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CRISPR/Cas9

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https://www.readbyqxmd.com/read/29036671/crispr-cas9-mediated-gene-knockout-is-insensitive-to-target-copy-number-but-is-dependent-on-guide-rna-potency-and-cas9-sgrna-threshold-expression-level
#1
Garmen Yuen, Fehad J Khan, Shaojian Gao, Jayne M Stommel, Eric Batchelor, Xiaolin Wu, Ji Luo
CRISPR/Cas9 is a powerful gene editing tool for gene knockout studies and functional genomic screens. Successful implementation of CRISPR often requires Cas9 to elicit efficient target knockout in a population of cells. In this study, we investigated the role of several key factors, including variation in target copy number, inherent potency of sgRNA guides, and expression level of Cas9 and sgRNA, in determining CRISPR knockout efficiency. Using isogenic, clonal cell lines with variable copy numbers of an EGFP transgene, we discovered that CRISPR knockout is relatively insensitive to target copy number, but is highly dependent on the potency of the sgRNA guide sequence...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036432/copb2-is-essential-for-embryogenesis-and-hypomorphic-mutations-cause-human-microcephaly
#2
Andrew DiStasio, Ashley Driver, Kristen Sund, Milene Donlin, Ranjith M Muraleedharan, Shabnam Pooya, Beth Kline-Fath, Kenneth M Kaufman, Cynthia A Prows, Elizabeth Schorry, Biplab DasGupta, Rolf W Stottmann
Primary microcephaly is a congenital brain malformation characterized by a head circumference less than three standard deviations below the mean for age and sex and results in moderate to severe mental deficiencies and decreased lifespan. We recently studied two children with primary microcephaly in an otherwise unaffected family. Exome sequencing identified an autosomal recessive mutation leading to an amino acid substitution in a WD40 domain of the highly conserved Coatomer Protein Complex, Subunit Beta 2 (COPB2)...
September 19, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29036339/contribution-of-major-flm-isoforms-to-temperature-dependent-flowering-in-arabidopsis-thaliana
#3
Giovanna Capovilla, Efthymia Symeonidi, Rui Wu, Markus Schmid
FLOWERING LOCUS M (FLM), a component of the thermosensory flowering time pathway in Arabidopsis thaliana, is regulated by temperature-dependent alternative splicing (AS). The main splicing variant, FLM-β, is a well-documented floral repressor that is down-regulated in response to increasing ambient growth temperature. Two hypotheses have been formulated to explain how flowering time is modulated by AS of FLM. In the first model a second splice variant, FLM-δ, acts as a dominant negative isoform that competes with FLM-β at elevated ambient temperatures, thereby indirectly promoting flowering...
September 25, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29036337/a-collection-of-mutants-for-cle-peptide-encoding-genes-in-arabidopsis-generated-by-crispr-cas9-mediated-gene-targeting
#4
Yasuka L Yamaguchi, Takashi Ishida, Mika Yoshimura, Yuko Imamura, Chie Shimaoka, Shinichiro Sawa
The ligand-receptor-mediated intercellular communication system plays important roles in coordinating developmental and physiological events in multicellular organisms. In plants, CLE peptides and their cognate receptors are thought to be involved in various aspects of the plant life cycle. Although the importance of this communication is broadly recognized, most CLE peptides are yet to be functionally characterized. A major problem in research on small signaling peptide-encoding genes is the limited number of loss-of-function mutants available due to their small gene size...
September 25, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29036168/a-machine-learning-approach-for-predicting-crispr-cas9-cleavage-efficiencies-and-patterns-underlying-its-mechanism-of-action
#5
Shiran Abadi, Winston X Yan, David Amar, Itay Mayrose
The adaptation of the CRISPR-Cas9 system as a genome editing technique has generated much excitement in recent years owing to its ability to manipulate targeted genes and genomic regions that are complementary to a programmed single guide RNA (sgRNA). However, the efficacy of a specific sgRNA is not uniquely defined by exact sequence homology to the target site, thus unintended off-targets might additionally be cleaved. Current methods for sgRNA design are mainly concerned with predicting off-targets for a given sgRNA using basic sequence features and employ elementary rules for ranking possible sgRNAs...
