@article {pmid31801211,
year = {2019},
author = {Brezgin, S and Kostyusheva, A and Kostyushev, D and Chulanov, V},
title = {Dead Cas Systems: Types, Principles, and Applications.},
journal = {International journal of molecular sciences},
volume = {20},
number = {23},
pages = {},
doi = {10.3390/ijms20236041},
pmid = {31801211},
issn = {1422-0067},
abstract = {The gene editing tool CRISPR-Cas has become the foundation for developing numerous molecular systems used in research and, increasingly, in medical practice. In particular, Cas proteins devoid of nucleolytic activity (dead Cas proteins; dCas) can be used to deliver functional cargo to programmed sites in the genome. In this review, we describe current CRISPR systems used for developing different dCas-based molecular approaches and summarize their most significant applications. We conclude with comments on the state-of-art in the CRISPR field and future directions.},
}

@article {pmid31800219,
year = {2019},
author = {Xiong, Y and Zhang, J and Yang, Z and Mou, Q and Ma, Y and Xiong, Y and Lu, Y},
title = {Functional DNA Regulated CRISPR-Cas12a Sensors for Point-of-Care Diagnostics of Non-Nucleic Acid Targets.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.9b09211},
pmid = {31800219},
issn = {1520-5126},
abstract = {Beyond its extraordinary genome editing ability, the CRISPR-Cas system has opened a new era of biosensing applications due to its high base resolution and isothermal signal amplification. However, the reported CRISPR-Cas sensors are largely only used for the detection of nucleic acids with limited application for non-nucleic acid targets. To realize the full potential of the CRISPR-Cas sensors and broaden their applications for detection and quantitation of non-nucleic acid targets, we herein re-port CRISPR-Cas12a sensors that are regulated by functional DNA (fDNA) molecules such as aptamers and DNAzymes that are selective for small organic molecule and metal ion detections. The sensor is based on the Cas12a dependent reporter sys-tem consisting of Cas12a, CRISPR RNA (crRNA) and its single stranded DNA substrate labeled with a fluorophore and quencher at each end (ssDNA-FQ), and fDNA molecules that can lock a DNA activator for Cas12a-crRNA, preventing the ssD-NA cleavage function of Cas12a in the absence of the fDNA targets. The presence of fDNA targets can trigger the unlocking of the DNA activator, which can then activate the cleavage of ssDNA-FQ by Cas12a, resulting in an increase of the fluorescent signal detectable by commercially available portable fluorimeters. Using this method, ATP and Na+ have been detected quan-titatively under ambient temperature (25 ℃) using a simple and fast detection workflow (two steps and <15 min), making the fDNA-regulated CRISPR system suitable for field tests or point-of-care diagnostics. Since fDNAs can be obtained to recog-nize a wide range of targets, the methods demonstrated here can expand this powerful CRISPR-Cas sensor system signifi-cantly to many other targets and thus provide a new toolbox to significantly expand the CRISPR-Cas system into many areas of bioanalytical and biomedical applications.},
}

@article {pmid31798958,
year = {2019},
author = {Buyukyoruk, M and Wiedenheft, B},
title = {Type I-F CRISPR-Cas provides protection from DNA, but not RNA phages.},
journal = {Cell discovery},
volume = {5},
number = {},
pages = {54},
doi = {10.1038/s41421-019-0123-9},
pmid = {31798958},
issn = {2056-5968},
}

@article {pmid31797930,
year = {2019},
author = {Liu, RM and Liang, LL and Freed, E and Chang, H and Oh, E and Liu, ZY and Garst, A and Eckert, CA and Gill, RT},
title = {Synthetic chimeric nucleases function for efficient genome editing.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {5524},
doi = {10.1038/s41467-019-13500-y},
pmid = {31797930},
issn = {2041-1723},
abstract = {CRISPR-Cas systems have revolutionized genome editing across a broad range of biotechnological endeavors. Many CRISPR-Cas nucleases have been identified and engineered for improved capabilities. Given the modular structure of such enzymes, we hypothesized that engineering chimeric sequences would generate non-natural variants that span the kinetic parameter landscape, and thus provide for the rapid selection of nucleases fit for a particular editing system. Here, we design a chimeric Cas12a-type library with approximately 560 synthetic chimeras, and select several functional variants. We demonstrate that certain nuclease domains can be recombined across distantly related nuclease templates to produce variants that function in bacteria, yeast, and human cell lines. We further characterize selected chimeric nucleases and find that they have different protospacer adjacent motif (PAM) preferences and the M44 chimera has higher specificity relative to wild-type (WT) sequences. This demonstration opens up the possibility of generating nuclease sequences with implications across biotechnology.},
}

@article {pmid31797922,
year = {2019},
author = {Watson, BNJ and Vercoe, RB and Salmond, GPC and Westra, ER and Staals, RHJ and Fineran, PC},
title = {Type I-F CRISPR-Cas resistance against virulent phages results in abortive infection and provides population-level immunity.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {5526},
doi = {10.1038/s41467-019-13445-2},
pmid = {31797922},
issn = {2041-1723},
abstract = {Type I CRISPR-Cas systems are abundant and widespread adaptive immune systems in bacteria and can greatly enhance bacterial survival in the face of phage infection. Upon phage infection, some CRISPR-Cas immune responses result in bacterial dormancy or slowed growth, which suggests the outcomes for infected cells may vary between systems. Here we demonstrate that type I CRISPR immunity of Pectobacterium atrosepticum leads to suppression of two unrelated virulent phages, ɸTE and ɸM1. Immunity results in an abortive infection response, where infected cells do not survive, but viral propagation is severely decreased, resulting in population protection due to the reduced phage epidemic. Our findings challenge the view of CRISPR-Cas as a system that protects the individual cell and supports growing evidence of abortive infection by some types of CRISPR-Cas systems.},
}

@article {pmid31797562,
year = {2019},
author = {Chen, F and Alphonse, M and Liu, Q},
title = {Strategies for nonviral nanoparticle-based delivery of CRISPR/Cas9 therapeutics.},
journal = {Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology},
volume = {},
number = {},
pages = {e1609},
doi = {10.1002/wnan.1609},
pmid = {31797562},
issn = {1939-0041},
abstract = {CRISPR-based genome editing technology has become an important potential therapeutic tool for various diseases. A vital challenge is to reach a safe, efficient, and clinically suitable delivery of a CRISPR-associated protein and a single-guide RNA. A possible translational approach to applying CRISPR-based technology is the use of viral vectors such as adeno-associated virus. However, such vectors give long-term exposure in vivo that may increase potential off-target effects as well as the risk of immunogenicity. Therefore, limitations to clinical applications are addressed using nonviral delivery systems such as nanoparticle-based delivery strategies. Today, the nanoparticle-based delivery approach is becoming more and more attractive in gene therapeutics because of its specific targeting, scale-up efficiency, efficacy of customization, minor stimulation of immune response, and minimal exposure to nucleases. In this review, we will present the most recent advances in developing innovations and potential advantages of the nanoparticle delivery system in CRISPR genome editing. We will also propose potential strategies of CRISPR-based technology for therapeutic and industrial applications. Our review will differ in focus from previous reviews and advance the literature on the subject by (a) focusing on the challenges of the CRISPR/Cas9 delivery system; (b) focusing on the application of nanoparticle-based delivery of CRISPR components (Cas9 and sgRNA), such as lipids and polymeric vectors; (c) discussing the potential nanoparticle-based delivery approaches for CRISPR/Cas9 application. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.},
}

@article {pmid31793351,
year = {2019},
author = {Safari, F and Sharifi, M and Farajnia, S and Akbari, B and Karimi Baba Ahmadi, M and Negahdaripour, M and Ghasemi, Y},
title = {The interaction of phages and bacteria: the co-evolutionary arms race.},
journal = {Critical reviews in biotechnology},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/07388551.2019.1674774},
pmid = {31793351},
issn = {1549-7801},
abstract = {Since the dawn of life, bacteria and phages are locked in a constant battle and both are perpetually changing their tactics to overcome each other. Bacteria use various strategies to overcome the invading phages, including adsorption inhibition, restriction-modification (R/E) systems, CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) systems, abortive infection (Abi), etc. To counteract, phages employ intelligent tactics for the nullification of bacterial defense systems, such as accessing host receptors, evading R/E systems, and anti-CRISPR proteins. Intense knowledge about the details of these defense pathways is the basis for their broad utilities in various fields of research from microbiology to biotechnology. Hence, in this review, we discuss some strategies used by bacteria to inhibit phage infections as well as phage tactics to circumvent bacterial defense systems. In addition, the application of these strategies will be described as a lesson learned from bacteria and phage combats. The ecological factors that affect the evolution of bacterial immune systems is the other issue represented in this review.},
}

@article {pmid31791381,
year = {2019},
author = {Mahas, A and Aman, R and Mahfouz, M},
title = {CRISPR-Cas13d mediates robust RNA virus interference in plants.},
journal = {Genome biology},
volume = {20},
number = {1},
pages = {263},
doi = {10.1186/s13059-019-1881-2},
pmid = {31791381},
issn = {1474-760X},
support = {CRG4//King Abdullah University of Science and Technology/ ; },
abstract = {BACKGROUND: CRISPR-Cas systems endow bacterial and archaeal species with adaptive immunity mechanisms to fend off invading phages and foreign genetic elements. CRISPR-Cas9 has been harnessed to confer virus interference against DNA viruses in eukaryotes, including plants. In addition, CRISPR-Cas13 systems have been used to target RNA viruses and the transcriptome in mammalian and plant cells. Recently, CRISPR-Cas13a has been shown to confer modest interference against RNA viruses. Here, we characterized a set of different Cas13 variants to identify those with the most efficient, robust, and specific interference activities against RNA viruses in planta using Nicotiana benthamiana.

RESULTS: Our data show that LwaCas13a, PspCas13b, and CasRx variants mediate high interference activities against RNA viruses in transient assays. Moreover, CasRx mediated robust interference in both transient and stable overexpression assays when compared to the other variants tested. CasRx targets either one virus alone or two RNA viruses simultaneously, with robust interference efficiencies. In addition, CasRx exhibits strong specificity against the target virus and does not exhibit collateral activity in planta.

CONCLUSIONS: Our data establish CasRx as the most robust Cas13 variant for RNA virus interference applications in planta and demonstrate its suitability for studying key questions relating to virus biology.},
}

@article {pmid31610539,
year = {2019},
author = {Němečková, A and Wäsch, C and Schubert, V and Ishii, T and Hřibová, E and Houben, A},
title = {CRISPR/Cas9-Based RGEN-ISL Allows the Simultaneous and Specific Visualization of Proteins, DNA Repeats, and Sites of DNA Replication.},
journal = {Cytogenetic and genome research},
volume = {159},
number = {1},
pages = {48-53},
doi = {10.1159/000502600},
pmid = {31610539},
issn = {1424-859X},
mesh = {Amaryllidaceae/*genetics ; Arabidopsis/*genetics ; CRISPR-Cas Systems/*genetics ; Chromatin/metabolism ; Chromosomes/genetics ; DNA Replication/*genetics ; DNA, Plant/genetics ; Endonucleases/genetics ; In Situ Hybridization, Fluorescence/methods ; RNA, Guide/genetics ; Telomere/genetics ; Zea mays/*genetics ; },
abstract = {Visualizing the spatiotemporal organization of the genome will improve our understanding of how chromatin structure and function are intertwined. Here, we describe a further development of the CRISPR/Cas9-based RNA-guided endonuclease-in situ labeling (RGEN-ISL) method. RGEN-ISL allowed the differentiation between vertebrate-type (TTAGGG)n and Arabidopsis-type (TTTAGGG)n telomere repeats. Using maize as an example, we established a combination of RGEN-ISL, immunostaining, and EdU labeling to visualize in situ specific repeats, histone marks, and DNA replication sites, respectively. The effects of the non-denaturing RGEN-ISL and standard denaturing FISH on the chromatin structure were compared using super-resolution microscopy. 3D structured illumination microscopy revealed that denaturation and acetic acid fixation impaired and flattened the chromatin. The broad range of adaptability of RGEN-ISL to different combinations of methods has the potential to advance the field of chromosome biology.},
}

Amaryllidaceae/*genetics
Arabidopsis/*genetics
CRISPR-Cas Systems/*genetics
Chromatin/metabolism
Chromosomes/genetics
DNA Replication/*genetics
DNA, Plant/genetics
Endonucleases/genetics
In Situ Hybridization, Fluorescence/methods
RNA, Guide/genetics
Telomere/genetics
Zea mays/*genetics

@article {pmid31410472,
year = {2019},
author = {Josipović, G and Tadić, V and Klasić, M and Zanki, V and Bečeheli, I and Chung, F and Ghantous, A and Keser, T and Madunić, J and Bošković, M and Lauc, G and Herceg, Z and Vojta, A and Zoldoš, V},
title = {Antagonistic and synergistic epigenetic modulation using orthologous CRISPR/dCas9-based modular system.},
journal = {Nucleic acids research},
volume = {47},
number = {18},
pages = {9637-9657},
pmid = {31410472},
issn = {1362-4962},
mesh = {Acyltransferases/genetics ; CRISPR-Cas Systems/*genetics ; Catalytic Domain/genetics ; DNA (Cytosine-5-)-Methyltransferases/genetics ; DNA Methylation/genetics ; *Epigenesis, Genetic ; Gene Editing/*methods ; Gene Expression Regulation/genetics ; Genome/genetics ; Glycosylation ; Hepatocyte Nuclear Factor 1-alpha/genetics ; Humans ; Mixed Function Oxygenases/genetics ; Promoter Regions, Genetic ; Proto-Oncogene Proteins/genetics ; RNA, Guide/genetics ; *Transcription, Genetic ; },
abstract = {Establishing causal relationship between epigenetic marks and gene transcription requires molecular tools, which can precisely modify specific genomic regions. Here, we present a modular and extensible CRISPR/dCas9-based toolbox for epigenetic editing and direct gene regulation. It features a system for expression of orthogonal dCas9 proteins fused to various effector domains and includes a multi-gRNA system for simultaneous targeting dCas9 orthologs to up to six loci. The C- and N-terminal dCas9 fusions with DNMT3A and TET1 catalytic domains were thoroughly characterized. We demonstrated simultaneous use of the DNMT3A-dSpCas9 and TET1-dSaCas9 fusions within the same cells and showed that imposed cytosine hyper- and hypo-methylation altered level of gene transcription if targeted CpG sites were functionally relevant. Dual epigenetic manipulation of the HNF1A and MGAT3 genes, involved in protein N-glycosylation, resulted in change of the glycan phenotype in BG1 cells. Furthermore, simultaneous targeting of the TET1-dSaCas9 and VPR-dSpCas9 fusions to the HNF1A regulatory region revealed strong and persistent synergistic effect on gene transcription, up to 30 days following cell transfection, suggesting involvement of epigenetic mechanisms in maintenance of the reactivated state. Also, modulation of dCas9 expression effectively reduced off-target effects while maintaining the desired effects on target regions.},
}

Acyltransferases/genetics
CRISPR-Cas Systems/*genetics
Catalytic Domain/genetics
DNA (Cytosine-5-)-Methyltransferases/genetics
DNA Methylation/genetics
*Epigenesis, Genetic
Gene Editing/*methods
Gene Expression Regulation/genetics
Genome/genetics
Glycosylation
Hepatocyte Nuclear Factor 1-alpha/genetics
Humans
Mixed Function Oxygenases/genetics
Promoter Regions, Genetic
Proto-Oncogene Proteins/genetics
RNA, Guide/genetics
*Transcription, Genetic

@article {pmid31372658,
year = {2019},
author = {Gam, JJ and DiAndreth, B and Jones, RD and Huh, J and Weiss, R},
title = {A 'poly-transfection' method for rapid, one-pot characterization and optimization of genetic systems.},
journal = {Nucleic acids research},
volume = {47},
number = {18},
pages = {e106},
pmid = {31372658},
issn = {1362-4962},
support = {P50 GM098792/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; CRISPR-Cas Systems/genetics ; Gene Expression/genetics ; High-Throughput Screening Assays/*methods ; Humans ; MicroRNAs/genetics ; Transfection/*methods ; },
abstract = {Biological research is relying on increasingly complex genetic systems and circuits to perform sophisticated operations in living cells. Performing these operations often requires simultaneous delivery of many genes, and optimizing the stoichiometry of these genes can yield drastic improvements in performance. However, sufficiently sampling the large design space of gene expression stoichiometries in mammalian cells using current methods is cumbersome, complex, or expensive. We present a 'poly-transfection' method as a simple yet high-throughput alternative that enables comprehensive evaluation of genetic systems in a single, readily-prepared transfection sample. Each cell in a poly-transfection represents an independent measurement at a distinct gene expression stoichiometry, fully leveraging the single-cell nature of transfection experiments. We first benchmark poly-transfection against co-transfection, showing that titration curves for commonly-used regulators agree between the two methods. We then use poly-transfections to efficiently generate new insights, for example in CRISPRa and synthetic miRNA systems. Finally, we use poly-transfection to rapidly engineer a difficult-to-optimize miRNA-based cell classifier for discriminating cancerous cells. One-pot evaluation enabled by poly-transfection accelerates and simplifies the design of genetic systems, providing a new high-information strategy for interrogating biology.},
}

Animals
CRISPR-Cas Systems/genetics
Gene Expression/genetics
High-Throughput Screening Assays/*methods
Humans
MicroRNAs/genetics
Transfection/*methods

@article {pmid31372638,
year = {2019},
author = {Korkmaz, G and Manber, Z and Lopes, R and Prekovic, S and Schuurman, K and Kim, Y and Teunissen, H and Flach, K and Wit, E and Galli, GG and Zwart, W and Elkon, R and Agami, R},
title = {A CRISPR-Cas9 screen identifies essential CTCF anchor sites for estrogen receptor-driven breast cancer cell proliferation.},
journal = {Nucleic acids research},
volume = {47},
number = {18},
pages = {9557-9572},
pmid = {31372638},
issn = {1362-4962},
mesh = {Binding Sites/genetics ; Breast Neoplasms/*genetics/pathology ; CCCTC-Binding Factor/*genetics ; CRISPR-Cas Systems/genetics ; Cell Proliferation/*genetics ; Chromatin/genetics ; Enhancer Elements, Genetic/genetics ; Estrogen Receptor alpha/*genetics ; Female ; Humans ; MCF-7 Cells ; Protein Binding/genetics ; },
abstract = {Estrogen receptor α (ERα) is an enhancer activating transcription factor, a key driver of breast cancer and a main target for cancer therapy. ERα-mediated gene regulation requires proper chromatin-conformation to facilitate interactions between ERα-bound enhancers and their target promoters. A major determinant of chromatin structure is the CCCTC-binding factor (CTCF), that dimerizes and together with cohesin stabilizes chromatin loops and forms the boundaries of topologically associated domains. However, whether CTCF-binding elements (CBEs) are essential for ERα-driven cell proliferation is unknown. To address this question in a global manner, we implemented a CRISPR-based functional genetic screen targeting CBEs located in the vicinity of ERα-bound enhancers. We identified four functional CBEs and demonstrated the role of one of them in inducing chromatin conformation changes in favor of activation of PREX1, a key ERα target gene in breast cancer. Indeed, high PREX1 expression is a bona-fide marker of ERα-dependency in cell lines, and is associated with good outcome after anti-hormonal treatment. Altogether, our data show that distinct CTCF-mediated chromatin structures are required for ERα- driven breast cancer cell proliferation.},
}

Binding Sites/genetics
Breast Neoplasms/*genetics/pathology
CCCTC-Binding Factor/*genetics
CRISPR-Cas Systems/genetics
Cell Proliferation/*genetics
Chromatin/genetics
Enhancer Elements, Genetic/genetics
Estrogen Receptor alpha/*genetics
Female
Humans
MCF-7 Cells
Protein Binding/genetics

@article {pmid31328227,
year = {2019},
author = {van Tran, N and Ernst, FGM and Hawley, BR and Zorbas, C and Ulryck, N and Hackert, P and Bohnsack, KE and Bohnsack, MT and Jaffrey, SR and Graille, M and Lafontaine, DLJ},
title = {The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112.},
journal = {Nucleic acids research},
volume = {47},
number = {15},
pages = {7719-7733},
doi = {10.1093/nar/gkz619},
pmid = {31328227},
issn = {1362-4962},
mesh = {Adenosine/*chemistry/genetics/metabolism ; Base Sequence ; Binding Sites ; CRISPR-Associated Protein 9/genetics/metabolism ; CRISPR-Cas Systems ; Cell Line, Tumor ; Crystallography, X-Ray ; Gene Deletion ; *Gene Expression Regulation, Neoplastic ; HCT116 Cells ; Humans ; Methyltransferases/*chemistry/deficiency/genetics/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Protein Stability ; RNA, Guide/genetics/metabolism ; RNA, Messenger/*chemistry/genetics/metabolism ; RNA, Ribosomal, 18S/*chemistry/genetics/metabolism ; Signal Transduction ; Substrate Specificity ; },
abstract = {N6-methyladenosine (m6A) has recently been found abundantly on messenger RNA and shown to regulate most steps of mRNA metabolism. Several important m6A methyltransferases have been described functionally and structurally, but the enzymes responsible for installing one m6A residue on each subunit of human ribosomes at functionally important sites have eluded identification for over 30 years. Here, we identify METTL5 as the enzyme responsible for 18S rRNA m6A modification and confirm ZCCHC4 as the 28S rRNA modification enzyme. We show that METTL5 must form a heterodimeric complex with TRMT112, a known methyltransferase activator, to gain metabolic stability in cells. We provide the first atomic resolution structure of METTL5-TRMT112, supporting that its RNA-binding mode differs distinctly from that of other m6A RNA methyltransferases. On the basis of similarities with a DNA methyltransferase, we propose that METTL5-TRMT112 acts by extruding the adenosine to be modified from a double-stranded nucleic acid.},
}

Adenosine/*chemistry/genetics/metabolism
Base Sequence
Binding Sites
CRISPR-Associated Protein 9/genetics/metabolism
CRISPR-Cas Systems
Cell Line, Tumor
Crystallography, X-Ray
Gene Deletion
*Gene Expression Regulation, Neoplastic
HCT116 Cells
Humans
Methyltransferases/*chemistry/deficiency/genetics/metabolism
Models, Molecular
Nucleic Acid Conformation
Protein Binding
Protein Conformation, alpha-Helical
Protein Conformation, beta-Strand
Protein Interaction Domains and Motifs
Protein Stability
RNA, Guide/genetics/metabolism
RNA, Messenger/*chemistry/genetics/metabolism
RNA, Ribosomal, 18S/*chemistry/genetics/metabolism
Signal Transduction
Substrate Specificity

@article {pmid31287866,
year = {2019},
author = {Shinoda, S and Kitagawa, S and Nakagawa, S and Wei, FY and Tomizawa, K and Araki, K and Araki, M and Suzuki, T and Suzuki, T},
title = {Mammalian NSUN2 introduces 5-methylcytidines into mitochondrial tRNAs.},
journal = {Nucleic acids research},
volume = {47},
number = {16},
pages = {8734-8745},
doi = {10.1093/nar/gkz575},
pmid = {31287866},
issn = {1362-4962},
mesh = {5-Methylcytosine/*metabolism ; Animals ; CRISPR-Cas Systems ; Fibroblasts/metabolism/pathology ; Gene Editing ; Gene Knockout Techniques ; HEK293 Cells ; HeLa Cells ; Humans ; Methylation ; Methyltransferases/deficiency/*genetics ; Mice ; Mice, Knockout ; Mitochondria/*genetics/metabolism ; Nucleic Acid Conformation ; Oxidative Phosphorylation ; Primary Cell Culture ; Protein Transport ; *RNA Processing, Post-Transcriptional ; RNA, Messenger/genetics/metabolism ; RNA, Mitochondrial/*genetics/metabolism ; RNA, Transfer/*genetics/metabolism ; S-Adenosylmethionine/metabolism ; },
abstract = {Post-transcriptional modifications in mitochondrial tRNAs (mt-tRNAs) play critical roles in mitochondrial protein synthesis, which produces respiratory chain complexes. In this study, we took advantage of mass spectrometric analysis to map 5-methylcytidine (m5C) at positions 48-50 in eight mouse and six human mt-tRNAs. We also confirmed the absence of m5C in mt-tRNAs isolated from Nsun2 knockout (KO) mice, as well as from NSUN2 KO human culture cells. In addition, we successfully reconstituted m5C at positions 48-50 of mt-tRNA in vitro with NSUN2 protein in the presence of S-adenosylmethionine. Although NSUN2 is predominantly localized to the nucleus and introduces m5C into cytoplasmic tRNAs and mRNAs, structured illumination microscopy clearly revealed NSUN2 foci inside mitochondria. These observations provide novel insights into the role of NSUN2 in the physiology and pathology of mitochondrial functions.},
}

5-Methylcytosine/*metabolism
Animals
CRISPR-Cas Systems
Fibroblasts/metabolism/pathology
Gene Editing
Gene Knockout Techniques
HEK293 Cells
HeLa Cells
Humans
Methylation
Methyltransferases/deficiency/*genetics
Mice
Mice, Knockout
Mitochondria/*genetics/metabolism
Nucleic Acid Conformation
Oxidative Phosphorylation
Primary Cell Culture
Protein Transport
*RNA Processing, Post-Transcriptional
RNA, Messenger/genetics/metabolism
RNA, Mitochondrial/*genetics/metabolism
RNA, Transfer/*genetics/metabolism
S-Adenosylmethionine/metabolism

@article {pmid31276587,
year = {2019},
author = {Van Haute, L and Lee, SY and McCann, BJ and Powell, CA and Bansal, D and Vasiliauskaitė, L and Garone, C and Shin, S and Kim, JS and Frye, M and Gleeson, JG and Miska, EA and Rhee, HW and Minczuk, M},
title = {NSUN2 introduces 5-methylcytosines in mammalian mitochondrial tRNAs.},
journal = {Nucleic acids research},
volume = {47},
number = {16},
pages = {8720-8733},
pmid = {31276587},
issn = {1362-4962},
support = {MC_UU_00015/4/MRC_/Medical Research Council/United Kingdom ; C13474/A18583/CRUK_/Cancer Research UK/United Kingdom ; C6946/A14492/CRUK_/Cancer Research UK/United Kingdom ; 104640/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; 092096/Z/10/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {5-Methylcytosine/*metabolism ; Animals ; CRISPR-Cas Systems ; Eczema/*genetics/metabolism/pathology ; Facies ; Fibroblasts/metabolism/pathology ; Gene Editing ; Gene Knockout Techniques ; Growth Disorders/*genetics/metabolism/pathology ; HEK293 Cells ; Humans ; Intellectual Disability/*genetics/metabolism/pathology ; Methylation ; Methyltransferases/deficiency/*genetics ; Mice ; Mice, Knockout ; Microcephaly/*genetics/metabolism/pathology ; Mitochondria/genetics/metabolism ; Nucleic Acid Conformation ; Oxidative Phosphorylation ; Primary Cell Culture ; Protein Transport ; *RNA Processing, Post-Transcriptional ; RNA, Messenger/genetics/metabolism ; RNA, Mitochondrial/*genetics/metabolism ; RNA, Transfer/*genetics/metabolism ; },
abstract = {Expression of human mitochondrial DNA is indispensable for proper function of the oxidative phosphorylation machinery. The mitochondrial genome encodes 22 tRNAs, 2 rRNAs and 11 mRNAs and their post-transcriptional modification constitutes one of the key regulatory steps during mitochondrial gene expression. Cytosine-5 methylation (m5C) has been detected in mitochondrial transcriptome, however its biogenesis has not been investigated in details. Mammalian NOP2/Sun RNA Methyltransferase Family Member 2 (NSUN2) has been characterized as an RNA methyltransferase introducing m5C in nuclear-encoded tRNAs, mRNAs and microRNAs and associated with cell proliferation and differentiation, with pathogenic variants in NSUN2 being linked to neurodevelopmental disorders. Here we employ spatially restricted proximity labelling and immunodetection to demonstrate that NSUN2 is imported into the matrix of mammalian mitochondria. Using three genetic models for NSUN2 inactivation-knockout mice, patient-derived fibroblasts and CRISPR/Cas9 knockout in human cells-we show that NSUN2 is necessary for the generation of m5C at positions 48, 49 and 50 of several mammalian mitochondrial tRNAs. Finally, we show that inactivation of NSUN2 does not have a profound effect on mitochondrial tRNA stability and oxidative phosphorylation in differentiated cells. We discuss the importance of the newly discovered function of NSUN2 in the context of human disease.},
}

5-Methylcytosine/*metabolism
Animals
CRISPR-Cas Systems
Eczema/*genetics/metabolism/pathology
Facies
Fibroblasts/metabolism/pathology
Gene Editing
Gene Knockout Techniques
Growth Disorders/*genetics/metabolism/pathology
HEK293 Cells
Humans
Intellectual Disability/*genetics/metabolism/pathology
Methylation
Methyltransferases/deficiency/*genetics
Mice
Mice, Knockout
Microcephaly/*genetics/metabolism/pathology
Mitochondria/genetics/metabolism
Nucleic Acid Conformation
Oxidative Phosphorylation
Primary Cell Culture
Protein Transport
*RNA Processing, Post-Transcriptional
RNA, Messenger/genetics/metabolism
RNA, Mitochondrial/*genetics/metabolism
RNA, Transfer/*genetics/metabolism

@article {pmid31226203,
year = {2019},
author = {Kitsera, N and Rodriguez-Alvarez, M and Emmert, S and Carell, T and Khobta, A},
title = {Nucleotide excision repair of abasic DNA lesions.},
journal = {Nucleic acids research},
volume = {47},
number = {16},
pages = {8537-8547},
doi = {10.1093/nar/gkz558},
pmid = {31226203},
issn = {1362-4962},
mesh = {Base Sequence ; CRISPR-Associated Protein 9/genetics/metabolism ; CRISPR-Cas Systems ; Cell Line, Transformed ; DNA/chemistry/*genetics/metabolism ; DNA Damage ; *DNA Repair ; DNA-(Apurinic or Apyrimidinic Site) Lyase/*genetics/metabolism ; DNA-Binding Proteins/deficiency/*genetics ; Fibroblasts/cytology/metabolism ; Gene Editing/methods ; Gene Knockout Techniques ; Genome, Human ; Humans ; Mutation ; Protein Binding ; Skin/cytology/metabolism ; Transcription, Genetic ; Xeroderma Pigmentosum Group A Protein/*genetics/metabolism ; },
abstract = {Apurinic/apyrimidinic (AP) sites are a class of highly mutagenic and toxic DNA lesions arising in the genome from a number of exogenous and endogenous sources. Repair of AP lesions takes place predominantly by the base excision pathway (BER). However, among chemically heterogeneous AP lesions formed in DNA, some are resistant to the endonuclease APE1 and thus refractory to BER. Here, we employed two types of reporter constructs accommodating synthetic APE1-resistant AP lesions to investigate the auxiliary repair mechanisms in human cells. By combined analyses of recovery of the transcription rate and suppression of transcriptional mutagenesis at specifically positioned AP lesions, we demonstrate that nucleotide excision repair pathway (NER) efficiently removes BER-resistant AP lesions and significantly enhances the repair of APE1-sensitive ones. Our results further indicate that core NER components XPA and XPF are equally required and that both global genome (GG-NER) and transcription coupled (TC-NER) subpathways contribute to the repair.},
}

Base Sequence
CRISPR-Associated Protein 9/genetics/metabolism
CRISPR-Cas Systems
Cell Line, Transformed
DNA/chemistry/*genetics/metabolism
DNA Damage
*DNA Repair
DNA-(Apurinic or Apyrimidinic Site) Lyase/*genetics/metabolism
DNA-Binding Proteins/deficiency/*genetics
Fibroblasts/cytology/metabolism
Gene Editing/methods
Gene Knockout Techniques
Genome, Human
Humans
Mutation
Protein Binding
Skin/cytology/metabolism
Transcription, Genetic
Xeroderma Pigmentosum Group A Protein/*genetics/metabolism

@article {pmid31165880,
year = {2019},
author = {Hardigan, AA and Roberts, BS and Moore, DE and Ramaker, RC and Jones, AL and Myers, RM},
title = {CRISPR/Cas9-targeted removal of unwanted sequences from small-RNA sequencing libraries.},
journal = {Nucleic acids research},
volume = {47},
number = {14},
pages = {e84},
doi = {10.1093/nar/gkz425},
pmid = {31165880},
issn = {1362-4962},
mesh = {Base Sequence ; *CRISPR-Cas Systems ; Gene Expression Regulation ; *Gene Library ; High-Throughput Nucleotide Sequencing/methods ; Humans ; MicroRNAs/genetics ; Models, Genetic ; Nucleic Acid Hybridization/*methods ; RNA, Ribosomal/genetics ; RNA, Small Untranslated/*genetics ; Sequence Analysis, RNA/methods ; },
abstract = {In small RNA (smRNA) sequencing studies, highly abundant molecules such as adapter dimer products and tissue-specific microRNAs (miRNAs) inhibit accurate quantification of lowly expressed species. We previously developed a method to selectively deplete highly abundant miRNAs. However, this method does not deplete adapter dimer ligation products that, unless removed by gel-separation, comprise most of the library. Here, we have adapted and modified recently described methods for CRISPR/Cas9-based Depletion of Abundant Species by Hybridization ('DASH') to smRNA-seq, which we have termed miRNA and Adapter Dimer-DASH (MAD-DASH). In MAD-DASH, Cas9 is complexed with single guide RNAs (sgRNAs) targeting adapter dimer ligation products, alongside highly expressed tissue-specific smRNAs, for cleavage in vitro. This process dramatically reduces adapter dimer and targeted smRNA sequences, can be multiplexed, shows minimal off-target effects, improves the quantification of lowly expressed miRNAs from human plasma and tissue derived RNA, and obviates the need for gel-separation, greatly increasing sample throughput. Additionally, the method is fully customizable to other smRNA-seq preparation methods. Like depletion of ribosomal RNA for mRNA-seq and mitochondrial DNA for ATAC-seq, our method allows for greater proportional read-depth of non-targeted sequences.},
}

Base Sequence
*CRISPR-Cas Systems
Gene Expression Regulation
*Gene Library
High-Throughput Nucleotide Sequencing/methods
Humans
MicroRNAs/genetics
Models, Genetic
Nucleic Acid Hybridization/*methods
RNA, Ribosomal/genetics
RNA, Small Untranslated/*genetics
Sequence Analysis, RNA/methods

@article {pmid31165872,
year = {2019},
author = {Huang, H and Kong, W and Jean, M and Fiches, G and Zhou, D and Hayashi, T and Que, J and Santoso, N and Zhu, J},
title = {A CRISPR/Cas9 screen identifies the histone demethylase MINA53 as a novel HIV-1 latency-promoting gene (LPG).},
journal = {Nucleic acids research},
volume = {47},
number = {14},
pages = {7333-7347},
doi = {10.1093/nar/gkz493},
pmid = {31165872},
issn = {1362-4962},
support = {R01 DE025447/DE/NIDCR NIH HHS/United States ; R01 GM117838/GM/NIGMS NIH HHS/United States ; R33 AI116180/AI/NIAID NIH HHS/United States ; },
mesh = {Aminopyridines/pharmacology ; CD4-Positive T-Lymphocytes/drug effects/metabolism/virology ; *CRISPR-Cas Systems ; Cell Line, Tumor ; Cells, Cultured ; Demethylation/drug effects ; Dioxygenases/antagonists & inhibitors/*genetics/metabolism ; Gene Expression Regulation, Viral/drug effects ; HEK293 Cells ; HIV Infections/*genetics/metabolism/virology ; HIV-1/drug effects/*genetics/physiology ; Histone Deacetylase Inhibitors/pharmacology ; Histone Demethylases/antagonists & inhibitors/*genetics/metabolism ; Histones/metabolism ; Host-Pathogen Interactions/drug effects/genetics ; Humans ; Hydrazones/pharmacology ; Methylation/drug effects ; Nuclear Proteins/antagonists & inhibitors/*genetics/metabolism ; RNA Interference ; Virus Latency/*genetics ; },
abstract = {Although combination antiretroviral therapy is potent to block active replication of HIV-1 in AIDS patients, HIV-1 persists as transcriptionally inactive proviruses in infected cells. These HIV-1 latent reservoirs remain a major obstacle for clearance of HIV-1. Investigation of host factors regulating HIV-1 latency is critical for developing novel antiretroviral reagents to eliminate HIV-1 latent reservoirs. From our recently accomplished CRISPR/Cas9 sgRNA screens, we identified that the histone demethylase, MINA53, is potentially a novel HIV-1 latency-promoting gene (LPG). We next validated MINA53's function in maintenance of HIV-1 latency by depleting MINA53 using the alternative RNAi approach. We further identified that in vitro MINA53 preferentially demethylates the histone substrate, H3K36me3 and that in cells MINA53 depletion by RNAi also increases the local level of H3K36me3 at LTR. The effort to map the downstream effectors unraveled that H3K36me3 has the cross-talk with another epigenetic mark H4K16ac, mediated by KAT8 that recognizes the methylated H3K36 and acetylated H4K16. Removing the MINA53-mediated latency mechanisms could benefit the reversal of post-integrated latent HIV-1 proviruses for purging of reservoir cells. We further demonstrated that a pan jumonji histone demethylase inhibitor, JIB-04, inhibits MINA53-mediated demethylation of H3K36me3, and JIB-04 synergizes with other latency-reversing agents (LRAs) to reactivate latent HIV-1.},
}

Aminopyridines/pharmacology
CD4-Positive T-Lymphocytes/drug effects/metabolism/virology
*CRISPR-Cas Systems
Cell Line, Tumor
Cells, Cultured
Demethylation/drug effects
Dioxygenases/antagonists & inhibitors/*genetics/metabolism
Gene Expression Regulation, Viral/drug effects
HEK293 Cells
HIV Infections/*genetics/metabolism/virology
HIV-1/drug effects/*genetics/physiology
Histone Deacetylase Inhibitors/pharmacology
Histone Demethylases/antagonists & inhibitors/*genetics/metabolism
Histones/metabolism
Host-Pathogen Interactions/drug effects/genetics
Humans
Hydrazones/pharmacology
Methylation/drug effects
Nuclear Proteins/antagonists & inhibitors/*genetics/metabolism
RNA Interference
Virus Latency/*genetics

@article {pmid31143069,
year = {2019},
author = {Limanskiy, V and Vyas, A and Chaturvedi, LS and Vyas, D},
title = {Harnessing the potential of gene editing technology using CRISPR in inflammatory bowel disease.},
journal = {World journal of gastroenterology},
volume = {25},
number = {18},
pages = {2177-2187},
doi = {10.3748/wjg.v25.i18.2177},
pmid = {31143069},
issn = {2219-2840},
mesh = {Adaptive Immunity/genetics ; CRISPR-Cas Systems/*genetics ; Gene Editing/*methods/trends ; Genetic Therapy/*methods/trends ; Humans ; Inflammatory Bowel Diseases/genetics/immunology/*therapy ; },
abstract = {The molecular scalpel of clustered regularly interspersed short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9) technology may be sharp enough to begin cutting the genes implicated in inflammatory bowel disease (IBD) and consequently decrease the 6.3 billion dollar annual financial healthcare burden in the treatment of IBD. For the past few years CRISPR technology has drastically revolutionized DNA engineering and biomedical research field. We are beginning to see its application in gene manipulation of sickle cell disease, human immunodeficiency virus resistant embryologic twin gene modification and IBD genes such as Gatm (Glycine amidinotransferase, mitochondrial), nucleotide-binding oligomerization domain-containing protein 2, KRT12 and other genes implicated in adaptive immune convergence pathways have been subjected to gene editing, however there are very few publications. Furthermore, since Crohn's disease and ulcerative colitis have shared disease susceptibility and share genetic gene profile, it is paramount and is more advantageous to use CRISPR technology to maximize impact. Although, currently CRISPR does have its limitations due to limited number of specific Cas enzymes, off-target activity, protospacer adjacent motifs and crossfire between different target sites. However, these limitations have given researchers further insight on how to augment and manipulate enzymes to enable precise gene excision and limit crossfire between target sites.},
}

Adaptive Immunity/genetics
CRISPR-Cas Systems/*genetics
Gene Editing/*methods/trends
Genetic Therapy/*methods/trends
Humans
Inflammatory Bowel Diseases/genetics/immunology/*therapy

@article {pmid31114866,
year = {2019},
author = {Quan, J and Langelier, C and Kuchta, A and Batson, J and Teyssier, N and Lyden, A and Caldera, S and McGeever, A and Dimitrov, B and King, R and Wilheim, J and Murphy, M and Ares, LP and Travisano, KA and Sit, R and Amato, R and Mumbengegwi, DR and Smith, JL and Bennett, A and Gosling, R and Mourani, PM and Calfee, CS and Neff, NF and Chow, ED and Kim, PS and Greenhouse, B and DeRisi, JL and Crawford, ED},
title = {FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences.},
journal = {Nucleic acids research},
volume = {47},
number = {14},
pages = {e83},
doi = {10.1093/nar/gkz418},
pmid = {31114866},
issn = {1362-4962},
support = {R35 HL140026/HL/NHLBI NIH HHS/United States ; //Wellcome Trust/United Kingdom ; K23 HL138461/HL/NHLBI NIH HHS/United States ; K24 HL133390/HL/NHLBI NIH HHS/United States ; R01 HL110969/HL/NHLBI NIH HHS/United States ; },
mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/drug effects/genetics ; Bacterial Infections/diagnosis/genetics/prevention & control ; *CRISPR-Cas Systems ; Computational Biology/*methods ; Drug Resistance, Bacterial/*drug effects/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/methods ; Reproducibility of Results ; Sensitivity and Specificity ; },
abstract = {The growing prevalence of deadly microbes with resistance to previously life-saving drug therapies is a dire threat to human health. Detection of low abundance pathogen sequences remains a challenge for metagenomic Next Generation Sequencing (NGS). We introduce FLASH (Finding Low Abundance Sequences by Hybridization), a next-generation CRISPR/Cas9 diagnostic method that takes advantage of the efficiency, specificity and flexibility of Cas9 to enrich for a programmed set of sequences. FLASH-NGS achieves up to 5 orders of magnitude of enrichment and sub-attomolar gene detection with minimal background. We provide an open-source software tool (FLASHit) for guide RNA design. Here we applied it to detection of antimicrobial resistance genes in respiratory fluid and dried blood spots, but FLASH-NGS is applicable to all areas that rely on multiplex PCR.},
}

Anti-Bacterial Agents/*pharmacology
Bacteria/classification/drug effects/genetics
Bacterial Infections/diagnosis/genetics/prevention & control
*CRISPR-Cas Systems
Computational Biology/*methods
Drug Resistance, Bacterial/*drug effects/genetics
High-Throughput Nucleotide Sequencing/*methods
Humans
Metagenomics/methods
Reproducibility of Results
Sensitivity and Specificity

@article {pmid31062017,
year = {2019},
author = {Asoshina, M and Myo, G and Tada, N and Tajino, K and Shimizu, N},
title = {Targeted amplification of a sequence of interest in artificial chromosome in mammalian cells.},
journal = {Nucleic acids research},
volume = {47},
number = {11},
pages = {5998-6006},
doi = {10.1093/nar/gkz343},
pmid = {31062017},
issn = {1362-4962},
mesh = {Animals ; CHO Cells ; CRISPR-Cas Systems ; Chromosomes, Artificial/*genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; Cricetinae ; Cricetulus ; *DNA Replication ; Endonucleases/genetics ; Gene Amplification ; Homologous Recombination ; *Matrix Attachment Regions ; Mice ; Plasmids/*metabolism ; *Replication Origin ; },
abstract = {A plasmid with a replication initiation region (IR) and a matrix attachment region (MAR) initiates gene amplification in mammalian cells at a random chromosomal location. A mouse artificial chromosome (MAC) vector can stably carry a large genomic region. In this study we combined these two technologies with the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease (Cas)9 strategy to achieve targeted amplification of a sequence of interest. We previously showed that the IR/MAR plasmid was amplified up to the extrachromosomal tandem repeat; here we demonstrate that cleavage of these tandem plasmids and MAC by Cas9 facilitates homologous recombination between them. The plasmid array on the MAC could be further extended to form a ladder structure with high gene expression by a breakage-fusion-bridge cycle involving breakage at mouse major satellites. Amplification of genes on the MAC has the advantage that the MAC can be transferred between cells. We visualized the MAC in live cells by amplifying the lactose operator array on the MAC in cells expressing lactose repressor-green fluorescent protein fusion protein. This targeted amplification strategy is in theory be applicable to any sequence at any chromosomal site, and provides a novel tool for animal cell technology.},
}

Animals
CHO Cells
CRISPR-Cas Systems
Chromosomes, Artificial/*genetics
Clustered Regularly Interspaced Short Palindromic Repeats
Cricetinae
Cricetulus
*DNA Replication
Endonucleases/genetics
Gene Amplification
Homologous Recombination
*Matrix Attachment Regions
Mice
Plasmids/*metabolism
*Replication Origin

@article {pmid31006810,
year = {2019},
author = {Kounatidou, E and Nakjang, S and McCracken, SRC and Dehm, SM and Robson, CN and Jones, D and Gaughan, L},
title = {A novel CRISPR-engineered prostate cancer cell line defines the AR-V transcriptome and identifies PARP inhibitor sensitivities.},
journal = {Nucleic acids research},
volume = {47},
number = {11},
pages = {5634-5647},
doi = {10.1093/nar/gkz286},
pmid = {31006810},
issn = {1362-4962},
support = {MR/P009972/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Algorithms ; *CRISPR-Cas Systems ; Cell Line, Tumor ; Cell Proliferation ; DNA Damage ; DNA Repair ; Drug Screening Assays, Antitumor ; Genetic Techniques ; Humans ; Lentivirus ; Male ; Poly(ADP-ribose) Polymerase Inhibitors/*pharmacology ; Prostatic Neoplasms/*genetics/*metabolism ; Receptors, Androgen/biosynthesis/*genetics ; Sequence Analysis, RNA ; Transcriptome ; },
abstract = {Resistance to androgen receptor (AR)-targeted therapies in prostate cancer (PC) is a major clinical problem. A key mechanism of treatment resistance in advanced PC is the generation of alternatively spliced forms of the AR termed AR variants (AR-Vs) that are refractory to targeted agents and drive tumour progression. Our understanding of how AR-Vs function is limited due to difficulties in distinguishing their discriminate activities from full-length AR (FL-AR). Here we report the development of a novel CRISPR-derived cell line which is a derivative of CWR22Rv1 cells, called CWR22Rv1-AR-EK, that has lost expression of FL-AR, but retains all endogenous AR-Vs. From this, we show that AR-Vs act unhindered by loss of FL-AR to drive cell growth and expression of androgenic genes. Global transcriptomics demonstrate that AR-Vs drive expression of a cohort of DNA damage response genes and depletion of AR-Vs sensitises cells to ionising radiation. Moreover, we demonstrate that AR-Vs interact with PARP1 and PARP2 and are dependent upon their catalytic function for transcriptional activation. Importantly, PARP blockade compromises expression of AR-V-target genes and reduces growth of CRPC cell lines suggesting a synthetic lethality relationship between AR-Vs and PARP, advocating the use of PARP inhibitors in AR-V positive PC.},
}