October 16, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29035510/crispri-and-crispra-screens-in-mammalian-cells-for-precision-biology-and-medicine
#6
Martin Kampmann
Next-generation DNA sequencing technologies have led to a massive accumulation of genomic and transcriptomic data from patients and healthy individuals. The major challenge ahead is to understand the functional significance of the elements of the human genome and transcriptome, and implications for diagnosis and treatment. Genetic screens in mammalian cells are a powerful approach to systematically elucidate gene function in health and disease states. In particular, recently developed CRISPR/Cas9-based screening approaches have enormous potential to uncover mechanisms and therapeutic strategies for human diseases...
October 16, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29035385/class-2-crispr-cas-rna-guided-endonucleases-swiss-army-knives-of-genome-editing
#7
REVIEW
Stefano Stella, Pablo Alcón, Guillermo Montoya
CRISPR-Cas is a bacterial defense system against phage infection and nucleic acid invasion. Class 2 type II CRISPR-Cas9 has also been widely used for genome engineering. Here, we review novel insights into the CRISPR class 2 type V enzymes, specifically Cpf1 and C2c1, which display different DNA-recognition and cleavage characteristics than those of Cas9, the best-characterized member of class 2. Recent structures of these ribonucleoprotein complexes that capture several stages of the endonuclease reaction have provided molecular details of recognition, unzipping and cleavage of the target DNA, allowing their comparison with Cas9...
October 16, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29034901/generation-of-a-kcnj11-homozygous-knockout-human-embryonic-stem-cell-line-wae001-a-12-using-crispr-cas9
#8
Fang Yuan, Dongsheng Guo, Ge Gao, Yanli Liu, Yingying Xu, Yuhang Wu, Fan Yang, Xinrong Ke, Keyu Lai, Liangqing Hong, Yin-Xiong Li
The ATP-sensitive potassium channel is an octameric complex, and one of its subunits, namely Kir6.2, is encoded by the KCNJ11 gene. Mutations in KCNJ11 result in hyperinsulinism or diabetes mellitus, associated with abnormal insulin secretion. Here, using CRISPR/Cas9 editing, we established a homozygous mutant KCNJ11 cell line, WAe001-A-12, which was generated by a 62-bp deletion in the coding sequence of the human embryonic stem cell line H1. It was confirmed that this deletion in the KCNJ11 gene did not affect the protein expression levels of key pluripotent factors...
October 2017: Stem Cell Research
https://www.readbyqxmd.com/read/29034888/generation-of-two-men1-knockout-lines-from-a-human-embryonic-stem-cell-line
#9
Yanli Liu, Aynisahan Ruzi, Dongsheng Guo, Feima Wu, Haikun Liu, Han Wu, Yuhang Wu, Fang Yuan, Yuanqi Zhuang, Fan Yang, Keyu Lai, Liangxue Lai, Yin-Xiong Li
The MEN1 gene is cytogenetically located at 11q13.1 and encodes the nuclear protein menin, which is involved in cell proliferation, apoptosis, differentiation, and metabolism. Here, we generated two MEN1 knockout human embryonic stem cell lines, WAe001-A-4 and WAe001-A-5, by targeting exon-2 and exon-9 of MEN1 using the CRISPR/Cas9 technique. These cell lines maintained their pluripotency, in vitro differentiation potential, normal morphology, and karyotype. These human MEN1-mutated cell lines not only enlarge the pool of lab resources but also provide ideal models to dissect the detailed physio-pathological roles of the menin protein...
October 2017: Stem Cell Research
https://www.readbyqxmd.com/read/29034887/generation-of-three-mir-122-knockout-lines-from-a-human-embryonic-stem-cell-line
#10
Yanli Liu, Feima Wu, Yuanqi Zhuang, Dongsheng Guo, Nasir Abbas, Ruzi Wei, Kepin Wang, Yan Chen, Jiawang Tao, Yuhang Wu, Fang Yuan, Tingcai Pan, Fan Yang, Keyu Lai, Liangxue Lai, Yin-Xiong Li
miR-122 is the most abundant miRNA in the human liver, accounting for 52% of the entire hepatic miRNome. Previous studies have demonstrated that miR-122 plays key roles in hepatocyte growth, metabolism, and homeostasis. Here, we created three miR-122 knockout human embryonic stem cell line lines, WAe001-A-7, WAe001-A-8, and WAe001-A-9, using the CRISPR/Cas9 technique. These mutated cell lines retained their pluripotency, in vitro differentiation potential, normal morphology, and karyotype.