Algorithms
*CRISPR-Cas Systems
Cell Line, Tumor
Cell Proliferation
DNA Damage
DNA Repair
Drug Screening Assays, Antitumor
Genetic Techniques
Humans
Lentivirus
Male
Poly(ADP-ribose) Polymerase Inhibitors/*pharmacology
Prostatic Neoplasms/*genetics/*metabolism
Receptors, Androgen/biosynthesis/*genetics
Sequence Analysis, RNA
Transcriptome

@article {pmid30982901,
year = {2019},
author = {Chiang, HC and Zhang, X and Li, J and Zhao, X and Chen, J and Wang, HT and Jatoi, I and Brenner, A and Hu, Y and Li, R},
title = {BRCA1-associated R-loop affects transcription and differentiation in breast luminal epithelial cells.},
journal = {Nucleic acids research},
volume = {47},
number = {10},
pages = {5086-5099},
doi = {10.1093/nar/gkz262},
pmid = {30982901},
issn = {1362-4962},
support = {R01 CA212674/CA/NCI NIH HHS/United States ; R01 CA220578/CA/NCI NIH HHS/United States ; T32 CA148724/CA/NCI NIH HHS/United States ; },
mesh = {BRCA1 Protein/*genetics/metabolism ; Breast/*metabolism ; CRISPR-Cas Systems ; Carcinogenesis ; Cell Differentiation ; *Enhancer Elements, Genetic ; Epithelial Cells/*metabolism ; Estrogen Receptor alpha/genetics ; Female ; Gene Deletion ; *Gene Expression Regulation, Neoplastic ; Genes, BRCA1 ; HEK293 Cells ; Heterozygote ; Humans ; MCF-7 Cells ; Mutation ; Transcription, Genetic ; },
abstract = {BRCA1-associated basal-like breast cancer originates from luminal progenitor cells. Breast epithelial cells from cancer-free BRCA1 mutation carriers are defective in luminal differentiation. However, how BRCA1 deficiency leads to lineage-specific differentiation defect is not clear. BRCA1 is implicated in resolving R-loops, DNA-RNA hybrid structures associated with genome instability and transcriptional regulation. We recently showed that R-loops are preferentially accumulated in breast luminal epithelial cells of BRCA1 mutation carriers. Here, we interrogate the impact of a BRCA1 mutation-associated R-loop located in a putative transcriptional enhancer upstream of the ERα-encoding ESR1 gene. Genetic ablation confirms the relevance of this R-loop-containing region to enhancer-promoter interactions and transcriptional activation of the corresponding neighboring genes, including ESR1, CCDC170 and RMND1. BRCA1 knockdown in ERα+ luminal breast cancer cells increases intensity of this R-loop and reduces transcription of its neighboring genes. The deleterious effect of BRCA1 depletion on transcription is mitigated by ectopic expression of R-loop-removing RNase H1. Furthermore, RNase H1 overexpression in primary breast cells from BRCA1 mutation carriers results in a shift from luminal progenitor cells to mature luminal cells. Our findings suggest that BRCA1-dependent R-loop mitigation contributes to luminal cell-specific transcription and differentiation, which could in turn suppress BRCA1-associated tumorigenesis.},
}

BRCA1 Protein/*genetics/metabolism
Breast/*metabolism
CRISPR-Cas Systems
Carcinogenesis
Cell Differentiation
*Enhancer Elements, Genetic
Epithelial Cells/*metabolism
Estrogen Receptor alpha/genetics
Female
Gene Deletion
*Gene Expression Regulation, Neoplastic
Genes, BRCA1
HEK293 Cells
Heterozygote
Humans
MCF-7 Cells
Mutation
Transcription, Genetic

@article {pmid30957847,
year = {2019},
author = {Gong, L and Li, M and Cheng, F and Zhao, D and Chen, Y and Xiang, H},
title = {Primed adaptation tolerates extensive structural and size variations of the CRISPR RNA guide in Haloarcula hispanica.},
journal = {Nucleic acids research},
volume = {47},
number = {11},
pages = {5880-5891},
doi = {10.1093/nar/gkz244},
pmid = {30957847},
issn = {1362-4962},
mesh = {Adaptation, Physiological ; CRISPR-Associated Proteins/metabolism ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; DNA Primers/genetics ; Escherichia coli/genetics ; Escherichia coli Proteins/metabolism ; Gene Deletion ; Haloarcula/*genetics ; Mutation ; Plasmids/metabolism ; *RNA, Guide ; },
abstract = {Recent studies on CRISPR adaptation revealed that priming is a major pathway of spacer acquisition, at least for the most prevalent type I systems. Priming is guided by a CRISPR RNA which fully/partially matches the invader DNA, but the plasticity of this RNA guide has not yet been characterized. In this study, we extensively modified the two conserved handles of a priming crRNA in Haloarcula hispanica, and altered the size of its central spacer part. Interestingly, priming is insusceptible to the full deletion of 3' handle, which seriously impaired crRNA stability and interference effects. With 3' handle deletion, further truncation of 5' handle revealed that its spacer-proximal 6 nucleotides could provide the least conserved sequence required for priming. Subsequent scanning mutation further identified critical nucleotides within 5' handle. Besides, priming was also shown to tolerate a wider size variation of the spacer part, compared to interference. These data collectively illustrate the high tolerance of priming to extensive structural/size variations of the crRNA guide, which highlights the structural flexibility of the crRNA-effector ribonucleoprotein complex. The observed high priming effectiveness suggests that primed adaptation promotes clearance of the fast-replicating and ever-evolving viral DNA, by rapidly and persistently multiplexing the interference pathway.},
}

Adaptation, Physiological
CRISPR-Associated Proteins/metabolism
*CRISPR-Cas Systems
*Clustered Regularly Interspaced Short Palindromic Repeats
DNA Primers/genetics
Escherichia coli/genetics
Escherichia coli Proteins/metabolism
Gene Deletion
Haloarcula/*genetics
Mutation
Plasmids/metabolism
*RNA, Guide

@article {pmid30949703,
year = {2019},
author = {Liu, H and Huang, T and Li, M and Li, M and Zhang, C and Jiang, J and Yu, X and Yin, Y and Zhang, F and Lu, G and Luo, MC and Zhang, LR and Li, J and Liu, K and Chen, ZJ},
title = {SCRE serves as a unique synaptonemal complex fastener and is essential for progression of meiosis prophase I in mice.},
journal = {Nucleic acids research},
volume = {47},
number = {11},
pages = {5670-5683},
doi = {10.1093/nar/gkz226},
pmid = {30949703},
issn = {1362-4962},
mesh = {Animals ; CRISPR-Cas Systems ; Chromosome Segregation ; Female ; HEK293 Cells ; Humans ; Male ; Meiosis ; *Meiotic Prophase I ; Mice ; Mice, Knockout ; Nuclear Proteins/genetics/*physiology ; Protein Binding ; Recombination, Genetic ; Spermatocytes/metabolism ; Synaptonemal Complex/*physiology ; Testis/metabolism ; },
abstract = {Meiosis is a specialized cell division for producing haploid gametes from diploid germ cells. During meiosis, synaptonemal complex (SC) mediates the alignment of homologs and plays essential roles in homologous recombination and therefore in promoting accurate chromosome segregation. In this study, we have identified a novel protein SCRE (synaptonemal complex reinforcing element) as a key molecule in maintaining the integrity of SC during meiosis prophase I in mice. Deletion of Scre (synaptonemal complex reinforcing element) caused germ cell death in both male and female mice, resulting in infertility. Our mechanistic studies showed that the synapses and SCs in Scre knockout mice were unstable due to the lack of the SC reinforcing function of SCRE, which is sparsely localized as discrete foci along the central elements in normal synaptic homologous chromosomes. The lack of Scre leads to meiosis collapse at the late zygotene stage. We further showed that SCRE interacts with synaptonemal complex protein 1 (SYCP1) and synaptonemal complex central element 3 (SYCE3). We conclude that the function of SCRE is to reinforce the integrity of the central elements, thereby stabilizing the SC and ensuring meiotic cell cycle progression. Our study identified SCRE as a novel SC fastener protein that is distinct from other known SC proteins.},
}

Animals
CRISPR-Cas Systems
Chromosome Segregation
Female
HEK293 Cells
Humans
Male
Meiosis
*Meiotic Prophase I
Mice
Mice, Knockout
Nuclear Proteins/genetics/*physiology
Protein Binding
Recombination, Genetic
Spermatocytes/metabolism
Synaptonemal Complex/*physiology
Testis/metabolism

@article {pmid30935995,
year = {2019},
author = {Aquino-Jarquin, G},
title = {CRISPR-Cas14 is now part of the artillery for gene editing and molecular diagnostic.},
journal = {Nanomedicine : nanotechnology, biology, and medicine},
volume = {18},
number = {},
pages = {428-431},
doi = {10.1016/j.nano.2019.03.006},
pmid = {30935995},
issn = {1549-9642},
mesh = {Base Sequence ; CRISPR-Cas Systems/*genetics ; *Gene Editing ; Genetic Loci ; *Pathology, Molecular ; },
abstract = {Recently Jennifer Doudna's group discovered the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated protein 14 (Cas14), identified almost exclusively in a superphylum of extremophile archaea. The newly discovered Cas14 possesses a single-stranded (ss)DNA targeting activity - despite being two times smaller than Cas9 - a capability that might confer a defense against viruses with ssDNA genomes. Furthermore, by combining the non-specific ssDNase cleavage activity of Cas14 with isothermal amplification method (DETECTR-Cas14), it can also be promisingly exploited for high-fidelity DNA single-nucleotide polymorphism genotyping, and potentially for detecting ssDNA viruses of undeniable clinical, ecological, and economic importance infecting hosts in all three domains of life. Thus, CRISPR-Cas14 might acquire an exponential expansion in the field of CRISPR diagnostic for infectious and noninfectious diseases.},
}

Base Sequence
CRISPR-Cas Systems/*genetics
*Gene Editing
Genetic Loci
*Pathology, Molecular

@article {pmid30916346,
year = {2019},
author = {Chen, D and Zhang, Z and Chen, C and Yao, S and Yang, Q and Li, F and He, X and Ai, C and Wang, M and Guan, MX},
title = {Deletion of Gtpbp3 in zebrafish revealed the hypertrophic cardiomyopathy manifested by aberrant mitochondrial tRNA metabolism.},
journal = {Nucleic acids research},
volume = {47},
number = {10},
pages = {5341-5355},
doi = {10.1093/nar/gkz218},
pmid = {30916346},
issn = {1362-4962},
mesh = {Aminoacylation ; Animals ; CRISPR-Cas Systems ; Cardiomyopathy, Hypertrophic/genetics/*metabolism ; GTP-Binding Proteins/*genetics/metabolism ; *Gene Deletion ; In Situ Hybridization ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/metabolism ; Mutation ; Myocytes, Cardiac/metabolism ; Phenotype ; Protein Conformation ; RNA, Transfer/*metabolism ; Transgenes ; Zebrafish/genetics ; Zebrafish Proteins/*genetics/metabolism ; },
abstract = {GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of τm5U at the wobble position of mitochondrial tRNAGlu, tRNAGln, tRNALys, tRNATrp and tRNALeu(UUR). The previous investigations showed that GTPBP3 mutations were associated with hypertrophic cardiomyopathy (HCM). However, the pathophysiology of GTPBP3 deficiency remains elusively. Using the gtpbp3 knockout zebrafish generated by CRISPR/Cas9 system, we demonstrated the aberrant mitochondrial tRNA metabolism in gtpbp3 knock-out zebrafish. The deletion of gtpbp3 may alter functional folding of tRNA, indicated by conformation changes and sensitivity to S1-mediated digestion of tRNAGlu, tRNALys, tRNATrp and tRNALeu(UUR). Strikingly, gtpbp3 knock-out zebrafish displayed the global increases in the aminoacylated efficiencies of mitochondrial tRNAs. The aberrant mitochondrial tRNA metabolisms impaired mitochondrial translation, produced proteostasis stress and altered activities of respiratory chain complexes. These mitochondria dysfunctions caused the alterations in the embryonic heart development and reduced fractional shortening of ventricles in mutant zebrafish. Notably, the gtpbp3 knock-out zebrafish exhibited hypertrophy of cardiomyocytes and myocardial fiber disarray in ventricles. These cardiac defects in the gtpbp3 knock-out zebrafish recapitulated the clinical phenotypes in HCM patients carrying the GTPBP3 mutation(s). Our findings highlight the fundamental role of defective nucleotide modifications of tRNAs in mitochondrial biogenesis and their pathological consequences in hypertrophic cardiomyopathy.},
}

Aminoacylation
Animals
CRISPR-Cas Systems
Cardiomyopathy, Hypertrophic/genetics/*metabolism
GTP-Binding Proteins/*genetics/metabolism
*Gene Deletion
In Situ Hybridization
Mitochondria/genetics/metabolism
Mitochondrial Proteins/metabolism
Mutation
Myocytes, Cardiac/metabolism
Phenotype
Protein Conformation
RNA, Transfer/*metabolism
Transgenes
Zebrafish/genetics
Zebrafish Proteins/*genetics/metabolism

@article {pmid30835740,
year = {2019},
author = {Hammouda, OT and Böttger, F and Wittbrodt, J and Thumberger, T},
title = {Swift Large-scale Examination of Directed Genome Editing.},
journal = {PloS one},
volume = {14},
number = {3},
pages = {e0213317},
doi = {10.1371/journal.pone.0213317},
pmid = {30835740},
issn = {1932-6203},
mesh = {Animals ; Animals, Genetically Modified/*genetics ; *CRISPR-Cas Systems ; Embryo, Nonmammalian/cytology/metabolism ; Gene Editing/*methods ; Gene Knockout Techniques/*methods ; Genome ; Oryzias/*genetics ; Zebrafish/*genetics ; },
abstract = {In the era of CRISPR gene editing and genetic screening, there is an increasing demand for quick and reliable nucleic acid extraction pipelines for rapid genotyping of large and diverse sample sets. Despite continuous improvements of current workflows, the handling-time and material costs per sample remain major limiting factors. Here we present a robust method for low-cost DIY-pipet tips addressing these needs; i.e. using a cellulose filter disc inserted into a regular pipet tip. These filter-in-tips allow for a rapid, stand-alone four-step genotyping workflow by simply binding the DNA contained in the primary lysate to the cellulose filter, washing it in water and eluting it directly into the buffer for the downstream application (e.g. PCR). This drastically cuts down processing time to maximum 30 seconds per sample, with the potential for parallelizing and automation. We show the ease and sensitivity of our procedure by genotyping genetically modified medaka (Oryzias latipes) and zebrafish (Danio rerio) embryos (targeted by CRISPR/Cas9 knock-out and knock-in) in a 96-well plate format. The robust isolation and detection of multiple alleles of various abundancies in a mosaic genetic background allows phenotype-genotype correlation already in the injected generation, demonstrating the reliability and sensitivity of the protocol. Our method is applicable across kingdoms to samples ranging from cells to tissues i. e. plant seedlings, adult flies, mouse cell culture and tissue as well as adult fish fin-clips.},
}

Animals
Animals, Genetically Modified/*genetics
*CRISPR-Cas Systems
Embryo, Nonmammalian/cytology/metabolism
Gene Editing/*methods
Gene Knockout Techniques/*methods
Genome
Oryzias/*genetics
Zebrafish/*genetics

@article {pmid30769094,
year = {2019},
author = {Raas, Q and Gondcaille, C and Hamon, Y and Leoni, V and Caccia, C and Ménétrier, F and Lizard, G and Trompier, D and Savary, S},
title = {CRISPR/Cas9-mediated knockout of Abcd1 and Abcd2 genes in BV-2 cells: novel microglial models for X-linked Adrenoleukodystrophy.},
journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids},
volume = {1864},
number = {5},
pages = {704-714},
doi = {10.1016/j.bbalip.2019.02.006},
pmid = {30769094},
issn = {1879-2618},
mesh = {ATP Binding Cassette Transporter, Subfamily D/*genetics/metabolism ; ATP Binding Cassette Transporter, Subfamily D, Member 1/*genetics/metabolism ; Adrenoleukodystrophy/*genetics/metabolism/pathology ; Animals ; CRISPR-Cas Systems ; Cell Line ; Fatty Acids/metabolism ; Female ; Gene Deletion ; Mice, Inbred C57BL ; Microglia/metabolism/pathology ; },
abstract = {X-linked adrenoleukodystrophy (X-ALD), the most frequent peroxisomal disorder, is associated with mutation in the ABCD1 gene which encodes a peroxisomal ATP-binding cassette transporter for very long-chain fatty acids (VLCFA). The biochemical hallmark of the disease is the accumulation of VLCFA. Peroxisomal defect in microglia being now considered a priming event in the pathology, we have therefore generated murine microglial cells mutated in the Abcd1 gene and its closest homolog, the Abcd2 gene. Using CRISPR/Cas9 gene editing strategy, we obtained 3 cell clones with a single or double deficiency. As expected, only the combined absence of ABCD1 and ABCD2 proteins resulted in the accumulation of VLCFA. Ultrastructural analysis by electron microscopy revealed in the double mutant cells the presence of lipid inclusions similar to those observed in brain macrophages of patients. These observations are likely related to the increased level of cholesterol and the accumulation of neutral lipids that we noticed in mutant cells. A preliminary characterization of the impact of peroxisomal defects on the expression of key microglial genes such as Trem2 suggests profound changes in microglial functions related to inflammation and phagocytosis. The expression levels of presumed modifier genes have also been found modified in mutant cells, making these novel cell lines relevant for use as in vitro models to better understand the physiopathogenesis of X-ALD and to discover new therapeutic targets.},
}

ATP Binding Cassette Transporter, Subfamily D/*genetics/metabolism
ATP Binding Cassette Transporter, Subfamily D, Member 1/*genetics/metabolism
Adrenoleukodystrophy/*genetics/metabolism/pathology
Animals
CRISPR-Cas Systems
Cell Line
Fatty Acids/metabolism
Female
Gene Deletion
Mice, Inbred C57BL
Microglia/metabolism/pathology

@article {pmid30717310,
year = {2019},
author = {Lu, C and Pang, D and Li, M and Yuan, H and Yu, T and Huang, P and Li, J and Chen, X and Jiao, H and Xie, Z and Ouyang, H},
title = {CRISPR/Cas9-Mediated Hitchhike Expression of Functional shRNAs at the Porcine miR-17-92 Cluster.},
journal = {Cells},
volume = {8},
number = {2},
pages = {},
doi = {10.3390/cells8020113},
pmid = {30717310},
issn = {2073-4409},
mesh = {Animals ; Animals, Genetically Modified ; Base Sequence ; Blastocyst/metabolism ; CRISPR-Associated Protein 9/*metabolism ; CRISPR-Cas Systems/*genetics ; Cell Line ; Fetus/cytology ; Fibroblasts/metabolism ; Genes, Reporter ; Genome ; Green Fluorescent Proteins/metabolism ; MicroRNAs/*genetics/metabolism ; RNA, Guide/genetics ; RNA, Small Interfering/*metabolism ; Swine ; Transgenes ; },
abstract = {Successful RNAi applications depend on strategies allowing stable and persistent expression of minimal gene silencing triggers without perturbing endogenous gene expression. In this study, we proposed an endogenous microRNA (miRNA) cluster as a novel integration site for small hairpin RNAs (shRNAs). We successfully integrated exogenous shRNAs at the porcine miRNA-17-92 (pmiR-17-92) cluster via a CRISPR/Cas9-mediated knock-in strategy. The anti-EGFP or anti-CSFV shRNAs could be stably and effectively expressed at the control of the endogenous promoter of the pmiR-17-92 cluster. Importantly, we confirmed that hitchhike expression of anti- classical swine fever (CSFV) shRNA had no effect on cell growth, blastocyst development and endogenous pmiR-17-92 expression in selected transgene (TG) porcine fetal fibroblasts (PFFs) clones. Moreover, these TG PFFs could inhibit the replication of CSFV by half and could be further used for generation of transgenic pigs. Taken together, these results show that our RNA interference (RNAi) expression strategy benefits numerous applications, from miRNA, genome and transgenic research, to gene therapy.},
}

Animals
Animals, Genetically Modified
Base Sequence
Blastocyst/metabolism
CRISPR-Associated Protein 9/*metabolism
CRISPR-Cas Systems/*genetics
Cell Line
Fetus/cytology
Fibroblasts/metabolism
Genes, Reporter
Genome
Green Fluorescent Proteins/metabolism
MicroRNAs/*genetics/metabolism
RNA, Guide/genetics
RNA, Small Interfering/*metabolism
Swine
Transgenes

@article {pmid30639098,
year = {2019},
author = {Henriksson, J and Chen, X and Gomes, T and Ullah, U and Meyer, KB and Miragaia, R and Duddy, G and Pramanik, J and Yusa, K and Lahesmaa, R and Teichmann, SA},
title = {Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation.},
journal = {Cell},
volume = {176},
number = {4},
pages = {882-896.e18},
doi = {10.1016/j.cell.2018.11.044},
pmid = {30639098},
issn = {1097-4172},
support = {/WT_/Wellcome Trust/United Kingdom ; WT206194/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; CRISPR-Cas Systems/genetics ; Cell Differentiation/genetics/immunology ; Chromatin ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Genome ; High-Throughput Nucleotide Sequencing ; Humans ; Lymphocyte Activation/genetics/immunology ; Mice ; Mice, Inbred C57BL ; Receptor Cross-Talk/*immunology ; T-Lymphocytes, Helper-Inducer/metabolism ; Th2 Cells/*immunology/*metabolism ; Transcription Factors/metabolism ; },
abstract = {T helper type 2 (Th2) cells are important regulators of mammalian adaptive immunity and have relevance for infection, autoimmunity, and tumor immunology. Using a newly developed, genome-wide retroviral CRISPR knockout (KO) library, combined with RNA-seq, ATAC-seq, and ChIP-seq, we have dissected the regulatory circuitry governing activation and differentiation of these cells. Our experiments distinguish cell activation versus differentiation in a quantitative framework. We demonstrate that these two processes are tightly coupled and are jointly controlled by many transcription factors, metabolic genes, and cytokine/receptor pairs. There are only a small number of genes regulating differentiation without any role in activation. By combining biochemical and genetic data, we provide an atlas for Th2 differentiation, validating known regulators and identifying factors, such as Pparg and Bhlhe40, as part of the core regulatory network governing Th2 helper cell fates.},
}

Animals
CRISPR-Cas Systems/genetics
Cell Differentiation/genetics/immunology
Chromatin
Clustered Regularly Interspaced Short Palindromic Repeats/genetics
Genome
High-Throughput Nucleotide Sequencing
Humans
Lymphocyte Activation/genetics/immunology
Mice
Mice, Inbred C57BL
Receptor Cross-Talk/*immunology
T-Lymphocytes, Helper-Inducer/metabolism
Th2 Cells/*immunology/*metabolism
Transcription Factors/metabolism

@article {pmid30590039,
year = {2018},
author = {Hung, COY and Livesey, FJ},
title = {Altered γ-Secretase Processing of APP Disrupts Lysosome and Autophagosome Function in Monogenic Alzheimer's Disease.},
journal = {Cell reports},
volume = {25},
number = {13},
pages = {3647-3660.e2},
doi = {10.1016/j.celrep.2018.11.095},
pmid = {30590039},
issn = {2211-1247},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Alzheimer Disease/genetics/*metabolism/pathology ; Amyloid Precursor Protein Secretases/antagonists & inhibitors/*metabolism ; Amyloid beta-Protein Precursor/genetics/*metabolism ; Autophagosomes/*metabolism ; Autophagy ; Axons/metabolism ; CRISPR-Cas Systems/genetics ; Cerebral Cortex/pathology ; Endosomes/metabolism ; Humans ; Lysosomes/*metabolism ; Mutation/genetics ; Presenilin-1/genetics ; *Protein Processing, Post-Translational ; Proteolysis ; },
abstract = {Abnormalities of the endolysosomal and autophagy systems are found in Alzheimer's disease, but it is not clear whether defects in these systems are a cause or consequence of degenerative processes in the disease. In human neuronal models of monogenic Alzheimer's disease, APP and PSEN1 mutations disrupt lysosome function and autophagy, leading to impaired lysosomal proteolysis and defective autophagosome clearance. Processing of APP by γ-secretase is central to the pathogenic changes in the lysosome-autophagy system caused by PSEN1 and APP mutations: reducing production of C-terminal APP by inhibition of BACE1 rescued these phenotypes in both APP and PSEN1 mutant neurons, whereas inhibition of γ-secretase induced lysosomal and autophagic pathology in healthy neurons. Defects in lysosomes and autophagy due to PSEN1 mutations are rescued by CRISPR-knockout of APP. These data demonstrate a key role for proteolysis of the C-terminal of APP by γ-secretase in neuronal dysfunction in monogenic Alzheimer's disease.},
}

Alzheimer Disease/genetics/*metabolism/pathology
Amyloid Precursor Protein Secretases/antagonists & inhibitors/*metabolism
Amyloid beta-Protein Precursor/genetics/*metabolism
Autophagosomes/*metabolism
Autophagy
Axons/metabolism
CRISPR-Cas Systems/genetics
Cerebral Cortex/pathology
Endosomes/metabolism
Humans
Lysosomes/*metabolism
Mutation/genetics
Presenilin-1/genetics
*Protein Processing, Post-Translational
Proteolysis

@article {pmid30485088,
year = {2019},
author = {Xue, L and Tang, B and Chen, W and Luo, J},
title = {Prediction of CRISPR sgRNA Activity Using a Deep Convolutional Neural Network.},
journal = {Journal of chemical information and modeling},
volume = {59},
number = {1},
pages = {615-624},
doi = {10.1021/acs.jcim.8b00368},
pmid = {30485088},
issn = {1549-960X},
mesh = {CRISPR-Cas Systems/*genetics ; Computational Biology/*methods ; *Deep Learning ; Gene Editing ; Models, Molecular ; Nucleic Acid Conformation ; RNA, Guide/chemistry/*genetics ; },
abstract = {The CRISPR-Cas9 system derived from adaptive immunity in bacteria and archaea has been developed into a powerful tool for genome engineering with wide-ranging applications. Optimizing single-guide RNA (sgRNA) design to improve efficiency of target cleavage is a key step for successful gene editing using the CRISPR-Cas9 system. Because not all sgRNAs that cognate to a given target gene are equally effective, computational tools have been developed based on experimental data to increase the likelihood of selecting effective sgRNAs. Despite considerable efforts to date, it still remains a big challenge to accurately predict functional sgRNAs directly from large-scale sequence data. We propose DeepCas9, a deep-learning framework based on the convolutional neural network (CNN), to automatically learn the sequence determinants and further enable the identification of functional sgRNAs for the CRISPR-Cas9 system. We show that the CNN method outperforms previous methods in both (i) the ability to correctly identify highly active sgRNAs in experiments not used in the training and (ii) the ability to accurately predict the target efficacies of sgRNAs in different organisms. Besides, we further visualize the convolutional kernels and show the match of identified sequence signatures and known nucleotide preferences. We finally demonstrate the application of our method to the design of next-generation genome-scale CRISPRi and CRISPRa libraries targeting human and mouse genomes. We expect that DeepCas9 will assist in reducing the numbers of sgRNAs that must be experimentally validated to enable more effective and efficient genetic screens and genome engineering. DeepCas9 can be freely accessed via the Internet at https://github.com/lje00006/DeepCas9 .},
}

CRISPR-Cas Systems/*genetics
Computational Biology/*methods
*Deep Learning
Gene Editing
Models, Molecular
Nucleic Acid Conformation
RNA, Guide/chemistry/*genetics

@article {pmid30252203,
year = {2018},
author = {Ding, M and Liu, Y and Li, J and Yao, L and Liao, X and Xie, H and Yang, K and Zhou, Q and Liu, Y and Huang, W and Cai, Z},
title = {Oestrogen promotes tumorigenesis of bladder cancer by inducing the enhancer RNA-eGREB1.},
journal = {Journal of cellular and molecular medicine},
volume = {22},
number = {12},
pages = {5919-5927},
pmid = {30252203},
issn = {1582-4934},
mesh = {Aged ; Apoptosis/drug effects ; CRISPR-Cas Systems/genetics ; Carcinogenesis/drug effects/genetics/*pathology ; Cell Line, Tumor ; Cell Movement/drug effects/genetics ; Cell Proliferation/drug effects/genetics ; Down-Regulation/drug effects ; Enhancer Elements, Genetic/*genetics ; Estrogens/*adverse effects ; Female ; Gene Expression Regulation, Neoplastic/drug effects ; Gene Knockdown Techniques ; Humans ; Male ; Middle Aged ; Neoplasm Invasiveness ; RNA/*genetics ; RNA, Small Interfering/metabolism ; Up-Regulation/drug effects/genetics ; Urinary Bladder Neoplasms/genetics/*pathology ; },
abstract = {In recent years, studies have shown that enhancer RNAs (eRNAs) can be transcribed from enhancers. Increasing evidence has revealed that eRNAs play critical roles in the development of various cancers. Oestrogen-associated eRNAs are closely related to breast cancer. In view of the gender differences in bladder cancer (BCa), we suppose that oestrogen-associated eRNAs are also involved in tumorigenesis of BCa. In our study, we first demonstrated that eGREB1 derived from the enhancer of an oestrogen-responsive gene-GREB1 was up-regulated in BCa tissues, and the expression level of eGREB1 is positively associated with the histological grade and TNM stage of BCa. Knockdown of eGREB1 by CRISPR-Cas13a could inhibit cell proliferation, migration and invasion and induce apoptosis in BCa cells T24 and 5637. Besides, we exhibited the promoting effect of oestrogen on BCa cells. What's more, down-regulation of eGREB1 could improve the malignant biological characteristics of BCa cells induced by oestrogen. In conclusion, our data indicated that eGREB1 plays oncogenic role and oestrogen may promote the occurrence and progression of BCa by inducing eGREB1 production. Our findings provide new insights into the prevention of BCa and develop a novel therapeutic target for the treatment of BCa.},
}

Aged
Apoptosis/drug effects
CRISPR-Cas Systems/genetics
Carcinogenesis/drug effects/genetics/*pathology
Cell Line, Tumor
Cell Movement/drug effects/genetics
Cell Proliferation/drug effects/genetics
Down-Regulation/drug effects
Enhancer Elements, Genetic/*genetics
Estrogens/*adverse effects
Female
Gene Expression Regulation, Neoplastic/drug effects
Gene Knockdown Techniques
Humans
Male
Middle Aged
Neoplasm Invasiveness
RNA/*genetics
RNA, Small Interfering/metabolism
Up-Regulation/drug effects/genetics
Urinary Bladder Neoplasms/genetics/*pathology

@article {pmid29808941,
year = {2018},
author = {Roux, LN and Petit, I and Domart, R and Concordet, JP and Qu, J and Zhou, H and Joliot, A and Ferrigno, O and Aberdam, D},
title = {Modeling of Aniridia-Related Keratopathy by CRISPR/Cas9 Genome Editing of Human Limbal Epithelial Cells and Rescue by Recombinant PAX6 Protein.},
journal = {Stem cells (Dayton, Ohio)},
volume = {36},
number = {9},
pages = {1421-1429},
doi = {10.1002/stem.2858},
pmid = {29808941},
issn = {1549-4918},
mesh = {Aniridia/*genetics/pathology ; CRISPR-Cas Systems/*physiology ; Epithelium, Corneal/*metabolism ; Gene Editing/*methods ; Humans ; PAX6 Transcription Factor/*genetics ; },
abstract = {Heterozygous PAX6 gene mutations leading to haploinsufficiency are the main cause of congenital aniridia, a rare and progressive panocular disease characterized by reduced visual acuity. Up to 90% of patients suffer from aniridia-related keratopathy (ARK), caused by a combination of factors including limbal epithelial stem cell (LSC) deficiency, impaired healing response and abnormal differentiation of the corneal epithelium. It usually begins in the first decade of life, resulting in recurrent corneal erosions, sub-epithelial fibrosis, and corneal opacification. Unfortunately, there are currently no efficient treatments available for these patients and no in vitro model for this pathology. We used CRISPR/Cas9 technology to introduce into the PAX6 gene of LSCs a heterozygous nonsense mutation found in ARK patients. Nine clones carrying a p.E109X mutation on one allele were obtained with no off-target mutations. Compared with the parental LSCs, heterozygous mutant LSCs displayed reduced expression of PAX6 and marked slow-down of cell proliferation, migration and detachment. Moreover, addition to the culture medium of recombinant PAX6 protein fused to a cell penetrating peptide was able to activate the endogenous PAX6 gene and to rescue phenotypic defects of mutant LSCs, suggesting that administration of such recombinant PAX6 protein could be a promising therapeutic approach for aniridia-related keratopathy. More generally, our results demonstrate that introduction of disease mutations into LSCs by CRISPR/Cas9 genome editing allows the creation of relevant cellular models of ocular disease that should greatly facilitate screening of novel therapeutic approaches. Stem Cells 2018;36:1421-1429.},
}

Aniridia/*genetics/pathology
CRISPR-Cas Systems/*physiology
Epithelium, Corneal/*metabolism
Gene Editing/*methods
Humans
PAX6 Transcription Factor/*genetics

@article {pmid29768208,
year = {2018},
author = {Barazas, M and Annunziato, S and Pettitt, SJ and de Krijger, I and Ghezraoui, H and Roobol, SJ and Lutz, C and Frankum, J and Song, FF and Brough, R and Evers, B and Gogola, E and Bhin, J and van de Ven, M and van Gent, DC and Jacobs, JJL and Chapman, R and Lord, CJ and Jonkers, J and Rottenberg, S},
title = {The CST Complex Mediates End Protection at Double-Strand Breaks and Promotes PARP Inhibitor Sensitivity in BRCA1-Deficient Cells.},
journal = {Cell reports},
volume = {23},
number = {7},
pages = {2107-2118},
pmid = {29768208},
issn = {2211-1247},
support = {MR/M009971/1//Medical Research Council/United Kingdom ; C52690/A19270/CRUK_/Cancer Research UK/United Kingdom ; CRUK/A14276/CRUK_/Cancer Research UK/United Kingdom ; 090532/Z/09/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; BRCA1 Protein/*deficiency/metabolism ; CRISPR-Cas Systems/genetics ; Cell Line, Tumor ; *DNA Breaks, Double-Stranded/drug effects ; Disease Models, Animal ; Drug Resistance, Neoplasm/drug effects ; Female ; Mice ; Mouse Embryonic Stem Cells/drug effects/metabolism ; Multiprotein Complexes/*metabolism ; Poly(ADP-ribose) Polymerase Inhibitors/*pharmacology ; Telomere/metabolism ; },
abstract = {Selective elimination of BRCA1-deficient cells by inhibitors of poly(ADP-ribose) polymerase (PARP) is a prime example of the concept of synthetic lethality in cancer therapy. This interaction is counteracted by the restoration of BRCA1-independent homologous recombination through loss of factors such as 53BP1, RIF1, and REV7/MAD2L2, which inhibit end resection of DNA double-strand breaks (DSBs). To identify additional factors involved in this process, we performed CRISPR/SpCas9-based loss-of-function screens and selected for factors that confer PARP inhibitor (PARPi) resistance in BRCA1-deficient cells. Loss of members of the CTC1-STN1-TEN1 (CST) complex were found to cause PARPi resistance in BRCA1-deficient cells in vitro and in vivo. We show that CTC1 depletion results in the restoration of end resection and that the CST complex may act downstream of 53BP1/RIF1. These data suggest that, in addition to its role in protecting telomeres, the CST complex also contributes to protecting DSBs from end resection.},
}

Animals
BRCA1 Protein/*deficiency/metabolism
CRISPR-Cas Systems/genetics
Cell Line, Tumor
*DNA Breaks, Double-Stranded/drug effects
Disease Models, Animal
Drug Resistance, Neoplasm/drug effects
Female
Mice
Mouse Embryonic Stem Cells/drug effects/metabolism
Multiprotein Complexes/*metabolism
Poly(ADP-ribose) Polymerase Inhibitors/*pharmacology
Telomere/metabolism

@article {pmid29741611,
year = {2018},
author = {Mosqueira, D and Mannhardt, I and Bhagwan, JR and Lis-Slimak, K and Katili, P and Scott, E and Hassan, M and Prondzynski, M and Harmer, SC and Tinker, A and Smith, JGW and Carrier, L and Williams, PM and Gaffney, D and Eschenhagen, T and Hansen, A and Denning, C},
title = {CRISPR/Cas9 editing in human pluripotent stem cell-cardiomyocytes highlights arrhythmias, hypocontractility, and energy depletion as potential therapeutic targets for hypertrophic cardiomyopathy.},
journal = {European heart journal},
volume = {39},
number = {43},
pages = {3879-3892},
pmid = {29741611},
issn = {1522-9645},
support = {NC/C013202/1//National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; RG/15/6/31436//British Heart Foundation/United Kingdom ; NC/K000225/1//National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; SP/15/9/31605//British Heart Foundation/United Kingdom ; 340248//European Research Council/International ; RM/13/1/30157//British Heart Foundation/United Kingdom ; PG/14/59/31000//British Heart Foundation/United Kingdom ; RG/14/1/30588//British Heart Foundation/United Kingdom ; MR/M017354/1//Medical Research Council/United Kingdom ; RG/11/19/29264//British Heart Foundation/United Kingdom ; },
mesh = {Arrhythmias, Cardiac/*genetics ; CRISPR-Cas Systems/genetics ; Cardiomyopathy, Hypertrophic/*genetics ; Cells, Cultured ; Gene Editing ; Humans ; Models, Cardiovascular ; Myocardial Contraction/*genetics ; Myocytes, Cardiac/*physiology ; Pluripotent Stem Cells/*physiology ; },
abstract = {Aims: Sarcomeric gene mutations frequently underlie hypertrophic cardiomyopathy (HCM), a prevalent and complex condition leading to left ventricle thickening and heart dysfunction. We evaluated isogenic genome-edited human pluripotent stem cell-cardiomyocytes (hPSC-CM) for their validity to model, and add clarity to, HCM.

Methods and results: CRISPR/Cas9 editing produced 11 variants of the HCM-causing mutation c.C9123T-MYH7 [(p.R453C-β-myosin heavy chain (MHC)] in 3 independent hPSC lines. Isogenic sets were differentiated to hPSC-CMs for high-throughput, non-subjective molecular and functional assessment using 12 approaches in 2D monolayers and/or 3D engineered heart tissues. Although immature, edited hPSC-CMs exhibited the main hallmarks of HCM (hypertrophy, multi-nucleation, hypertrophic marker expression, sarcomeric disarray). Functional evaluation supported the energy depletion model due to higher metabolic respiration activity, accompanied by abnormalities in calcium handling, arrhythmias, and contraction force. Partial phenotypic rescue was achieved with ranolazine but not omecamtiv mecarbil, while RNAseq highlighted potentially novel molecular targets.

Conclusion: Our holistic and comprehensive approach showed that energy depletion affected core cardiomyocyte functionality. The engineered R453C-βMHC-mutation triggered compensatory responses in hPSC-CMs, causing increased ATP production and αMHC to energy-efficient βMHC switching. We showed that pharmacological rescue of arrhythmias was possible, while MHY7: MYH6 and mutant: wild-type MYH7 ratios may be diagnostic, and previously undescribed lncRNAs and gene modifiers are suggestive of new mechanisms.},
}

Arrhythmias, Cardiac/*genetics
CRISPR-Cas Systems/genetics
Cardiomyopathy, Hypertrophic/*genetics
Cells, Cultured
Gene Editing
Humans
Models, Cardiovascular
Myocardial Contraction/*genetics
Myocytes, Cardiac/*physiology
Pluripotent Stem Cells/*physiology

@article {pmid31782599,
year = {2019},
author = {Li, J and Qin, R and Zhang, Y and Xu, S and Liu, X and Yang, J and Zhang, X and Wei, P},
title = {Optimizing plant adenine base editor systems by modifying the transgene selection system.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.13304},
pmid = {31782599},
issn = {1467-7652},
abstract = {Classical CRISPR-Cas systems introduce a DNA double-strand break (DSB) at target genomic loci. In plant, DSBs are typically repaired through the error-prone nonhomologous end joining (NHEJ) pathway and result in small InDels (Chen et al., 2019). Recently, base editors (BEs), including cytosine BEs (CBEs) and adenine BEs (ABEs), were developed to introduce precise nucleotide substitutions by combining the CRISPR-Cas system with engineered nucleotide deaminases (Gaudelli et al., 2017; Komor et al., 2016). These BEs enable precise conversions between A∙T and G∙C pairs in the eukaryotic genome without introducing DSBs.},
}

@article {pmid31781808,
year = {2019},
author = {Hu, T and Cui, Y and Qu, X},
title = {Characterization and comparison of CRISPR Loci in Streptococcus thermophilus.},
journal = {Archives of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00203-019-01780-3},
pmid = {31781808},
issn = {1432-072X},
support = {31471712//National Natural Science Foundation of China/ ; 31371827//National Natural Science Foundation of China/ ; },
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) consists of a series of regular repeat-spacer sequences. It can not only act as a natural immune system in most prokaryotes, but also be utilized as the tool of newly developed genome modification and evolutionary researches. Streptococcus thermophilus is an important model organism for the study and application of CRISPR systems. In present study, the occurrence and diversity of CRISPR-Cas systems in the genomes of S. thermophilus were investigated including 4 new sequenced strains CS5, CS9, CS18, CS20, and other 23 strains downloaded from NCBI website. 66 CRISPR/Cas systems were identified among these 27 strains and could divided into four subsystems according to the arrangement of Cas proteins, notably I-E, II-A, II-C and III-A. Overall, 26 type II-C systems, 18 type II-A systems, 13 type III-A systems, 9 type I-E systems were identified. It was mentioned that CS20 contained two type II-C systems which had not been identified in the other 26 S. thermophilus strains. Overall, 1,080 spacers were analyzed and blasted. Sequence identity searches of spacers implied that most spacers derived from partial sequences of exogenous DNA, including various bacteriophages and plasmids. Of note, a large number of novel spacers were found in this study, indicating the unique phage environment they have undergone, especially CS20 strain. In addition, the analysis of the cas1 and cas9 genes revealed the genetic relationship among CRISPR-Cas system in these strains. Furthermore, the analysis of CRISPR spacers also indicated protospacer adjacent motif (PAM) sequences. Summary of PAM sequences could lay the foundations for the application of S. thermophilus CRISPR-Cas system. Our results suggested CS5 and CS18 can be used as model strains in the research of CRISPR-Cas system, and CS20 might have greater application potential in gene editing.},
}

@article {pmid31775607,
year = {2019},
author = {Nethery, MA and Henriksen, ED and Daughtry, KV and Johanningsmeier, SD and Barrangou, R},
title = {Comparative genomics of eight Lactobacillus buchneri strains isolated from food spoilage.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {902},
doi = {10.1186/s12864-019-6274-0},
pmid = {31775607},
issn = {1471-2164},
support = {Lactobacillus research//North Carolina Ag Foundation/ ; Internal support//Agricultural Research Service/ ; },
abstract = {BACKGROUND: Lactobacillus buchneri is a lactic acid bacterium frequently associated with food bioprocessing and fermentation and has been found to be either beneficial or detrimental to industrial food processes depending on the application. The ability to metabolize lactic acid into acetic acid and 1,2-propandiol makes L. buchneri invaluable to the ensiling process, however, this metabolic activity leads to spoilage in other applications, and is especially damaging to the cucumber fermentation industry. This study aims to augment our genomic understanding of L. buchneri in order to make better use of the species in a wide range of applicable industrial settings.

RESULTS: Whole-genome sequencing (WGS) was performed on seven phenotypically diverse strains isolated from spoiled, fermented cucumber and the ATCC type strain for L. buchneri, ATCC 4005. Here, we present our findings from the comparison of eight newly-sequenced and assembled genomes against two publicly available closed reference genomes, L. buchneri CD034 and NRRL B-30929. Overall, we see ~ 50% of all coding sequences are conserved across these ten strains. When these coding sequences are clustered by functional description, the strains appear to be enriched in mobile genetic elements, namely transposons. All isolates harbor at least one CRISPR-Cas system, and many contain putative prophage regions, some of which are targeted by the host's own DNA-encoded spacer sequences.