October 2017: Stem Cell Research
https://www.readbyqxmd.com/read/29034883/establishment-of-a-congenital-tooth-agenesis-related-gene-msx1-knockout-human-embryonic-stem-cell-lines-by-crispr-cas9-technology
#11
Yanting Xue, Minghui Zhu, Dajiang Qin, Yongjin Li, Xiaotong Cen, Xiaofang Sun, Wenwei Lian, Baojian Liao
Human MSX1 gene is mapped to chromosome 4 and encodes a 303aa homeobox protein MSX1. MSX1 expression appears during early tooth development of vertebrate embryogenesis. Mutations in this protein are related to human tooth anomalie, cleft lip and palate and congenital ectodermal dysplasia syndrome. Most of the confirmed pathogenic mutations are located in exon2 encoded homeobox domain. Here, we report the establishment of MSX1 gene knockout human embryonic stem (hES) cell lines by CRISPR-Cas9 technology. These cell lines provide good materials for further studies of the roles MSX1 plays in human tooth development and congenital tooth agenesis...
October 2017: Stem Cell Research
https://www.readbyqxmd.com/read/29033363/convergent-transcriptional-programs-regulate-camp-levels-in-c-%C3%A2-elegans-gabaergic-motor-neurons
#12
Bin Yu, Xiaolin Wang, Shuai Wei, Tao Fu, Emmanuel Enoch Dzakah, Ahmed Waqas, Walter W Walthall, Ge Shan
Both transcriptional regulation and signaling pathways play crucial roles in neuronal differentiation and plasticity. Caenorhabditis elegans possesses 19 GABAergic motor neurons (MNs) called D MNs, which are divided into two subgroups: DD and VD. DD, but not VD, MNs reverse their cellular polarity in a developmental process called respecification. UNC-30 and UNC-55 are two critical transcription factors in D MNs. By using chromatin immunoprecipitation with CRISPR/Cas9 knockin of GFP fusion, we uncovered the global targets of UNC-30 and UNC-55...
October 11, 2017: Developmental Cell
https://www.readbyqxmd.com/read/29032444/modulating-signaling-networks-by-crispr-cas9-mediated-transposable-element-insertion
#13
REVIEW
Luis María Vaschetto
In a recent past, transposable elements (TEs) were referred to as selfish genetic components only capable of copying themselves with the aim of increasing the odds of being inherited. Nonetheless, TEs have been initially proposed as positive control elements acting in synergy with the host. Nowadays, it is well known that TE movement into host genome comprises an important evolutionary mechanism capable of increasing the adaptive fitness. As insights into TE functioning are increasing day to day, the manipulation of transposition has raised an interesting possibility of setting the host functions, although the lack of appropriate genome engineering tools has unpaved it...
October 14, 2017: Current Genetics
https://www.readbyqxmd.com/read/29031777/new-applications-of-crispr-cas9-system-on-mutant-dna-detection
#14
Chenqiang Jia, Cong Huai, Jiaqi Ding, Lingna Hu, Bo Su, Hongyan Chen, Daru Lu
The detection of mutant DNA is critical for precision medicine, but low-frequency DNA mutation is very hard to be determined. CRISPR/Cas9 is a robust tool for in vivo gene editing, and shows the potential for precise in vitro DNA cleavage. Here we developed a DNA mutation detection system based on CRISPR/Cas9 that can detect gene mutation efficiently even in a low-frequency condition. The system of CRISPR/Cas9 cleavage in vitro showed a high accuracy similar to traditional T7 endonuclease I (T7E1) assay in estimating mutant DNA proportion in the condition of normal frequency...
October 11, 2017: Gene
https://www.readbyqxmd.com/read/29031730/bidirectional-manipulation-of-gene-expression-in-adipocytes-using-crispra-and-sirna
#15
Morten Lundh, Kaja Pluciñska, Marie S Isidor, Patricia S S Petersen, Brice Emanuelli
OBJECTIVE: Functional investigation of novel gene/protein targets associated with adipocyte differentiation or function heavily relies on efficient and accessible tools to manipulate gene expression in adipocytes in vitro. Recent advances in gene-editing technologies such as CRISPR-Cas9 have not only eased gene editing but also greatly facilitated modulation of gene expression without altering the genome. Here, we aimed to develop and validate a competent in vitro adipocyte model of controllable functionality as well as multiplexed gene manipulation in adipocytes, using the CRISPRa "SAM" system and siRNAs to simultaneously overexpress and silence selected genes in the same cell populations...