CONCLUSIONS: Our findings provide new insights into the genomics of L. buchneri through whole genome sequencing and subsequent characterization of genomic features, building a platform for future studies and identifying elements for potential strain manipulation or engineering.},
}

@article {pmid30948423,
year = {2019},
author = {Hu, XF and Zhang, B and Liao, CH and Zeng, ZJ},
title = {High-Efficiency CRISPR/Cas9-Mediated Gene Editing in Honeybee (Apis mellifera) Embryos.},
journal = {G3 (Bethesda, Md.)},
volume = {9},
number = {5},
pages = {1759-1766},
doi = {10.1534/g3.119.400130},
pmid = {30948423},
issn = {2160-1836},
mesh = {Animals ; Base Sequence ; Bees/*genetics ; *CRISPR-Cas Systems ; *Embryo, Nonmammalian ; *Gene Editing ; Gene Knockdown Techniques ; Glycoproteins/chemistry/genetics ; Insect Proteins/chemistry/genetics ; Mutagenesis ; Mutation ; PAX6 Transcription Factor/chemistry/genetics ; RNA, Guide ; },
abstract = {The honeybee (Apis mellifera) is an important insect pollinator of wild flowers and crops, playing critical roles in the global ecosystem. Additionally, the honeybee serves as an ideal social insect model. Therefore, functional studies on honeybee genes are of great interest. However, until now, effective gene manipulation methods have not been available in honeybees. Here, we reported an improved CRISPR/Cas9 gene-editing method by microinjecting sgRNA and Cas9 protein into the region of zygote formation within 2 hr after queen oviposition, which allows one-step generation of biallelic knockout mutants in honeybee with high efficiency. We first targeted the Mrjp1 gene. Two batches of honeybee embryos were collected and injected with Mrjp1 sgRNA and Cas9 protein at the ventral cephalic side and the dorsal posterior side of the embryos, respectively. The gene-editing rate at the ventral cephalic side was 93.3%, which was much higher than that (11.8%) of the dorsal-posterior-side injection. To validate the high efficiency of our honeybee gene-editing system, we targeted another gene, Pax6, and injected Pax6 sgRNA and Cas9 protein at the ventral cephalic side in the third batch. A 100% editing rate was obtained. Sanger sequencing of the TA clones showed that 73.3% (for Mrjp1) and 76.9% (for Pax6) of the edited current-generation embryos were biallelic knockout mutants. These results suggest that the CRISPR/Cas9 method we established permits one-step biallelic knockout of target genes in honeybee embryos, thereby demonstrating an efficient application to functional studies of honeybee genes. It also provides a useful reference to gene editing in other insects with elongated eggs.},
}

Animals
Base Sequence
Bees/*genetics
*CRISPR-Cas Systems
*Embryo, Nonmammalian
*Gene Editing
Gene Knockdown Techniques
Glycoproteins/chemistry/genetics
Insect Proteins/chemistry/genetics
Mutagenesis
Mutation
PAX6 Transcription Factor/chemistry/genetics
RNA, Guide

@article {pmid31771992,
year = {2019},
author = {Emmert, AS and Iwasawa, E and Shula, C and Schultz, P and Lindquist, D and Dunn, RS and Fugate, EM and Hu, YC and Mangano, FT and Goto, J},
title = {Impaired neural differentiation and glymphatic CSF flow in the Ccdc39 rat model of neonatal hydrocephalus: genetic interaction with L1cam.},
journal = {Disease models & mechanisms},
volume = {12},
number = {11},
pages = {},
doi = {10.1242/dmm.040972},
pmid = {31771992},
issn = {1754-8411},
abstract = {Neonatal hydrocephalus affects about one child per 1000 births and is a major congenital brain abnormality. We previously discovered a gene mutation within the coiled-coil domain-containing 39 (Ccdc39) gene, which causes the progressive hydrocephalus (prh) phenotype in mice due to lack of ependymal-cilia-mediated cerebrospinal fluid (CSF) flow. In this study, we used CRISPR/Cas9 to introduce the Ccdc39 gene mutation into rats, which are more suitable for imaging and surgical experiments. The Ccdc39prh/prh mutants exhibited mild ventriculomegaly at postnatal day (P)5 that progressed into severe hydrocephalus by P11 (P<0.001). After P11, macrophage and neutrophil invasion along with subarachnoid hemorrhage were observed in mutant brains showing reduced neurofilament density, hypomyelination and increased cell death signals compared with wild-type brains. Significantly more macrophages entered the brain parenchyma at P5 before hemorrhaging was noted and increased expression of a pro-inflammatory factor (monocyte chemoattractant protein-1) was found in the cortical neural and endothelial cells in the mutant brains at P11. Glymphatic-mediated CSF circulation was progressively impaired along the middle cerebral artery from P11 as mutants developed severe hydrocephalus (P<0.001). In addition, Ccdc39prh/prh mutants with L1 cell adhesion molecule (L1cam) gene mutation, which causes X-linked human congenital hydrocephalus, showed an accelerated early hydrocephalus phenotype (P<0.05-0.01). Our findings in Ccdc39prh/prh mutant rats demonstrate a possible causal role of neuroinflammation in neonatal hydrocephalus development, which involves impaired cortical development and glymphatic CSF flow. Improved understanding of inflammatory responses and the glymphatic system in neonatal hydrocephalus could lead to new therapeutic strategies for this condition.This article has an associated First Person interview with the joint first authors of the paper.},
}

@article {pmid31197108,
year = {2019},
author = {Miltner, AM and Mercado-Ayon, Y and Cheema, SK and Zhang, P and Zawadzki, RJ and La Torre, A},
title = {A Novel Reporter Mouse Uncovers Endogenous Brn3b Expression.},
journal = {International journal of molecular sciences},
volume = {20},
number = {12},
pages = {},
doi = {10.3390/ijms20122903},
pmid = {31197108},
issn = {1422-0067},
support = {Catalyst for a cure//The Glaucoma Research Foundation/ ; R25 GM116690/GM/NIGMS NIH HHS/United States ; P30 EY012576/NH/NIH HHS/United States ; R01 EY026942/EY/NEI NIH HHS/United States ; P30 EY012576/EY/NEI NIH HHS/United States ; R01EY026942/NH/NIH HHS/United States ; },
mesh = {Animals ; CRISPR-Cas Systems ; Genes, Reporter ; Homeodomain Proteins/*genetics/metabolism ; Luminescent Proteins/genetics/*metabolism ; Mice ; Mice, Inbred C57BL ; Recombinant Proteins/genetics/metabolism ; Retina/diagnostic imaging/*metabolism ; Transcription Factor Brn-3B/*genetics/metabolism ; Visual Pathways/diagnostic imaging/metabolism ; },
abstract = {Brn3b (Pou4f2) is a class-4 POU domain transcription factor known to play central roles in the development of different neuronal populations of the Central Nervous System, including retinal ganglion cells (RGCs), the neurons that connect the retina with the visual centers of the brain. Here, we have used CRISPR-based genetic engineering to generate a Brn3b-mCherry reporter mouse without altering the endogenous expression of Brn3b. In our mouse line, mCherry faithfully recapitulates normal Brn3b expression in the retina, the optic tracts, the midbrain tectum, and the trigeminal ganglia. The high sensitivity of mCherry also revealed novel expression of Brn3b in the neuroectodermal cells of the optic stalk during early stages of eye development. Importantly, the fluorescent intensity of Brn3b-mCherry in our reporter mice allows for noninvasive live imaging of RGCs using Scanning Laser Ophthalmoscopy (SLO), providing a novel tool for longitudinal monitoring of RGCs.},
}

Animals
CRISPR-Cas Systems
Genes, Reporter
Homeodomain Proteins/*genetics/metabolism
Luminescent Proteins/genetics/*metabolism
Mice
Mice, Inbred C57BL
Recombinant Proteins/genetics/metabolism
Retina/diagnostic imaging/*metabolism
Transcription Factor Brn-3B/*genetics/metabolism
Visual Pathways/diagnostic imaging/metabolism

@article {pmid31180051,
year = {2019},
author = {DI Felice, F and Micheli, G and Camilloni, G},
title = {Restriction enzymes and their use in molecular biology: An overview.},
journal = {Journal of biosciences},
volume = {44},
number = {2},
pages = {},
pmid = {31180051},
issn = {0973-7138},
mesh = {CRISPR-Cas Systems ; Chromatin/chemistry/metabolism ; Chromosome Mapping/*history/methods ; Cloning, Molecular/*methods ; DNA/chemistry/genetics/*history/metabolism ; DNA Methylation ; DNA Restriction Enzymes/genetics/*history/metabolism ; History, 20th Century ; History, 21st Century ; Humans ; Molecular Biology/*history/methods ; Nobel Prize ; Nucleotide Mapping/*history/methods ; Transcription Activator-Like Effector Nucleases/genetics/history/metabolism ; },
abstract = {Restriction enzymes have been identified in the early 1950s of the past century and have quickly become key players in the molecular biology of DNA. Forty years ago, the scientists whose pioneering work had explored the activity and sequence specificity of these enzymes, contributing to the definition of their enormous potential as tools for DNA characterization, mapping and manipulation, were awarded the Nobel Prize. In this short review, we celebrate the history of these enzymes in the light of their many different uses, as these proteins have accompanied the history of DNA for over 50 years representing active witnesses of major steps in the field.},
}

CRISPR-Cas Systems
Chromatin/chemistry/metabolism
Chromosome Mapping/*history/methods
Cloning, Molecular/*methods
DNA/chemistry/genetics/*history/metabolism
DNA Methylation
DNA Restriction Enzymes/genetics/*history/metabolism
History, 20th Century
History, 21st Century
Humans
Molecular Biology/*history/methods
Nobel Prize
Nucleotide Mapping/*history/methods
Transcription Activator-Like Effector Nucleases/genetics/history/metabolism

@article {pmid31069679,
year = {2019},
author = {Warner, BK and Alder, JK and Suli, A},
title = {Genome Editing in Zebrafish Using CRISPR-Cas9: Applications for Developmental Toxicology.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1965},
number = {},
pages = {235-250},
doi = {10.1007/978-1-4939-9182-2_16},
pmid = {31069679},
issn = {1940-6029},
support = {R00 HL113105/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; CRISPR-Cas Systems ; Embryonic Development/drug effects ; Gene Editing/*methods ; Gene-Environment Interaction ; Teratogens/toxicity ; Zebrafish/embryology/*genetics ; },
abstract = {Environment-gene interactions have a powerful impact on embryo development. The ability to precisely edit the genome makes it possible to address questions concerning the specific roles that genes or variants play in modulating the response to environmental challenges. In this chapter, we provide a simplified protocol using CRISPR-Cas9 ribonucleoproteins for genome editing in the zebrafish model organism. The genetic manipulation can then be coupled with chemical screens to identify and understand the mechanism behind toxicants or compounds that modulate development.},
}

Animals
CRISPR-Cas Systems
Embryonic Development/drug effects
Gene Editing/*methods
Gene-Environment Interaction
Teratogens/toxicity
Zebrafish/embryology/*genetics

@article {pmid30959888,
year = {2019},
author = {Ilyechova, EY and Bonaldi, E and Orlov, IA and Skomorokhova, EA and Puchkova, LV and Broggini, M},
title = {CRISP-R/Cas9 Mediated Deletion of Copper Transport Genes CTR1 and DMT1 in NSCLC Cell Line H1299. Biological and Pharmacological Consequences.},
journal = {Cells},
volume = {8},
number = {4},
pages = {},
doi = {10.3390/cells8040322},
pmid = {30959888},
issn = {2073-4409},
mesh = {CRISPR-Cas Systems/*genetics ; Carcinoma, Non-Small-Cell Lung/*genetics ; Cation Transport Proteins/*genetics/metabolism ; Cell Line, Tumor ; Cell Survival/genetics ; Copper/*metabolism ; Gene Expression Regulation, Neoplastic ; Humans ; Ion Transport ; Lung Neoplasms/*genetics ; Transcription Factors/*genetics/metabolism ; },
abstract = {Copper, the highly toxic micronutrient, plays two essential roles: it is a catalytic and structural cofactor for Cu-dependent enzymes, and it acts as a secondary messenger. In the cells, copper is imported by CTR1 (high-affinity copper transporter 1), a transmembrane high-affinity copper importer, and DMT1 (divalent metal transporter). In cytosol, enzyme-specific chaperones receive copper from CTR1 C-terminus and deliver it to their apoenzymes. DMT1 cannot be a donor of catalytic copper because it does not have a cytosol domain which is required for copper transfer to the Cu-chaperons that assist the formation of cuproenzymes. Here, we assume that DMT1 can mediate copper way required for a regulatory copper pool. To verify this hypothesis, we used CRISPR/Cas9 to generate H1299 cell line with CTR1 or DMT1 single knockout (KO) and CTR1/DMT1 double knockout (DKO). To confirm KOs of the genes qRT-PCR were used. Two independent clones for each gene were selected for further studies. In CTR1 KO cells, expression of the DMT1 gene was significantly increased and vice versa. In subcellular compartments of the derived cells, copper concentration dropped, however, in nuclei basal level of copper did not change dramatically. CTR1 KO cells, but not DMT1 KO, demonstrated reduced sensitivity to cisplatin and silver ions, the agents that enter the cell through CTR1. Using single CTR1 and DMT1 KO, we were able to show that both, CTR1 and DMT1, provided the formation of vital intracellular cuproenzymes (SOD1, COX), but not secretory ceruloplasmin. The loss of CTR1 resulted in a decrease in the level of COMMD1, XIAP, and NF-κB. Differently, the DMT1 deficiency induced increase of the COMMD1, HIF1α, and XIAP levels. The possibility of using CTR1 KO and DMT1 KO cells to study homeodynamics of catalytic and signaling copper selectively is discussed.},
}

CRISPR-Cas Systems/*genetics
Carcinoma, Non-Small-Cell Lung/*genetics
Cation Transport Proteins/*genetics/metabolism
Cell Line, Tumor
Cell Survival/genetics
Copper/*metabolism
Gene Expression Regulation, Neoplastic
Humans
Ion Transport
Lung Neoplasms/*genetics
Transcription Factors/*genetics/metabolism

@article {pmid30850374,
year = {2019},
author = {Labun, K and Guo, X and Chavez, A and Church, G and Gagnon, JA and Valen, E},
title = {Accurate analysis of genuine CRISPR editing events with ampliCan.},
journal = {Genome research},
volume = {29},
number = {5},
pages = {843-847},
doi = {10.1101/gr.244293.118},
pmid = {30850374},
issn = {1549-5469},
mesh = {CRISPR-Cas Systems/*genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; DNA End-Joining Repair/genetics ; Gene Editing/*methods ; High-Throughput Nucleotide Sequencing/*methods ; *Mutation Rate ; Recombinational DNA Repair/genetics ; Sequence Alignment/methods ; Software ; },
abstract = {We present ampliCan, an analysis tool for genome editing that unites highly precise quantification and visualization of genuine genome editing events. ampliCan features nuclease-optimized alignments, filtering of experimental artifacts, event-specific normalization, and off-target read detection and quantifies insertions, deletions, HDR repair, as well as targeted base editing. It is scalable to thousands of amplicon sequencing-based experiments from any genome editing experiment, including CRISPR. It enables automated integration of controls and accounts for biases at every step of the analysis. We benchmarked ampliCan on both real and simulated data sets against other leading tools, demonstrating that it outperformed all in the face of common confounding factors.},
}

CRISPR-Cas Systems/*genetics
Clustered Regularly Interspaced Short Palindromic Repeats
DNA End-Joining Repair/genetics
Gene Editing/*methods
High-Throughput Nucleotide Sequencing/*methods
*Mutation Rate
Recombinational DNA Repair/genetics
Sequence Alignment/methods
Software

@article {pmid30804513,
year = {2019},
author = {Newton, MD and Taylor, BJ and Driessen, RPC and Roos, L and Cvetesic, N and Allyjaun, S and Lenhard, B and Cuomo, ME and Rueda, DS},
title = {DNA stretching induces Cas9 off-target activity.},
journal = {Nature structural & molecular biology},
volume = {26},
number = {3},
pages = {185-192},
doi = {10.1038/s41594-019-0188-z},
pmid = {30804513},
issn = {1545-9985},
support = {MC_UP_1102/1/MRC_/Medical Research Council/United Kingdom ; MC_UP_1102/5/MRC_/Medical Research Council/United Kingdom ; 206292/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; 106954/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Bacteriophage lambda/*genetics ; CRISPR-Associated Protein 9/*metabolism ; CRISPR-Cas Systems/*genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; DNA Cleavage ; DNA, Viral/genetics/*metabolism ; Escherichia coli/virology ; Fluorescence Resonance Energy Transfer ; Gene Editing ; Microfluidics ; Microscopy, Confocal ; Optical Tweezers ; RNA, Guide/genetics ; Streptococcus pyogenes/enzymology ; },
abstract = {CRISPR/Cas9 is a powerful genome-editing tool, but spurious off-target edits present a barrier to therapeutic applications. To understand how CRISPR/Cas9 discriminates between on-targets and off-targets, we have developed a single-molecule assay combining optical tweezers with fluorescence to monitor binding to λ-DNA. At low forces, the Streptococcus pyogenes Cas9 complex binds and cleaves DNA specifically. At higher forces, numerous off-target binding events appear repeatedly at the same off-target sites in a guide-RNA-sequence-dependent manner, driven by the mechanical distortion of the DNA. Using single-molecule Förster resonance energy transfer (smFRET) and cleavage assays, we show that DNA bubbles induce off-target binding and cleavage at these sites, even with ten mismatches, as well as at previously identified in vivo off-targets. We propose that duplex DNA destabilization during cellular processes (for example, transcription, replication, etc.) can expose these cryptic off-target sites to Cas9 activity, highlighting the need for improved off-target prediction algorithms.},
}

Bacteriophage lambda/*genetics
CRISPR-Associated Protein 9/*metabolism
CRISPR-Cas Systems/*genetics
Clustered Regularly Interspaced Short Palindromic Repeats/*genetics
DNA Cleavage
DNA, Viral/genetics/*metabolism
Escherichia coli/virology
Fluorescence Resonance Energy Transfer
Gene Editing
Microfluidics
Microscopy, Confocal
Optical Tweezers
RNA, Guide/genetics
Streptococcus pyogenes/enzymology

@article {pmid30669572,
year = {2019},
author = {Escobar-Aguirre, S and Arancibia, D and Escorza, A and Bravo, C and Andrés, ME and Zamorano, P and Martínez, V},
title = {Development of a Bicistronic Vector for the Expression of a CRISPR/Cas9-mCherry System in Fish Cell Lines.},
journal = {Cells},
volume = {8},
number = {1},
pages = {},
doi = {10.3390/cells8010075},
pmid = {30669572},
issn = {2073-4409},
mesh = {Animals ; CRISPR-Associated Protein 9/*metabolism ; CRISPR-Cas Systems/*genetics ; Cell Line ; Fishes/*genetics ; Genetic Vectors/*metabolism ; Genome ; HEK293 Cells ; Humans ; Mutation/genetics ; Promoter Regions, Genetic ; RNA, Guide/metabolism ; Ribonuclease III/metabolism ; Zebrafish ; },
abstract = {The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system has been widely used in animals as an efficient genome editing tool. In fish cells, the technique has been difficult to implement due to the lack of proper vectors that use active promoters to drive the expression of both small guide RNA (sgRNA) and the S. pyogenes Cas9 (spCas9) protein within a single expression platform. Until now, fish cells have been modified using co-transfection of the mRNA of both the sgRNA and the spCas9. In the present study, we describe the optimization of a new vector for the expression of a CRISPR/Cas9 system, designed to edit the genome of fish cell lines, that combines a gene reporter (mCherry), sgRNA, and spCas9 in a single vector, facilitating the study of the efficiency of piscine and non-piscine promoters. A cassette containing the zebrafish U6 RNA III polymerase (U6ZF) promoter was used for the expression of the sgRNA. The new plasmid displayed the expression of spCas9, mCherry, and sgRNA in CHSE/F fish cells. The results demonstrate the functionality of the mammalian promoter and the U6ZF promoter in fish cell lines. This is the first approach aimed at developing a unified genome editing system in fish cells using bicistronic vectors, thus creating a powerful biotechnological platform to study gene function.},
}

Animals
CRISPR-Associated Protein 9/*metabolism
CRISPR-Cas Systems/*genetics
Cell Line
Fishes/*genetics
Genetic Vectors/*metabolism
Genome
HEK293 Cells
Humans
Mutation/genetics
Promoter Regions, Genetic
RNA, Guide/metabolism
Ribonuclease III/metabolism
Zebrafish

@article {pmid30357811,
year = {2019},
author = {Jiao, J and Jin, Y and Zheng, M and Zhang, H and Yuan, M and Lv, Z and Odhiambo, W and Yu, X and Zhang, P and Li, C and Ma, Y and Ji, Y},
title = {AID and TET2 co-operation modulates FANCA expression by active demethylation in diffuse large B cell lymphoma.},
journal = {Clinical and experimental immunology},
volume = {195},
number = {2},
pages = {190-201},
doi = {10.1111/cei.13227},
pmid = {30357811},
issn = {1365-2249},
mesh = {Animals ; Antineoplastic Agents/pharmacology ; B-Lymphocytes/metabolism ; Bortezomib/pharmacology ; CRISPR-Cas Systems ; Cell Line, Tumor ; Cell Transformation, Neoplastic/metabolism ; Cytidine Deaminase/genetics/*metabolism ; *DNA Demethylation ; DNA-Binding Proteins/*metabolism ; Disease Models, Animal ; Fanconi Anemia Complementation Group A Protein/*genetics/metabolism ; Gene Expression Regulation/genetics ; Gene Knockout Techniques ; Humans ; Immunoglobulin Class Switching/genetics ; Lymphoma, Large B-Cell, Diffuse/*drug therapy/immunology/*pathology ; Mice ; Mice, Inbred NOD ; Mice, SCID ; Proto-Oncogene Proteins/*metabolism ; Somatic Hypermutation, Immunoglobulin/genetics ; },
abstract = {Diffuse large B cell lymphoma (DLBCL) is traced to a mature B malignance carrying abnormal activation-induced cytidine deaminase (AID) expression. AID activity initially focuses on deamination of cytidine to uracil to generate somatic hypermutation and class-switch recombination of the immunoglobulin (Ig), but recently it has been implicated in DNA demethylation of genes required for B cell development and proliferation in the germinal centre (GC). However, whether AID activity on mutation or demethylation of genes involves oncogenesis of DLBCL has not been well characterized. Our data demonstrate that the proto-oncogene Fanconi anaemia complementation group A (FANCA) is highly expressed in DLBCL patients and cell lines, respectively. AID recruits demethylation enzyme ten eleven translocation family member (TET2) to bind the FANCA promoter. As a result, FANCA is demethylated and its expression increases in DLBCL. On the basis of our findings, we have developed a new therapeutic strategy to significantly inhibit DLBCL cell growth by combination of the proteasome inhibitor bortezomib with AID and TET2 depletion. These findings support a novel mechanism that AID has a crucial role in active demethylation for oncogene activation in DLBCL.},
}

Animals
Antineoplastic Agents/pharmacology
B-Lymphocytes/metabolism
Bortezomib/pharmacology
CRISPR-Cas Systems
Cell Line, Tumor
Cell Transformation, Neoplastic/metabolism
Cytidine Deaminase/genetics/*metabolism
*DNA Demethylation
DNA-Binding Proteins/*metabolism
Disease Models, Animal
Fanconi Anemia Complementation Group A Protein/*genetics/metabolism
Gene Expression Regulation/genetics
Gene Knockout Techniques
Humans
Immunoglobulin Class Switching/genetics
Lymphoma, Large B-Cell, Diffuse/*drug therapy/immunology/*pathology
Mice
Mice, Inbred NOD
Mice, SCID
Proto-Oncogene Proteins/*metabolism
Somatic Hypermutation, Immunoglobulin/genetics

@article {pmid31768302,
year = {2019},
author = {Cabrera-Contreras, R and Santamaría, RI and Bustos, P and Martínez-Flores, I and Meléndez-Herrada, E and Morelos-Ramírez, R and Barbosa-Amezcua, M and González-Covarrubias, V and Silva-Herzog, E and Soberón, X and González, V},
title = {Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children's Hospital in México City in an eight-years survey.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e8068},
doi = {10.7717/peerj.8068},
pmid = {31768302},
issn = {2167-8359},
abstract = {Staphylococcus epidermidis is a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistant S. epidermidis strains in eight years at a children's health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study, including resistance to methicillin, beta-lactams, fluoroquinolones, and macrolides. To understand the genetic basis of antibiotic resistance and its association with virulence and gene exchange, we sequenced the genomes of 17 S. epidermidis isolates. Whole-genome nucleotide identities between all the pairs of S. epidermidis strains were about 97% to 99%. We inferred a clonal structure and eight Multilocus Sequence Types (MLSTs) in the S. epidermidis sequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). Half of the S. epidermidis analyzed lacked the ica operon for biofilm formation. Likely, they are commensal S. epidermidis strains but multi-antibiotic resistant. Uneven distribution of insertion sequences, phages, and CRISPR-Cas immunity phage systems suggest frequent horizontal gene transfer. Rates of recombination between S. epidermidis strains were more prevalent than the mutation rate and affected the whole genome. Therefore, the multidrug resistance, independently of the pathogenic traits, might explain the persistence of specific highly adapted S. epidermidis clonal lineages in nosocomial settings.},
}

@article {pmid31768221,
year = {2019},
author = {Valenti, MT and Serena, M and Carbonare, LD and Zipeto, D},
title = {CRISPR/Cas system: An emerging technology in stem cell research.},
journal = {World journal of stem cells},
volume = {11},
number = {11},
pages = {937-956},
doi = {10.4252/wjsc.v11.i11.937},
pmid = {31768221},
issn = {1948-0210},
abstract = {The identification of new and even more precise technologies for modifying and manipulating the genome has been a challenge since the discovery of the DNA double helix. The ability to modify selectively specific genes provides a powerful tool for characterizing gene functions, performing gene therapy, correcting specific genetic mutations, eradicating diseases, engineering cells and organisms to achieve new and different functions and obtaining transgenic animals as models for studying specific diseases. Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology has recently revolutionized genome engineering. The application of this new technology to stem cell research allows disease models to be developed to explore new therapeutic tools. The possibility of translating new systems of molecular knowledge to clinical research is particularly appealing for addressing degenerative diseases. In this review, we describe several applications of CRISPR/Cas9 to stem cells related to degenerative diseases. In addition, we address the challenges and future perspectives regarding the use of CRISPR/Cas9 as an important technology in the medical sciences.},
}

@article {pmid31767844,
year = {2019},
author = {McGrath, E and Shin, H and Zhang, L and Phue, JN and Wu, WW and Shen, RF and Jang, YY and Revollo, J and Ye, Z},
title = {Targeting specificity of APOBEC-based cytosine base editor in human iPSCs determined by whole genome sequencing.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {5353},
doi = {10.1038/s41467-019-13342-8},
pmid = {31767844},
issn = {2041-1723},
support = {R01EB023812//U.S. Department of Health & Human Services | NIH | National Institute of Biomedical Imaging and Bioengineering (NIBIB)/ ; R03HD091264//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; OCS Challenge Grant//U.S. Department of Health & Human Services | U.S. Food and Drug Administration (U.S. Food & Drug Administration)/ ; OCS Challenge Grant//U.S. Department of Health & Human Services | U.S. Food and Drug Administration (U.S. Food & Drug Administration)/ ; },
abstract = {DNA base editors have enabled genome editing without generating DNA double strand breaks. The applications of this technology have been reported in a variety of animal and plant systems, however, their editing specificity in human stem cells has not been studied by unbiased genome-wide analysis. Here we investigate the fidelity of cytidine deaminase-mediated base editing in human induced pluripotent stem cells (iPSCs) by whole genome sequencing after sustained or transient base editor expression. While base-edited iPSC clones without significant off-target modifications are identified, this study also reveals the potential of APOBEC-based base editors in inducing unintended point mutations outside of likely in silico-predicted CRISPR-Cas9 off-targets. The majority of the off-target mutations are C:G->T:A transitions or C:G->G:C transversions enriched for the APOBEC mutagenesis signature. These results demonstrate that cytosine base editor-mediated editing may result in unintended genetic modifications with distinct patterns from that of the conventional CRISPR-Cas nucleases.},
}

@article {pmid31767004,
year = {2019},
author = {Mougiakos, I and Orsi, E and Ghiffary, MR and Post, W and de Maria, A and Adiego-Perez, B and Kengen, SWM and Weusthuis, RA and van der Oost, J},
title = {Efficient Cas9-based genome editing of Rhodobacter sphaeroides for metabolic engineering.},
journal = {Microbial cell factories},
volume = {18},
number = {1},
pages = {204},
doi = {10.1186/s12934-019-1255-1},
pmid = {31767004},
issn = {1475-2859},
support = {870.15.130//NWO-Green Foundation/ ; 2015/05279/ALW//NWO-Green Foundation/ ; 834279//European Research Council (ERC)/ ; },
abstract = {BACKGROUND: Rhodobacter sphaeroides is a metabolically versatile bacterium that serves as a model for analysis of photosynthesis, hydrogen production and terpene biosynthesis. The elimination of by-products formation, such as poly-β-hydroxybutyrate (PHB), has been an important metabolic engineering target for R. sphaeroides. However, the lack of efficient markerless genome editing tools for R. sphaeroides is a bottleneck for fundamental studies and biotechnological exploitation. The Cas9 RNA-guided DNA-endonuclease from the type II CRISPR-Cas system of Streptococcus pyogenes (SpCas9) has been extensively employed for the development of genome engineering tools for prokaryotes and eukaryotes, but not for R. sphaeroides.

RESULTS: Here we describe the development of a highly efficient SpCas9-based genomic DNA targeting system for R. sphaeroides, which we combine with plasmid-borne homologous recombination (HR) templates developing a Cas9-based markerless and time-effective genome editing tool. We further employ the tool for knocking-out the uracil phosphoribosyltransferase (upp) gene from the genome of R. sphaeroides, as well as knocking it back in while altering its start codon. These proof-of-principle processes resulted in editing efficiencies of up to 100% for the knock-out yet less than 15% for the knock-in. We subsequently employed the developed genome editing tool for the consecutive deletion of the two predicted acetoacetyl-CoA reductase genes phaB and phbB in the genome of R. sphaeroides. The culturing of the constructed knock-out strains under PHB producing conditions showed that PHB biosynthesis is supported only by PhaB, while the growth of the R. sphaeroides ΔphbB strains under the same conditions is only slightly affected.

CONCLUSIONS: In this study, we combine the SpCas9 targeting activity with the native homologous recombination (HR) mechanism of R. sphaeroides for the development of a genome editing tool. We further employ the developed tool for the elucidation of the PHB production pathway of R. sphaeroides. We anticipate that the presented work will accelerate molecular research with R. sphaeroides.},
}

@article {pmid31763794,
year = {2019},
author = {Kim, HM and Colaiácovo, MP},
title = {CRISPR-Cas9-Guided Genome Engineering in Caenorhabditis elegans.},
journal = {Current protocols in molecular biology},
volume = {129},
number = {1},
pages = {e106},
doi = {10.1002/cpmb.106},
pmid = {31763794},
issn = {1934-3647},
support = {R01 GM105853/NH/NIH HHS/United States ; },
abstract = {The CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated protein) system is being used successfully for efficient and targeted genome editing in various organisms, including the nematode Caenorhabditis elegans. Recent studies have developed a variety of CRISPR-Cas9 approaches to enhance genome engineering via two major DNA double-strand break repair pathways: nonhomologous end joining and homologous recombination. Here, we describe a protocol for Cas9-mediated C. elegans genome editing together with single guide RNA (sgRNA) and repair template cloning (canonical marker-free and cassette selection methods), as well as injection methods required for delivering Cas9, sgRNAs, and repair template DNA into the germline. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Guide RNA preparation Alternate Protocol 1: sgRNA cloning using fusion PCR Basic Protocol 2: Preparation of a repair template for homologous recombination Alternate Protocol 2: Preparation of repair template donors for the cassette selection method Basic Protocol 3: Injecting animals Basic Protocol 4: Screening transgenic worms with marker-free method Alternate Protocol 3: Screening transgenic worms with cassette selection method.},
}

@article {pmid31762718,
year = {2019},
author = {El-Kenawy, A and Benarba, B and Neves, AF and de Araujo, TG and Tan, BL and Gouri, A},
title = {Gene surgery: Potential applications for human diseases.},
journal = {EXCLI journal},
volume = {18},
number = {},
pages = {908-930},
doi = {10.17179/excli2019-1833},
pmid = {31762718},
issn = {1611-2156},
abstract = {Gene therapy became in last decade a new emerging therapeutic era showing promising results against different diseases such as cancer, cardiovascular diseases, diabetes, and neurological disorders. Recently, the genome editing technique for eukaryotic cells called CRISPR-Cas (Clustered Regulatory Interspaced Short Palindromic Repeats) has enriched the field of gene surgery with enhanced applications. In the present review, we summarized the different applications of gene surgery for treating human diseases such as cancer, diabetes, nervous, and cardiovascular diseases, besides the molecular mechanisms involved in these important effects. Several studies support the important therapeutic applications of gene surgery in a large number of health disorders and diseases including β-thalassemia, cancer, immunodeficiencies, diabetes, and neurological disorders. In diabetes, gene surgery was shown to be effective in type 1 diabetes by triggering different signaling pathways. Furthermore, gene surgery, especially that using CRISPR-Cas possessed important application on diagnosis, screening and treatment of several cancers such as lung, liver, pancreatic and colorectal cancer. Nevertheless, gene surgery still presents some limitations such as the design difficulties and costs regarding ZFNs (Zinc Finger Nucleases) and TALENs (Transcription Activator-Like Effector Nucleases) use, off-target effects, low transfection efficiency, in vivo delivery-safety and ethical issues.},
}

@article {pmid31759123,
year = {2019},
author = {Xu, CF and Chen, GJ and Luo, YL and Zhang, Y and Zhao, G and Lu, ZD and Czarna, A and Gu, Z and Wang, J},
title = {Rational designs of in vivo CRISPR-Cas delivery systems.},
journal = {Advanced drug delivery reviews},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.addr.2019.11.005},
pmid = {31759123},
issn = {1872-8294},
abstract = {The CRISPR-Cas system initiated a revolution in genome editing when it was, for the first time, demonstrated success in the mammalian cells. Today, scientists are able to readily edit the genome, regulate gene transcription, engineer posttranscriptional events, and image nucleic acids using CRISPR-Cas-based tools. However, to efficiently transport CRISPR-Cas into target tissues/cells remains challenging due to many extra- and intra-cellular barriers, therefore largely limiting the applications of CRISPR-based therapeutics in vivo. In this review, we summarize the features of plasmid-, RNA- and ribonucleoprotein (RNP)-based CRISPR-Cas therapeutics. Then, we survey the current in vivo delivery systems. Finally, we specify the requirements for efficient in vivo delivery in clinical settings, and highlight both efficiency and safety for different CRISPR-Cas tools.},
}

@article {pmid31756888,
year = {2019},
author = {Arizala, D and Arif, M},
title = {Genome-Wide Analyses Revealed Remarkable Heterogeneity in Pathogenicity Determinants, Antimicrobial Compounds, and CRISPR-Cas Systems of Complex Phytopathogenic Genus Pectobacterium.},
journal = {Pathogens (Basel, Switzerland)},
volume = {8},
number = {4},
pages = {},
doi = {10.3390/pathogens8040247},
pmid = {31756888},
issn = {2076-0817},
support = {Hatch project 9038H//National Institute of Food and Agriculture/ ; },
abstract = {The Pectobacterium genus comprises pectolytic enterobacteria defined as the causal agents of soft rot, blackleg, and aerial stem rot diseases of potato and economically important crops. In this study, we undertook extensive genome-wide comparative analyses of twelve species that conform the Pectobacterium genus. Bioinformatics approaches outlined a low nucleotide identity of P. parmentieri and P. wasabiae with other species, while P. carotovorum subsp. odoriferum was shown to harbor numerous pseudogenes, which suggests low coding capacity and genomic degradation. The genome atlases allowed for distinguishing distinct DNA structures and highlighted suspicious high transcription zones. The analyses unveiled a noteworthy heterogeneity in the pathogenicity determinants. Specifically, phytotoxins, polysaccharides, iron uptake systems, and the type secretion systems III-V were observed in just some species. Likewise, a comparison of gene clusters encoding antimicrobial compounds put in evidence for high conservation of carotovoricin, whereas a few species possessed the phenazine, carbapenem, and carocins. Moreover, three clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) systems: I-E, I-F, and III-A were identified. Surrounding some CRISPR-Cas regions, different toxin and antitoxin systems were found, which suggests bacterial suicide in the case of an immune system failure. Multiple whole-genome alignments shed light on to the presence of a novel cellobiose phosphotransferase system (PTS) exclusive to P. parmenteri, and an unreported T5SS conserved in almost all species. Several regions that were associated with virulence, microbe antagonism, and adaptive immune systems were predicted within genomic islands, which underscored the essential role that horizontal gene transfer has imparted in the dynamic evolution and speciation of Pectobacterium species. Overall, the results decipher the different strategies that each species has developed to infect their hosts, outcompete for food resources, and defend against bacteriophages. Our investigation provides novel genetic insights that will assist in understanding the pathogenic lifestyle of Pectobacterium, a genus that jeopardizes the agriculture sustainability of important crops worldwide.},
}

@article {pmid31753920,
year = {2019},
author = {Bhargava, R and Lopezcolorado, FW and Tsai, LJ and Stark, JM},
title = {The canonical non-homologous end joining factor XLF promotes chromosomal deletion rearrangements in human cells.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1074/jbc.RA119.010421},
pmid = {31753920},
issn = {1083-351X},
abstract = {Clastogen exposure can result in chromosomal rearrangements, including large deletions and inversions that are associated with cancer development. To examine such rearrangements in human cells, here we developed a reporter assay based on endogenous genes on chromosome 12. Using the RNA-guided nuclease Cas9, we induced two DNA double-strand breaks (DSBs), one each in the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and CD4 molecule (CD4) genes, that caused a deletion rearrangement leading to CD4 expression from the GAPDH promoter. We observed that this GAPDH-CD4 deletion rearrangement activates CD4+ cells that can be readily detected by flow cytometry. Similarly, DSBs in the lysophosphatidylcholine acyltransferase 3 (LPCAT3) and CD4 genes induced an LPCAT3-CD4 inversion rearrangement resulting in CD4 expression. Studying the GAPDH-CD4 deletion rearrangement in multiple cell lines, we found that the canonical non-homologous end joining (C-NHEJ) factor XLF promotes these rearrangements. Junction analysis uncovered that the relative contribution of C-NHEJ appears lower in U2OS than in HEK293 and A549 cells. Furthermore, an ATM kinase inhibitor increased C-NHEJ-mediated rearrangements only in U2OS cells. We also found that an XLF residue that is critical for an interaction with the C-NHEJ factor X-ray repair cross-complementing 4 (XRCC4), and XRCC4 itself, are each important for promoting both this deletion rearrangement and end joining without insertion/deletion mutations. In summary, a reporter assay based on endogenous genes on chromosome 12 reveals that XLF-dependent C-NHEJ promotes deletion rearrangements in human cells and that cell type-specific differences in the contribution of C-NHEJ and ATM kinase inhibition influence these rearrangements.},
}

@article {pmid31751606,
year = {2019},
author = {Hensel, G},
title = {Genetic transformation of Triticeae cereals - Summary of almost three-decade's development.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {107484},
doi = {10.1016/j.biotechadv.2019.107484},
pmid = {31751606},
issn = {1873-1899},
abstract = {Triticeae cereals are among the most important crop plants grown worldwide and being used for animal feed, food and beverages. Although breeding efforts evolved over the last ten thousand years our today's crop plants, biotechnological methods would help to speed up the process and incorporate traits impossible by conventional breeding. The main research topics were related to cover the future demand on our agricultural practices to supply sufficient food for a growing world population. Target traits are resistances against viral and fungal diseases, improvement of water and nitrogen use efficiency, to tackle plant architecture, both below and aboveground and to develop varieties that could grow on dry or salty locations. Other applications are considering accumulation of useful compounds or decreasing allergenicity. This review will summarize methods to generate the material including a section how genome engineering using gRNA/Cas (CRISPR/Cas) technology could further improve the methodology and will give an overview about recent and future applications.},
}

@article {pmid31748409,
year = {2019},
author = {Yoganand, KN and Muralidharan, M and Nimkar, S and Anand, B},
title = {Fidelity of prespacer capture and processing is governed by the PAM mediated interactions of Cas1-2 adaptation complex in CRISPR-Cas type I-E system.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1074/jbc.RA119.009438},
pmid = {31748409},
issn = {1083-351X},
abstract = {Prokaryotes deploy CRISPR-Cas based RNA guided adaptive immunity to fend off mobile genetic elements such as phages and plasmids. During CRISPR adaptation, which is the first stage of CRISPR immunity, the Cas1-2 integrase complex captures invader-derived prespacer DNA and specifically integrates it at the leader-repeat junction as spacers. For this integration, several variants of CRISPR-Cas systems use Cas4 as an indispensable nuclease for selectively processing the protospacer adjacent motif (PAM) containing prespacers to a defined length. Surprisingly, however, a few CRISPR-Cas systems such as type I-E are bereft of Cas4. Despite the absence of Cas4, how the prespacers show impeccable conservation for length and PAM selection in type I-E remains intriguing. Here, using in vivo and in vitro integration assays, deep sequencing and exonuclease footprinting, we show that Cas1-2/I-E- via the type I-E specific extended C-terminal tail of Cas1 -displays intrinsic affinity for PAM containing prespacers of variable length in Escherichia coli Although Cas1-2/I-E does not prune the prespacers, its binding protects the prespacer boundaries from exonuclease action. This ensures the pruning of exposed ends by exonucleases to aptly sized substrates for integration into the CRISPR locus. In summary, our work reveals that in few CRISPR-Cas variants such as type I-E, the specificity of PAM selection resides with Cas1-2, whereas the prespacer processing is co-opted by cellular non-Cas exonucleases, thereby offsetting the need for Cas4.},
}

@article {pmid31747398,
year = {2019},
author = {Mackow, NA and Shen, J and Adnan, M and Khan, AS and Fries, BC and Diago-Navarro, E},
title = {CRISPR-Cas influences the acquisition of antibiotic resistance in Klebsiella pneumoniae.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0225131},
doi = {10.1371/journal.pone.0225131},
pmid = {31747398},
issn = {1932-6203},
abstract = {In the US Carbapenem resistance in Klebsiella pneumoniae (Kp) is primarily attributed to the presence of the genes blaKPC-2 and blaKPC-3, which are transmitted via plasmids. Carbapenem-resistant Kp (CR-Kp) infections are associated with hospital outbreaks. They are difficult to treat, and associated with high mortality rates prompting studies of how resistance is obtained. In this study, we determined the presence of CRISPR-Cas in 304 clinical Kp strains. The CRISPR-Cas system has been found to prevent the spread of plasmids and bacteriophages, and therefore limits the horizontal gene transfer mediated by these mobile genetic elements. Here, we hypothesized that only those Kp strains that lack CRISPR-Cas can acquire CR plasmids, while those strains that have CRISPR-Cas are protected from gaining these plasmids and thus maintain sensitivity to antimicrobials. Our results show that CRISPR-Cas is absent in most clinical Kp strains including the clinically important ST258 clone. ST258 strains that continue to be sensitive to carbapenems also lack CRISPR-Cas. Interestingly, CRISPR-Cas positive strains, all non-ST258, exhibit lower resistance rates to antimicrobials than CRISPR-Cas negative strains. Importantly, we demonstrate that the presence of CRISPR-Cas appears to inhibit the acquisition of blaKPC plasmids in 7 Kp strains. Furthermore, we show that strains that are unable to acquire blaKPC plasmids contain CRISPR spacer sequences highly identical to those found in previously published multidrug-resistance-containing plasmids. Lastly, to our knowledge this is the first paper demonstrating that resistance to blaKPC plasmid invasion in a CRISPR-containing Kp strain can be reversed by deleting the CRISPR-cas cassette.},
}

@article {pmid31745933,
year = {2020},
author = {Swinnen, G and Jacobs, T and Pauwels, L and Goossens, A},
title = {CRISPR-Cas-Mediated Gene Knockout in Tomato.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2083},
number = {},
pages = {321-341},
doi = {10.1007/978-1-4939-9952-1_25},
pmid = {31745933},
issn = {1940-6029},
abstract = {Loss-of-function mutants are crucial for plant functional genomics studies. With the advent of CRISPR-Cas genome editing, generating null alleles for one or multiple specific gene(s) has become feasible for many plant species including tomato (Solanum lycopersicum). An easily programmable RNA-guided Cas endonuclease efficiently creates DNA double-strand breaks (DSBs) at targeted genomic sites that can be repaired by nonhomologous end joining (NHEJ) typically leading to small insertions or deletions that can produce null mutations. Here, we describe how to utilize CRISPR-Cas genome editing to obtain stable tomato gene knockout lines.},
}

@article {pmid31745554,
year = {2019},
author = {Bernheim, A and Bikard, D and Touchon, M and Rocha, EPC},
title = {Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkz1091},
pmid = {31745554},
issn = {1362-4962},
abstract = {Prokaryotes use CRISPR-Cas systems for adaptive immunity, but the reasons for the frequent existence of multiple CRISPRs and cas clusters remain poorly understood. Here, we analysed the joint distribution of CRISPR and cas genes in a large set of fully sequenced bacterial genomes and their mobile genetic elements. Our analysis suggests few negative and many positive epistatic interactions between Cas subtypes. The latter often result in complex genetic organizations, where a locus has a single adaptation module and diverse interference mechanisms that might provide more effective immunity. We typed CRISPRs that could not be unambiguously associated with a cas cluster and found that such complex loci tend to have unique type I repeats in multiple CRISPRs. Many chromosomal CRISPRs lack a neighboring Cas system and they often have repeats compatible with the Cas systems encoded in trans. Phages and 25 000 prophages were almost devoid of CRISPR-Cas systems, whereas 3% of plasmids had CRISPR-Cas systems or isolated CRISPRs. The latter were often compatible with the chromosomal cas clusters, suggesting that plasmids can co-opt the latter. These results highlight the importance of interactions between CRISPRs and cas present in multiple copies and in distinct genomic locations in the function and evolution of bacterial immunity.},
}

@article {pmid31742435,
year = {2019},
author = {Wierson, WA and Simone, BW and WareJoncas, Z and Mann, C and Welker, JM and Kar, B and Emch, MJ and Friedberg, I and Gendron, WAC and Barry, MA and Clark, KJ and Dobbs, DL and McGrail, MA and Ekker, SC and Essner, JJ},
title = {Expanding the CRISPR Toolbox with ErCas12a in Zebrafish and Human Cells.},
journal = {The CRISPR journal},
volume = {},
number = {},
pages = {},
doi = {10.1089/crispr.2019.0026},
pmid = {31742435},
issn = {2573-1602},
abstract = {CRISPR and CRISPR-Cas effector proteins enable the targeting of DNA double-strand breaks to defined loci based on a variable length RNA guide specific to each effector. The guide RNAs are generally similar in size and form, consisting of a ∼20 nucleotide sequence complementary to the DNA target and an RNA secondary structure recognized by the effector. However, the effector proteins vary in protospacer adjacent motif requirements, nuclease activities, and DNA binding kinetics. Recently, ErCas12a, a new member of the Cas12a family, was identified in Eubacterium rectale. Here, we report the first characterization of ErCas12a activity in zebrafish and expand on previously reported activity in human cells. Using a fluorescent reporter system, we show that CRISPR-ErCas12a elicits strand annealing mediated DNA repair more efficiently than CRISPR-Cas9. Further, using our previously reported gene targeting method that utilizes short homology, GeneWeld, we demonstrate the use of CRISPR-ErCas12a to integrate reporter alleles into the genomes of both zebrafish and human cells. Together, this work provides methods for deploying an additional CRISPR-Cas system, thus increasing the flexibility researchers have in applying genome engineering technologies.},
}

@article {pmid31742433,
year = {2019},
author = {Chen, SP and Wang, HH},
title = {An Engineered Cas-Transposon System for Programmable and Site-Directed DNA Transpositions.},
journal = {The CRISPR journal},
volume = {},
number = {},
pages = {},
doi = {10.1089/crispr.2019.0030},
pmid = {31742433},
issn = {2573-1602},
abstract = {Efficient site-directed insertion of heterologous DNA into a genome remains an outstanding challenge. Recombinases that can integrate kilobase-sized DNA constructs are difficult to reprogram to user-defined loci, while genomic insertion using CRISPR-Cas methods relies on inefficient host DNA repair machinery. Here, we describe a Cas-Transposon (CasTn) system for genomic insertions that uses a Himar1 transposase fused to a catalytically dead dCas9 nuclease to mediate programmable, site-directed transposition. Using cell-free in vitro assays, we demonstrated that the Himar-dCas9 fusion protein increased the frequency of transposon insertion at a single targeted TA dinucleotide by >300-fold compared to a random transposase, and that site-directed transposition is dependent on target choice while robust to log-fold variations in protein and DNA concentrations. We also showed that Himar-dCas9 mediates directed transposition into plasmids in Escherichia coli. This work highlights CasTn as a new modality for host-independent, programmable, site-directed DNA insertions.},
}

@article {pmid31740840,
year = {2019},
author = {Giesselmann, P and Brändl, B and Raimondeau, E and Bowen, R and Rohrandt, C and Tandon, R and Kretzmer, H and Assum, G and Galonska, C and Siebert, R and Ammerpohl, O and Heron, A and Schneider, SA and Ladewig, J and Koch, P and Schuldt, BM and Graham, JE and Meissner, A and Müller, FJ},
title = {Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41587-019-0293-x},
pmid = {31740840},
issn = {1546-1696},
support = {EXC 22167-390884018//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 13GW0128A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; },
abstract = {Expansions of short tandem repeats are genetic variants that have been implicated in several neuropsychiatric and other disorders, but their assessment remains challenging with current polymerase-based methods1-4. Here we introduce a CRISPR-Cas-based enrichment strategy for nanopore sequencing combined with an algorithm for raw signal analysis. Our method, termed STRique for short tandem repeat identification, quantification and evaluation, integrates conventional sequence mapping of nanopore reads with raw signal alignment for the localization of repeat boundaries and a hidden Markov model-based repeat counting mechanism. We demonstrate the precise quantification of repeat numbers in conjunction with the determination of CpG methylation states in the repeat expansion and in adjacent regions at the single-molecule level without amplification. Our method enables the study of previously inaccessible genomic regions and their epigenetic marks.},
}

@article {pmid31740839,
year = {2019},
author = {Cameron, P and Coons, MM and Klompe, SE and Lied, AM and Smith, SC and Vidal, B and Donohoue, PD and Rotstein, T and Kohrs, BW and Nyer, DB and Kennedy, R and Banh, LM and Williams, C and Toh, MS and Irby, MJ and Edwards, LS and Lin, CH and Owen, ALG and Künne, T and van der Oost, J and Brouns, SJJ and Slorach, EM and Fuller, CK and Gradia, S and Kanner, SB and May, AP and Sternberg, SH},
title = {Harnessing type I CRISPR-Cas systems for genome engineering in human cells.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41587-019-0310-0},
pmid = {31740839},
issn = {1546-1696},
abstract = {Type I CRISPR-Cas systems are the most abundant adaptive immune systems in bacteria and archaea1,2. Target interference relies on a multi-subunit, RNA-guided complex called Cascade3,4, which recruits a trans-acting helicase-nuclease, Cas3, for target degradation5-7. Type I systems have rarely been used for eukaryotic genome engineering applications owing to the relative difficulty of heterologous expression of the multicomponent Cascade complex. Here, we fuse Cascade to the dimerization-dependent, non-specific FokI nuclease domain8-11 and achieve RNA-guided gene editing in multiple human cell lines with high specificity and efficiencies of up to ~50%. FokI-Cascade can be reconstituted via an optimized two-component expression system encoding the CRISPR-associated (Cas) proteins on a single polycistronic vector and the guide RNA (gRNA) on a separate plasmid. Expression of the full Cascade-Cas3 complex in human cells resulted in targeted deletions of up to ~200 kb in length. Our work demonstrates that highly abundant, previously untapped type I CRISPR-Cas systems can be harnessed for genome engineering applications in eukaryotic cells.},
}

@article {pmid31735642,
year = {2019},
author = {Vink, JNA and Martens, KJA and Vlot, M and McKenzie, RE and Almendros, C and Estrada Bonilla, B and Brocken, DJW and Hohlbein, J and Brouns, SJJ},
title = {Direct Visualization of Native CRISPR Target Search in Live Bacteria Reveals Cascade DNA Surveillance Mechanism.},
journal = {Molecular cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molcel.2019.10.021},
pmid = {31735642},
issn = {1097-4164},
abstract = {CRISPR-Cas systems encode RNA-guided surveillance complexes to find and cleave invading DNA elements. While it is thought that invaders are neutralized minutes after cell entry, the mechanism and kinetics of target search and its impact on CRISPR protection levels have remained unknown. Here, we visualize individual Cascade complexes in a native type I CRISPR-Cas system. We uncover an exponential relation between Cascade copy number and CRISPR interference levels, pointing to a time-driven arms race between invader replication and target search, in which 20 Cascade complexes provide 50% protection. Driven by PAM-interacting subunit Cas8e, Cascade spends half its search time rapidly probing DNA (∼30 ms) in the nucleoid. We further demonstrate that target DNA transcription and CRISPR arrays affect the integrity of Cascade and affect CRISPR interference. Our work establishes the mechanism of cellular DNA surveillance by Cascade that allows the timely detection of invading DNA in a crowded, DNA-packed environment.},
}

@article {pmid31731968,
year = {2020},
author = {Lee, SS and Park, J and Heo, YB and Woo, HM},
title = {Case study of xylose conversion to glycolate in Corynebacterium glutamicum: Current limitation and future perspective of the CRISPR-Cas systems.},
journal = {Enzyme and microbial technology},
volume = {132},
number = {},
pages = {109395},
doi = {10.1016/j.enzmictec.2019.109395},
pmid = {31731968},
issn = {1879-0909},
abstract = {RNA-guided genome engineering technologies have been developed for the advanced metabolic engineering of microbial cells to enhance the production of value-added chemicals in Corynebacterium glutamicum as an industrial host. Here, we described the biotransformation of xylose to glycolate using engineered Corynebacterium glutamicum, a well-known industrial amino acid producer. A synthetic pathway involving heterologous D-tagatose 3-epimerase and L-fuculose kinase/aldolase reactions was introduced in C. glutamicum, resulting in 9.9 ± 0.01 g/L glycolate from 20 g/L xylose at a yield of 0.51 g/g (equal to 1.0 mol/mol). Additional glyoxylate reduction pathway developed by CRISPR-Cas12a recombineering has been introduced and attempted to increase the maximum theoretical molar yield of 2.0 (mol/mol). Due to the limitation of the CRISPR-Cas12a recombineering with TTTV PAM sites, advanced CRISPR-Cas systems were suggested for the next-round metabolic engineering for improving the glycolate yield to overcome the current genome-editing tool for metabolic engineering in C. glutamicum.},
}

@article {pmid31730297,
year = {2019},
author = {Liu, Q and Zhang, H and Huang, X},
title = {Anti-CRISPR proteins targeting the CRISPR-Cas system enrich the toolkit for genetic engineering.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.15139},
pmid = {31730297},
issn = {1742-4658},
abstract = {CRISPR-Cas adaptive immune defense systems, which are widely distributed in bacteria and Archaea, can provide sequence-specific protection against foreign DNA or RNA in some cases. However, the evolution of defense systems in bacterial hosts did not lead to the elimination of phages, and some phages carry anti-CRISPR genes that encode products that bind to the components mediating the defense mechanism and thus antagonize CRISPR-Cas immune systems of bacteria. Given the extensive application of CRISPR-Cas9 technologies in gene editing, in this review, we focus on the anti-CRISPR proteins (Acrs) that inhibit CRISPR-Cas systems for gene editing. We describe the discovery of Acrs in immune systems involving type I, II and V CRISPR-Cas immunity, discuss the potential function of Acrs in inactivating type II and V CRISPR-Cas systems for gene editing and gene modulation, and provide an outlook on the development of important biotechnology tools for genetic engineering using Acrs.},
}

@article {pmid31729390,
year = {2019},
author = {Medvedeva, S and Liu, Y and Koonin, EV and Severinov, K and Prangishvili, D and Krupovic, M},
title = {Virus-borne mini-CRISPR arrays are involved in interviral conflicts.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {5204},
pmid = {31729390},
issn = {2041-1723},
support = {ANR-17-CE15-0005-01//Agence Nationale de la Recherche (French National Research Agency)/ ; },
abstract = {CRISPR-Cas immunity is at the forefront of antivirus defense in bacteria and archaea and specifically targets viruses carrying protospacers matching the spacers catalogued in the CRISPR arrays. Here, we perform deep sequencing of the CRISPRome-all spacers contained in a microbiome-associated with hyperthermophilic archaea of the order Sulfolobales recovered directly from an environmental sample and from enrichment cultures established in the laboratory. The 25 million CRISPR spacers sequenced from a single sampling site dwarf the diversity of spacers from all available Sulfolobales isolates and display complex temporal dynamics. Comparison of closely related virus strains shows that CRISPR targeting drives virus genome evolution. Furthermore, we show that some archaeal viruses carry mini-CRISPR arrays with 1-2 spacers and preceded by leader sequences but devoid of cas genes. Closely related viruses present in the same population carry spacers against each other. Targeting by these virus-borne spacers represents a distinct mechanism of heterotypic superinfection exclusion and appears to promote archaeal virus speciation.},
}

@article {pmid31727474,
year = {2019},
author = {Manghwar, H and Lindsey, K and Zhang, X and Jin, S},
title = {CRISPR/Cas System: Recent Advances and Future Prospects for Genome Editing.},
journal = {Trends in plant science},
volume = {24},
number = {12},
pages = {1102-1125},
doi = {10.1016/j.tplants.2019.09.006},
pmid = {31727474},
issn = {1878-4372},
abstract = {Genome editing (GE) has revolutionized biological research through the new ability to precisely edit the genomes of living organisms. In recent years, various GE tools have been explored for editing simple and complex genomes. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has widely been used in GE due to its high efficiency, ease of use, and accuracy. It can be used to add desirable and remove undesirable alleles simultaneously in a single event. Here, we discuss various applications of CRISPR/Cas9 in a range of important crops, compare it with other GE tools, and review its mechanism, limitations, and future possibilities. Various newly emerging CRISPR/Cas systems, including base editing (BE), xCas9, and Cas12a (Cpf1), are also considered.},
}

@article {pmid31727255,
year = {2019},
author = {Liao, C and Slotkowski, RA and Beisel, CL},
title = {CRATES: A one-step assembly method for Class 2 CRISPR arrays.},
journal = {Methods in enzymology},
volume = {629},
number = {},
pages = {493-511},
doi = {10.1016/bs.mie.2019.04.011},
pmid = {31727255},
issn = {1557-7988},
abstract = {CRISPR-Cas systems naturally rely on CRISPR arrays to achieve immunity against multiple foreign invaders, where these arrays are also being utilized for multiplexed targeting as part of CRISPR technologies. However, CRISPR arrays have proven difficult to synthesize or assemble to-date due to the repetitive DNA repeats in each array. To overcome this barrier, we recently reported a cloning method we term CRATES (CRISPR Assembly through Trimmed Ends of Spacers) for the single-step, efficient generation of large Class 2 CRISPR arrays. CRATES generates CRISPR arrays through assembly of multiple repeat-spacer subunits using defined junction sequences within the trimmed portion of the CRISPR spacers. These arrays can be utilized by single-effector nucleases associated with Class 2 CRISPR-Cas systems, such as Cas9, Cas12a/Cpf1, or Cas13a/C2c2. Here, we describe in detail the steps for generating arrays utilized by Cas9 and Cas12a as well as composite arrays co-utilized by both nucleases. We also generate a representative three-spacer array and demonstrate multiplexed DNA cleavage through plasmid-clearance assays in Escherichia coli. This method is expected to simplify the study of natural CRISPR arrays and facilitate multiplexed targeting with programmable nucleases from Class 2 Cas nucleases across the myriad applications of CRISPR technologies.},
}

@article {pmid31727131,
year = {2019},
author = {Choi, BD and Yu, X and Castano, AP and Darr, H and Henderson, DB and Bouffard, AA and Larson, RC and Scarfò, I and Bailey, SR and Gerhard, GM and Frigault, MJ and Leick, MB and Schmidts, A and Sagert, JG and Curry, WT and Carter, BS and Maus, MV},
title = {CRISPR-Cas9 disruption of PD-1 enhances activity of universal EGFRvIII CAR T cells in a preclinical model of human glioblastoma.},
journal = {Journal for immunotherapy of cancer},
volume = {7},
number = {1},
pages = {304},
doi = {10.1186/s40425-019-0806-7},
pmid = {31727131},
issn = {2051-1426},
support = {NA//CRISPR Therapeutics/ ; R25NS065743/NH/NIH HHS/United States ; NA//Neurosurgery Research and Education Foundation/ ; NA//B*Cured/ ; NA//Society for Immunotherapy of Cancer/ ; NA/DRCRF/Damon Runyon Cancer Research Foundation/United States ; NA//Stand Up To Cancer/ ; NA//The Jenny Fund/ ; },
abstract = {Despite remarkable success in the treatment of hematological malignancies, CAR T-cell therapies for solid tumors have floundered, in large part due to local immune suppression and the effects of prolonged stimulation leading to T-cell dysfunction and exhaustion. One mechanism by which gliomas and other cancers can hamper CAR T cells is through surface expression of inhibitory ligands such as programmed cell death ligand 1 (PD-L1). Using the CRIPSR-Cas9 system, we created universal CAR T cells resistant to PD-1 inhibition through multiplexed gene disruption of endogenous T-cell receptor (TRAC), beta-2 microglobulin (B2M) and PD-1 (PDCD1). Triple gene-edited CAR T cells demonstrated enhanced activity in preclinical glioma models. Prolonged survival in mice bearing intracranial tumors was achieved after intracerebral, but not intravenous administration. CRISPR-Cas9 gene-editing not only provides a potential source of allogeneic, universal donor cells, but also enables simultaneous disruption of checkpoint signaling that otherwise impedes maximal antitumor functionality.},
}

@article {pmid31726388,
year = {2019},
author = {Lindel, F and Dodt, CR and Weidner, N and Noll, M and Bergemann, F and Behrendt, R and Fischer, S and Dietrich, J and Cartellieri, M and Hamann, MV and Lindemann, D},
title = {TraFo-CRISPR: Enhanced Genome Engineering by Transient Foamy Virus Vector-Mediated Delivery of CRISPR/Cas9 Components.},
journal = {Molecular therapy. Nucleic acids},
volume = {18},
number = {},
pages = {708-726},
pmid = {31726388},
issn = {2162-2531},
abstract = {The adaptation of CRISPR/Cas technology for use in mammals has revolutionized genome engineering. In particular with regard to clinical application, efficient expression of Cas9 within a narrow time frame is highly desirable to minimize the accumulation of off-target editing. We developed an effective, aptamer-independent retroviral delivery system for Cas9 mRNAs that takes advantage of a unique foamy virus (FV) capability: the efficient encapsidation and transfer of non-viral RNAs. This enabled us to create a FV vector toolbox for efficient, transient delivery (TraFo) of CRISPR/Cas9 components into different target tissues. Co-delivery of Cas9 mRNA by TraFo-Cas9 vectors in combination with retroviral, integration-deficient single guide RNA (sgRNA) expression enhanced efficacy and specificity of gene-inactivation compared with CRISPR/Cas9 lentiviral vector systems. Furthermore, separate TraFo-Cas9 delivery allowed the optional inclusion of a repair matrix for efficient gene correction or tagging as well as the addition of fluorescent negative selection markers for easy identification of off-target editing or incorrect repair events. Thus, the TraFo CRISPR toolbox represents an interesting alternative technology for gene inactivation and gene editing.},
}

@article {pmid31726224,
year = {2019},
author = {Creutzburg, SCA and Swartjes, T and van der Oost, J},
title = {Medium-throughput in vitro detection of DNA cleavage by CRISPR-Cas12a.},
journal = {Methods (San Diego, Calif.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymeth.2019.11.005},
pmid = {31726224},
issn = {1095-9130},
abstract = {Quantifying DNA cleavage by CRISPR-Cas nucleases is usually done by separating the cleaved products from the non-cleaved target by agarose gel electrophoresis. We devised a method that eliminates the quantification from band intensity on agarose gel, and uses a target with a fluorescent dye on the one end and a biotin on the other. Cleavage of the target will separate the dye from the biotin, and cause the dye to stay in solution when streptavidin beads are introduced. All non-cleaved target will be eliminated from solution and no longer contribute to detectable fluorescence. Cleavage will therefore increase the fluorescent signal. A control, which has no streptavidin treatment, is taken along to correct for any errors that might have been introduced by pipetting, inactivation of the fluorescent dye or release of the biotin during several steps of the procedure. With this method we were able to quantify the fraction of active Cas12a in a purification sample and assess the cleavage rate.},
}

@article {pmid31723075,
year = {2019},
author = {Zetsche, B and Strecker, J and Abudayyeh, OO and Gootenberg, JS and Scott, DA and Zhang, F},
title = {A Survey of Genome Editing Activity for 16 Cas12a Orthologs.},
journal = {The Keio journal of medicine},
volume = {},
number = {},
pages = {},
doi = {10.2302/kjm.2019-0009-OA},
pmid = {31723075},
issn = {1880-1293},
abstract = {The class 2 CRISPR-Cas endonuclease Cas12a (previously known as Cpf1) offers several advantages over Cas9, including the ability to process its own array and the requirement for just a single RNA guide. These attributes make Cas12a promising for many genome engineering applications. To further expand the suite of Cas12a tools available, we tested 16 Cas12a orthologs for activity in eukaryotic cells. Four of these new enzymes demonstrated targeted activity, one of which, from Moraxella bovoculi AAX11_00205 (Mb3Cas12a), exhibited robust indel formation. We also showed that Mb3Cas12a displays some tolerance for a shortened PAM (TTN versus the canonical Cas12a PAM TTTV). The addition of these enzymes to the genome editing toolbox will further expand the utility of this powerful technology.},
}

@article {pmid31722192,
year = {2019},
author = {Garcia, B and Lee, J and Edraki, A and Hidalgo-Reyes, Y and Erwood, S and Mir, A and Trost, CN and Seroussi, U and Stanley, SY and Cohn, RD and Claycomb, JM and Sontheimer, EJ and Maxwell, KL and Davidson, AR},
title = {Anti-CRISPR AcrIIA5 Potently Inhibits All Cas9 Homologs Used for Genome Editing.},
journal = {Cell reports},
volume = {29},
number = {7},
pages = {1739-1746.e5},
doi = {10.1016/j.celrep.2019.10.017},
pmid = {31722192},
issn = {2211-1247},
abstract = {CRISPR-Cas9 systems provide powerful tools for genome editing. However, optimal employment of this technology will require control of Cas9 activity so that the timing, tissue specificity, and accuracy of editing may be precisely modulated. Anti-CRISPR proteins, which are small, naturally occurring inhibitors of CRISPR-Cas systems, are well suited for this purpose. A number of anti-CRISPR proteins have been shown to potently inhibit subgroups of CRISPR-Cas9 systems, but their maximal inhibitory activity is generally restricted to specific Cas9 homologs. Since Cas9 homologs vary in important properties, differing Cas9s may be optimal for particular genome-editing applications. To facilitate the practical exploitation of multiple Cas9 homologs, here we identify one anti-CRISPR, called AcrIIA5, that potently inhibits nine diverse type II-A and type II-C Cas9 homologs, including those currently used for genome editing. We show that the activity of AcrIIA5 results in partial in vivo cleavage of a single-guide RNA (sgRNA), suggesting that its mechanism involves RNA interaction.},
}

@article {pmid31714905,
year = {2019},
author = {Anderson, ME and Mavica, J and Shackleford, L and Flis, I and Fochler, S and Basu, S and Alphey, L},
title = {CRISPR/Cas9 gene editing in the West Nile Virus vector, Culex quinquefasciatus Say.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0224857},
pmid = {31714905},
issn = {1932-6203},
abstract = {Culex quinquefasciatus Say is an opportunistic blood feeder with a wide geographic distribution which is also a major vector for a range of diseases of both animals and humans. CRISPR/Cas technologies have been applied to a wide variety of organisms for both applied and basic research purposes. CRISPR/Cas methods open new possibilities for genetic research in non-model organisms of public health importance. In this work we have adapted microinjection techniques commonly used in other mosquito species to Culex quinquefasciatus, and have shown these to be effective at generating homozygous knock-out mutations of a target gene in one generation. This is the first description of the kmo gene and mutant phenotype in this species.},
}

@article {pmid31711197,
year = {2019},
author = {Herrera-Carrillo, E and Gao, Z and Berkhout, B},
title = {CRISPR therapy towards an HIV cure.},
journal = {Briefings in functional genomics},
volume = {},
number = {},
pages = {},
doi = {10.1093/bfgp/elz021},
pmid = {31711197},
issn = {2041-2657},
abstract = {Tools based on RNA interference (RNAi) and the recently developed clustered regularly short palindromic repeats (CRISPR) system enable the selective modification of gene expression, which also makes them attractive therapeutic reagents for combating HIV infection and other infectious diseases. Several parallels can be drawn between the RNAi and CRISPR-Cas9 platforms. An ideal RNAi or CRISPR-Cas9 therapeutic strategy for treating infectious or genetic diseases should exhibit potency, high specificity and safety. However, therapeutic applications of RNAi and CRISPR-Cas9 have been challenged by several major limitations, some of which can be overcome by optimal design of the therapy or the design of improved reagents. In this review, we will discuss some advantages and limitations of anti-HIV strategies based on RNAi and CRISPR-Cas9 with a focus on the efficiency, specificity, off-target effects and delivery methods.},
}

@article {pmid31709036,
year = {2019},
author = {Tang, L and Yang, F and He, X and Xie, H and Liu, X and Fu, J and Xi, H and Lu, X and Liu, C and Song, Z and Qu, J and Zhao, J and Gu, F},
title = {Efficient cleavage resolves PAM preferences of CRISPR-Cas in human cells.},
journal = {Cell regeneration (London, England)},
volume = {8},
number = {2},
pages = {44-50},
pmid = {31709036},
issn = {2045-9769},
abstract = {Clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) of bacterial adaptive immunity have been adopted as a powerful and versatile tool for manipulation of the genome. This paradigm has been widely applied in biological research and treatments of animal or cellular disease models. A critical feature of CRISPR-Cas is the protospacer adjacent motif (PAM), which dictates the DNA target recognition mechanism of Cas proteins. While, direct identifying functional PAM sequences in human cells remains a challenge. Here, we developed a positive screen system termed PAM-DOSE (PAM Definition by Observable Sequence Excision) to delineate the functional PAMs in human cells. Specifically, the PAM libraries for CRISPR-Cas (SpCas9, SpCas9-NG, FnCas12a, AsCas12a, LbCas12a and MbCas12a) were generated and the corresponding CRISPR-Cas mediated cleaved fragments with functional PAM in human cells were harvested for DNA sequencing, which could be tracked and visualized with either florescence microscopy or flow cytometry analysis. With this system, we identified the functional PAMs of CRISPR-Cas members. We also found that spacer sequence affects the PAM preference of Cas proteins. This method will facilitate identification of functional PAMs for Cas-mediated human genome editing applications.},
}

@article {pmid31708910,
year = {2019},
author = {Li, Y and Peng, N},
title = {Endogenous CRISPR-Cas System-Based Genome Editing and Antimicrobials: Review and Prospects.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2471},
pmid = {31708910},
issn = {1664-302X},
abstract = {CRISPR-Cas systems adapt "memories" via spacers from viruses and plasmids to develop adaptive immunity against mobile genetic elements. Mature CRISPR RNAs guide CRISPR-associated nucleases to site-specifically cleave target DNA or RNA, providing an efficient genome engineering tool for organisms of all three kingdoms. Cas9, Cas12, and Cas13 are single proteins with multiple domains that are the most widely used CRISPR nucleases of the Class 2 system. However, these CRISPR endonucleases are large in size, leading to difficulty for manipulation and toxicity for cells. Most archaeal genomes and half of the bacterial genomes encode different types of CRISPR-Cas systems. Therefore, developing endogenous CRISPR-Cas systems-based genome editing will simplify manipulations and increase editing efficiency in prokaryotic cells. Here, we review the current applications and discuss the prospects of using endogenous CRISPR nucleases for genome engineering and CRISPR-based antimicrobials.},
}

@article {pmid31696232,
year = {2019},
author = {Davies, B},
title = {The technical risks of human gene editing.},
journal = {Human reproduction (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/humrep/dez162},
pmid = {31696232},
issn = {1460-2350},
abstract = {A recent report from Dr He Jiankui concerning the birth of twin girls harbouring mutations engineered by CRISPR/Cas nucleases has been met with international condemnation. Beside the serious ethical concerns, there are known technical risks associated with CRISPR/Cas gene editing which further raise questions about how these events could have been allowed to occur. Numerous studies have reported unexpected genomic mutation and mosaicism following the use of CRISPR/Cas nucleases, and it is currently unclear how prevalent these disadvantageous events are and how robust and sensitive the strategies to detect these unwanted events may be. Although Dr Jiankui's study appears to have involved certain checks to ascertain these risks, the decision to implant the manipulated embryos, given these unknowns, must nonetheless be considered reckless. Here I review the technical concerns surrounding genome editing and consider the available data from Dr Jiankui in this context. Although the data remains unpublished, preventing a thorough assessment of what was performed, it seems clear that the rationale behind the undertaking was seriously flawed; the procedures involved substantial technical risks which, when added to the serious ethical concerns, fully justify the widespread criticism that the events have received.},
}

@article {pmid31695072,
year = {2019},
author = {Scott, T and Urak, R and Soemardy, C and Morris, KV},
title = {Improved Cas9 activity by specific modifications of the tracrRNA.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {16104},
pmid = {31695072},
issn = {2045-2322},
support = {P01 AI099783/AI/NIAID NIH HHS/United States ; R01 AI111139/AI/NIAID NIH HHS/United States ; AI111139-01//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; 113407-01//U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH)/ ; },
abstract = {CRISPR/Cas is a transformative gene editing tool, that offers a simple and effective way to target a catalytic Cas9, the most widely used is derived from Streptococcus pyogenes (SpCas9), with a complementary small guide RNA (sgRNA) to inactivate endogenous genes resulting from insertions and deletions (indels). CRISPR/Cas9 has been rapidly applied to basic research as well as expanded for potential clinical applications. Utilization of spCas9 as an ribonuclearprotein complex (RNP) is considered the most safe and effective method to apply Cas9 technology, and the efficacy of this system is critically dependent on the ability of Cas9 to generate high levels of indels. We find here that novel sequence changes to the tracrRNA significantly improves Cas9 activity when delivered as an RNP. We demonstrate that a dual-guide RNA (dgRNA) with a modified tracrRNA can improve reporter knockdown and indel formation at several targets within the long terminal repeat (LTR) of HIV. Furthermore, the sequence-modified tracrRNAs improved Cas9-mediated reduction of CCR5 surface receptor expression in cell lines, which correlated with higher levels of indel formation. It was demonstrated that a Cas9 RNP with a sequence modified tracrRNA enhanced indel formation at the CCR5 target site in primary CD4+ T-cells. Finally, we show improved activity at two additional targets within the HBB locus and the BCL11A GATA site. Overall, the data presented here suggests that novel facile tracrRNA sequence changes could potentially be integrated with current dgRNA technology, and open up the possibility for the development of sequence modified tracrRNAs to improve Cas9 RNP activity.},
}

@article {pmid31693906,
year = {2019},
author = {Xu, Z and Li, M and Li, Y and Cao, H and Miao, L and Xu, Z and Higuchi, Y and Yamasaki, S and Nishino, K and Woo, PCY and Xiang, H and Yan, A},
title = {Native CRISPR-Cas-Mediated Genome Editing Enables Dissecting and Sensitizing Clinical Multidrug-Resistant P. aeruginosa.},
journal = {Cell reports},
volume = {29},
number = {6},
pages = {1707-1717.e3},
doi = {10.1016/j.celrep.2019.10.006},
pmid = {31693906},
issn = {2211-1247},
abstract = {Despite being fundamentally important and having direct therapeutic implications, the functional genomics of the clinical isolates of multidrug-resistant (MDR) pathogens is often impeded by the lack of genome-editing tools. Here, we report the establishment of a highly efficient, in situ genome-editing technique applicable in clinical and environmental isolates of the prototypic MDR pathogen P. aeruginosa by harnessing the endogenous type I-F CRISPR-Cas systems. Using this approach, we generate various reverse mutations in an epidemic MDR genotype, PA154197, and identify underlying resistance mechanisms that involve the extensive synergy among three different resistance determinants. Screening a series of "ancestor" mutant lines uncovers the remarkable sensitivity of the MDR line PA154197 to a class of small, cationic peptidomimetics, which sensitize PA154197 cells to antibiotics by perturbing outer-membrane permeability. These studies provide a framework for molecular genetics and anti-resistance drug discovery for clinically isolated MDR pathogens.},
}

@article {pmid31693467,
year = {2019},
author = {Valetdinova, KR and Ovechkina, VS and Zakian, SM},
title = {Methods for Correction of the Single-Nucleotide Substitution c.840C>T in Exon 7 of the SMN2 Gene.},
journal = {Biochemistry. Biokhimiia},
volume = {84},
number = {9},
pages = {1074-1084},
doi = {10.1134/S0006297919090104},
pmid = {31693467},
issn = {1608-3040},
mesh = {*CRISPR-Cas Systems/genetics ; Cells, Cultured ; Exons/*genetics ; Humans ; Polymorphism, Single Nucleotide/*genetics ; Survival of Motor Neuron 2 Protein/genetics ; },
abstract = {The CRISPR/Cas technology has a great potential in the treatment of many hereditary diseases. One of the prospective models for the CRISPR/Cas-mediated therapy is spinal muscular atrophy (SMA), a disease caused by deletion of the SMN1 gene that encodes the SMN protein required for the survival of motor neurons. SMA patients' genomes contain either single or several copies of SMN2 gene, which is a paralog of SMN1. Exon 7 of SMN2 has the single-nucleotide substitution c.840C>T leading to the defective splicing and decrease in the amounts of the full-length SMN. The objective of this study was to create and test gene-editing systems for correction of the single-nucleotide substitution c.840C>T in exon 7 of the SMN2 gene in fibroblasts, induced pluripotent stem cells, and motor neuron progenitors derived from a SMA patient. For this purpose, we used plasmid vectors expressing CRISPR/Cas9 and CRISPR/Cpf1, plasmid donor, and 90-nt single-stranded oligonucleotide templates that were delivered to the target cells by electroporation. Although sgRNA_T2 and sgRNA_T3 guiding RNAs were more efficient than sgRNA_T1 in fibroblasts (p < 0.05), no significant differences in the editing efficiency of sgRNA_T1, sgRNA_T2, and sgRNA_T3 was observed in patient-specific induced pluripotent stem cells and motor neuron progenitors. The highest editing efficiency in induced pluripotent stem cells and motor neuron progenitors was demonstrated by the sgRNA_T1 and 90-nt single-stranded oligonucleotide donors.},
}

*CRISPR-Cas Systems/genetics
Cells, Cultured
Exons/*genetics
Humans
Polymorphism, Single Nucleotide/*genetics
Survival of Motor Neuron 2 Protein/genetics

@article {pmid31691023,
year = {2019},
author = {Barman, A and Deb, B and Chakraborty, S},
title = {A glance at genome editing with CRISPR-Cas9 technology.},
journal = {Current genetics},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00294-019-01040-3},
pmid = {31691023},
issn = {1432-0983},
abstract = {In recent years, CRISPR-Cas9 technology is widely acknowledged for having major applications in the field of biotechnology for editing genome of any organism to treat a variety of complex diseases and for other purposes. The acronym 'CRISPR-Cas' stands for clustered regularly interspaced short palindromic repeats-CRISPR-associated genes. This genetic organization exists in prokaryotic organisms and aids in the development of adaptive immunity since a protein called Cas9 nuclease cleaves specific target nucleic acid sequences from foreign invaders and destroys them. This mode of action has gained interest of the researchers to understand the insights of CRISPR-Cas9 technology. Here, we review that CRISPR-Cas organization is restricted to two classes and possesses different protein effectors. We also review the architecture of CRISPR loci, mechanism involved in genome editing by CRISPR-Cas9 technology and pathways of repairing double-strand breaks (DSBs) generated during the process of genome editing. This review also presents the strategies to increase the Cas9 specificity and reduce off-target activity to achieve accurate genome editing. Further, this review provides information on CRISPR tools used for genome editing, databases that are required for storing data on loci, strategies for delivering CRISPR-Cas9 to cells under study and applications of CRISPR-Cas9 to various fields. Safety measures are implemented on this technology to avoid misuse or ethical issues. We also discuss about the future aspects and potential applications of CRISPR-Cas9 technology required mainly for the treatment of dreadful diseases, crop improvement as well as genetic improvement in human.},
}

@article {pmid31690864,
year = {2019},
author = {Niemiec, E and Howard, HC},
title = {Include egg donors in CRISPR gene-editing debate.},
journal = {Nature},
volume = {575},
number = {7781},
pages = {51},
doi = {10.1038/d41586-019-03388-5},
pmid = {31690864},
issn = {1476-4687},
mesh = {CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; *Gene Editing ; Humans ; Mutation ; },
}

CRISPR-Cas Systems
*Clustered Regularly Interspaced Short Palindromic Repeats
*Gene Editing
Humans
Mutation

@article {pmid31689989,
year = {2019},
author = {Vats, S and Kumawat, S and Kumar, V and Patil, GB and Joshi, T and Sonah, H and Sharma, TR and Deshmukh, R},
title = {Genome Editing in Plants: Exploration of Technological Advancements and Challenges.},
journal = {Cells},
volume = {8},
number = {11},
pages = {},
doi = {10.3390/cells8111386},
pmid = {31689989},
issn = {2073-4409},
support = {Ramalingaswami Fellowship//Department of Biotechnology , Ministry of Science and Technology/ ; },
abstract = {Genome-editing, a recent technological advancement in the field of life sciences, is one of the great examples of techniques used to explore the understanding of the biological phenomenon. Besides having different site-directed nucleases for genome editing over a decade ago, the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) based genome editing approach has become a choice of technique due to its simplicity, ease of access, cost, and flexibility. In the present review, several CRISPR/Cas based approaches have been discussed, considering recent advances and challenges to implicate those in the crop improvement programs. Successful examples where CRISPR/Cas approach has been used to improve the biotic and abiotic stress tolerance, and traits related to yield and plant architecture have been discussed. The review highlights the challenges to implement the genome editing in polyploid crop plants like wheat, canola, and sugarcane. Challenges for plants difficult to transform and germline-specific gene expression have been discussed. We have also discussed the notable progress with multi-target editing approaches based on polycistronic tRNA processing, Csy4 endoribonuclease, intron processing, and Drosha ribonuclease. Potential to edit multiple targets simultaneously makes it possible to take up more challenging tasks required to engineer desired crop plants. Similarly, advances like precision gene editing, promoter bashing, and methylome-editing will also be discussed. The present review also provides a catalog of available computational tools and servers facilitating designing of guide-RNA targets, construct designs, and data analysis. The information provided here will be useful for the efficient exploration of technological advances in genome editing field for the crop improvement programs.},
}

@article {pmid31685954,
year = {2019},
author = {Zlotorynski, E},
title = {CRISPR-Cas in its prime.},
journal = {Nature reviews. Molecular cell biology},
volume = {20},
number = {12},
pages = {718-719},
doi = {10.1038/s41580-019-0194-3},
pmid = {31685954},
issn = {1471-0080},
}

@article {pmid31685795,
year = {2019},
author = {Moon, SB and Kim, DY and Ko, JH and Kim, YS},
title = {Recent advances in the CRISPR genome editing tool set.},
journal = {Experimental & molecular medicine},
volume = {51},
number = {11},
pages = {130},
pmid = {31685795},
issn = {2092-6413},
support = {NRF-2016M3A9B6903343//National Research Foundation of Korea (NRF)/ ; NRF-2016M3A9B6903343//National Research Foundation of Korea (NRF)/ ; NRF-2016M3A9B6903343//National Research Foundation of Korea (NRF)/ ; NRF-2016M3A9B6903343//National Research Foundation of Korea (NRF)/ ; CAP-15-03-KRIBB//National Research Council of Science and Technology (National Research Council of Science & Technology)/ ; CAP-15-03-KRIBB//National Research Council of Science and Technology (National Research Council of Science & Technology)/ ; CAP-15-03-KRIBB//National Research Council of Science and Technology (National Research Council of Science & Technology)/ ; CAP-15-03-KRIBB//National Research Council of Science and Technology (National Research Council of Science & Technology)/ ; },
abstract = {Genome editing took a dramatic turn with the development of the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated proteins (Cas) system. The CRISPR-Cas system is functionally divided into classes 1 and 2 according to the composition of the effector genes. Class 2 consists of a single effector nuclease, and routine practice of genome editing has been achieved by the development of the Class 2 CRISPR-Cas system, which includes the type II, V, and VI CRISPR-Cas systems. Types II and V can be used for DNA editing, while type VI is employed for RNA editing. CRISPR techniques induce both qualitative and quantitative alterations in gene expression via the double-stranded breakage (DSB) repair pathway, base editing, transposase-dependent DNA integration, and gene regulation using the CRISPR-dCas or type VI CRISPR system. Despite significant technical improvements, technical challenges should be further addressed, including insufficient indel and HDR efficiency, off-target activity, the large size of Cas, PAM restrictions, and immune responses. If sophisticatedly refined, CRISPR technology will harness the process of DNA rewriting, which has potential applications in therapeutics, diagnostics, and biotechnology.},
}

@article {pmid31683605,
year = {2019},
author = {Kurilovich, E and Shiriaeva, A and Metlitskaya, A and Morozova, N and Ivancic-Bace, I and Severinov, K and Savitskaya, E},
title = {Genome Maintenance Proteins Modulate Autoimmunity Mediated Primed Adaptation by the Escherichia coli Type I-E CRISPR-Cas System.},
journal = {Genes},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/genes10110872},
pmid = {31683605},
issn = {2073-4425},
support = {19-74-20130 (E.S.)//Russian Science Foundation grant/ ; IP-2016-06-8861 (I.I.B.)//Croatian Science Foundation grant/ ; },
abstract = {Bacteria and archaea use CRISPR-Cas adaptive immunity systems to interfere with viruses, plasmids, and other mobile genetic elements. During the process of adaptation, CRISPR-Cas systems acquire immunity by incorporating short fragments of invaders' genomes into CRISPR arrays. The acquisition of fragments of host genomes leads to autoimmunity and may drive chromosomal rearrangements, negative cell selection, and influence bacterial evolution. In this study, we investigated the role of proteins involved in genome stability maintenance in spacer acquisition by the Escherichia coli type I-E CRISPR-Cas system targeting its own genome. We show here, that the deletion of recJ decreases adaptation efficiency and affects accuracy of spacers incorporation into CRISPR array. Primed adaptation efficiency is also dramatically inhibited in double mutants lacking recB and sbcD but not in single mutants suggesting independent involvement and redundancy of RecBCD and SbcCD pathways in spacer acquisition. While the presence of at least one of two complexes is crucial for efficient primed adaptation, RecBCD and SbcCD affect the pattern of acquired spacers. Overall, our data suggest distinct roles of the RecBCD and SbcCD complexes and of RecJ in spacer precursor selection and insertion into CRISPR array and highlight the functional interplay between CRISPR-Cas systems and host genome maintenance mechanisms.},
}

@article {pmid31682364,
year = {2019},
author = {Stasi, A and Rodrigues, IP},
title = {Dealing with Patent Fragmentation in Genetics: Can Patent Pools Facilitate the Development of CRISPR Gene-Editing Technology?.},
journal = {Journal of law and medicine},
volume = {26},
number = {4},
pages = {866-873},
pmid = {31682364},
issn = {1320-159X},
mesh = {CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; *Gene Editing ; Humans ; },
abstract = {The discovery of CRISPR systems has been one of the most exciting developments in the field of genetics in the past decade. The recent proliferation of intellectual property rights for CRISPR genome editing technology carries the risk of potential bottlenecks for further basic biological research and development of commercial products. To make CRISPR-based technology widely available, the reliance by the industry on efficient methods of collective management of intellectual property rights through patent pools seems inevitable. A packager of patent pools could be used as a mechanism to facilitate transactions in the market for technology and allow interested parties to deal with a single entity. This article argues that, while a global licensing platform could be effectively achieved in non-therapeutic applications of genome editing, it is questionable whether patent pooling would provide the ideal balance of incentive and reward for CRISPR genome editing technologies for human gene therapy.},
}

CRISPR-Cas Systems
*Clustered Regularly Interspaced Short Palindromic Repeats
*Gene Editing
Humans

@article {pmid31679813,
year = {2019},
author = {Ophinni, Y and Palatini, U and Hayashi, Y and Parrish, NF},
title = {piRNA-Guided CRISPR-like Immunity in Eukaryotes.},
journal = {Trends in immunology},
volume = {40},
number = {11},
pages = {998-1010},
doi = {10.1016/j.it.2019.09.003},
pmid = {31679813},
issn = {1471-4981},
abstract = {Eukaryotic genomes contain virus-derived sequences called endogenous virus elements (EVEs). The majority of EVEs are related to retroviruses, which integrate into the host genome in order to replicate. Some retroviral EVEs encode a function; for example, some produce proteins that block infection by related viruses. EVEs derived from nonretroviral viruses - also recently found in many eukaryotic genomes - are more enigmatic. Here, we summarize the evidence that EVEs can act as templates to generate Piwi-interacting RNAs (piRNAs), whose canonical function is sequence-specific silencing of transposable elements (TEs) to maintain genomic integrity. We argue that EVEs may thus enable heritable, sequence-specific antiviral immune memory in eukaryotes - analogous to CRISPR-Cas immunity in prokaryotes.},
}

@article {pmid31672965,
year = {2019},
author = {Jillette, N and Du, M and Zhu, JJ and Cardoz, P and Cheng, AW},
title = {Split selectable markers.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {4968},
pmid = {31672965},
issn = {2041-1723},
support = {R01 HG009900/HG/NHGRI NIH HHS/United States ; 1R01HG009900//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; P30CA034196//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Selectable markers are widely used in transgenesis and genome editing for selecting engineered cells with a desired genotype but the variety of markers is limited. Here we present split selectable markers that each allow for selection of multiple "unlinked" transgenes in the context of lentivirus-mediated transgenesis as well as CRISPR-Cas-mediated knock-ins. Split marker gene segments fused to protein splicing elements called "inteins" can be separately co-segregated with different transgenic vectors, and rejoin via protein trans-splicing to reconstitute a full-length marker protein in host cells receiving all intended vectors. Using a lentiviral system, we create and validate 2-split Hygromycin, Puromycin, Neomycin and Blasticidin resistance genes as well as mScarlet fluorescent proteins. By combining split points, we create 3- and 6-split Hygromycin resistance genes, demonstrating that higher-degree split markers can be generated by a "chaining" design. We adapt the split marker system for selecting biallelically engineered cells after CRISPR gene editing. Future engineering of split markers may allow selection of a higher number of genetic modifications in target cells.},
}

@article {pmid31671185,
year = {2019},
author = {Swarts, DC},
title = {Making the cut(s): how Cas12a cleaves target and non-target DNA.},
journal = {Biochemical Society transactions},
volume = {47},
number = {5},
pages = {1499-1510},
doi = {10.1042/BST20190564},
pmid = {31671185},
issn = {1470-8752},
abstract = {CRISPR-Cas12a (previously named Cpf1) is a prokaryotic deoxyribonuclease that can be programmed with an RNA guide to target complementary DNA sequences. Upon binding of the target DNA, Cas12a induces a nick in each of the target DNA strands, yielding a double-stranded DNA break. In addition to inducing cis-cleavage of the targeted DNA, target DNA binding induces trans-cleavage of non-target DNA. As such, Cas12a-RNA guide complexes can provide sequence-specific immunity against invading nucleic acids such as bacteriophages and plasmids. Akin to CRISPR-Cas9, Cas12a has been repurposed as a genetic tool for programmable genome editing and transcriptional control in both prokaryotic and eukaryotic cells. In addition, its trans-cleavage activity has been applied for high-sensitivity nucleic acid detection. Despite the demonstrated value of Cas12a for these applications, the exact molecular mechanisms of both cis- and trans-cleavage of DNA were not completely understood. Recent studies have revealed mechanistic details of Cas12a-mediates DNA cleavage: base pairing of the RNA guide and the target DNA induces major conformational changes in Cas12a. These conformational changes render Cas12a in a catalytically activated state in which it acts as deoxyribonuclease. This deoxyribonuclease activity mediates cis-cleavage of the displaced target DNA strand first, and the RNA guide-bound target DNA strand second. As Cas12a remains in the catalytically activated state after cis-cleavage, it subsequently demonstrates trans-cleavage of non-target DNA. Here, I review the mechanistic details of Cas12a-mediated cis- and trans-cleavage of DNA. In addition, I discuss how bacteriophage-derived anti-CRISPR proteins can inhibit Cas12a activity.},
}

@article {pmid31666940,
year = {2019},
author = {Yang, G and Huang, X},
title = {Methods and applications of CRISPR/Cas system for genome editing in stem cells.},
journal = {Cell regeneration (London, England)},
volume = {8},
number = {2},
pages = {33-41},
pmid = {31666940},
issn = {2045-9769},
abstract = {Genome editing technology holds great promise for genome manipulation and gene therapy. While widespread utilization, genome editing has been used to unravel the roles of specific genes in differentiation and pluripotency of stem cells, and reinforce the stem cell-based applications. In this review, we summarize the advances of genome editing technology, as well as the derivative technologies from CRISPR/Cas system, which show tremendous potential in various fields. We also highlight the key findings in the studies of stem cells and regeneration by genome editing technology.},
}

@article {pmid31665284,
year = {2019},
author = {Deaner, M and Alper, HS},
title = {Enhanced scale and scope of genome engineering and regulation using CRISPR/Cas in Saccharomyces cerevisiae.},
journal = {FEMS yeast research},
volume = {19},
number = {7},
pages = {},
doi = {10.1093/femsyr/foz076},
pmid = {31665284},
issn = {1567-1364},
abstract = {Although only 6 years old, the CRISPR system has blossomed into a tool for rapid, on-demand genome engineering and gene regulation in Saccharomyces cerevisiae. In this minireview, we discuss fundamental CRISPR technologies, tools to improve the efficiency and capabilities of gene targeting, and cutting-edge techniques to explore gene editing and transcriptional regulation at genome scale using pooled approaches. The focus is on applications to metabolic engineering with topics including development of techniques to edit the genome in multiplex, tools to enable large numbers of genetic modifications using pooled single-guide RNA libraries and efforts to enable programmable transcriptional regulation using endonuclease-null Cas enzymes.},
}

@article {pmid31663848,
year = {2019},
author = {Li, W and Zhang, Y and Han, B and Li, L and Li, M and Lu, X and Chen, C and Lu, M and Zhang, Y and Jia, X and Zhu, Z and Tong, X and Zhang, B},
title = {One-step efficient generation of dual-function conditional knockout and geno-tagging alleles in zebrafish.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
pmid = {31663848},
issn = {2050-084X},
support = {2018YFA0801000//National Key Research and Development Program of China/International ; 2016YFA0100500//National Key Research and Development Program of China/International ; 2015CB942803//National Key Basic Research Program of China/International ; 31671500//National Natural Science Foundation of China/International ; 31871458//National Natural Science Foundation of China/International ; 81371264//National Natural Science Foundation of China/International ; Qidong-SLS Innovation Fund//Peking University/International ; },
abstract = {CRISPR/Cas systems are widely used to knock out genes by inducing indel mutations, which are prone to genetic compensation. Complex genome modifications such as knockin (KI) might bypass compensation, though difficult to practice due to low efficiency. Moreover, no 'two-in-one' KI strategy combining conditional knockout (CKO) with fluorescent gene-labeling or further allele-labeling has been reported. Here, we developed a dual-cassette-donor strategy and achieved one-step and efficient generation of dual-function KI alleles at tbx5a and kctd10 loci in zebrafish via targeted insertion. These alleles display fluorescent gene-tagging and CKO effects before and after Cre induction, respectively. By introducing a second fluorescent reporter, geno-tagging effects were achieved at tbx5a and sox10 loci, exhibiting CKO coupled with fluorescent reporter switch upon Cre induction, enabling tracing of three distinct genotypes. We found that LiCl purification of gRNA is critical for highly efficient KI, and preselection of founders allows the efficient germline recovery of KI events.},
}