October 2017: Molecular Metabolism
https://www.readbyqxmd.com/read/29030852/genomic-tagging-of-ago1-using-crispr-cas9-mediated-homologous-recombination
#16
Sanjay Ghosh, Ji-Long Liu
Tagging of genes at the endogenous loci is a powerful strategy for the analysis of protein function. We have developed a homologous recombination-based approach for inserting epitope tag into Drosophila AGO1 locus by employing the CRISPR/Cas9 technology. The methodology involves co-expression of sgRNA (containing 20-nucleotide AGO1 targeting sequence) and Cas9 protein, together with a donor template that has HA-AGO1 cassette flanked by sequences homologous to the AGO1 locus. The integration is efficient and readily monitored by immunostaining of the transgenic cell line...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29029439/microrna-149-suppresses-hepatic-inflammatory-response-through-antagonizing-stat3-signaling-pathway
#17
Qiqi Zhang, Jia Su, Ziwei Wang, Hui Qi, Zeyong Ge, Zhijun Li, Wei-Dong Chen, Yan-Dong Wang
Chronic inflammation is increasingly recognized as an important component of tumorigenesis and metabolic diseases. The roles of microRNA149* (miRNA149*) in inflammation remain poorly understood. Here, we demonstrate that miR-149* is a suppressor of STAT3-mediated inflammation. MiR-149*(-/-) mice were generated with CRISPR/CAS9 technique. In a lipopolysaccharide (LPS)-induced inflammation model, miR-149*(-/-) mice show more severe liver injury and inflammation, compared with wild-type (WT) mice. MiR-149*(-/-) mice also displayed elevated messenger RNA (mRNA) levels of interleukin (IL)-6, inducible nitric oxide synthase (iNOS), complement C3 (C3) and IL-4 in response to LPS...
September 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29028833/merkel-cell-polyomavirus-recruits-mycl-to-the-ep400-complex-to-promote-oncogenesis
#18
Jingwei Cheng, Donglim Esther Park, Christian Berrios, Elizabeth A White, Reety Arora, Rosa Yoon, Timothy Branigan, Tengfei Xiao, Thomas Westerling, Alexander Federation, Rhamy Zeid, Benjamin Strober, Selene K Swanson, Laurence Florens, James E Bradner, Myles Brown, Peter M Howley, Megha Padi, Michael P Washburn, James A DeCaprio
Merkel cell carcinoma (MCC) frequently contains integrated copies of Merkel cell polyomavirus DNA that express a truncated form of Large T antigen (LT) and an intact Small T antigen (ST). While LT binds RB and inactivates its tumor suppressor function, it is less clear how ST contributes to MCC tumorigenesis. Here we show that ST binds specifically to the MYC homolog MYCL (L-MYC) and recruits it to the 15-component EP400 histone acetyltransferase and chromatin remodeling complex. We performed a large-scale immunoprecipitation for ST and identified co-precipitating proteins by mass spectrometry...
October 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/29028415/crispr-cas9-mediated-noncoding-rna-editing-in-human-cancers
#19
Jie Yang, Xiaodan Meng, Jinchang Pan, Nan Jiang, Chengwei Zhou, Zhenhua Wu, Zhaohui Gong
Cancer is characterized by multiple genetic and epigenetic alterations, including a higher prevalence of mutations of oncogenes and/or tumor suppressors. Mounting evidences have shown that noncoding RNAs (ncRNAs) are involved in the epigenetic regulation of cancer genes and their associated pathways. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease 9 (CRISPR/Cas9) system, a revolutionary genome-editing technology, has shed light on ncRNA-based cancer therapy. Here, we briefly introduce the classifications and mechanisms of CRISPR/Cas9 system...
October 13, 2017: RNA Biology
https://www.readbyqxmd.com/read/29025896/high-throughput-single-molecule-telomere-characterization
#20
Jennifer McCaffrey, Eleanor Young, Katy Lassahn, Justin Sibert, Steven Pastor, Harold Riethman, Ming Xiao
We have developed a novel method that enables global subtelomere and haplotype-resolved analysis of telomere lengths at the single-molecule level. An in vitro CRISPR/Cas9 RNA-directed nickase system directs the specific labeling of human (TTAGGG)n DNA tracts in genomes that have also been barcoded using a separate nickase enzyme that recognizes a 7-bp motif genome-wide. High-throughput imaging and analysis of large DNA single molecules from genomes labeled in this fashion using a nanochannel array system permits mapping through subtelomere repeat element (SRE) regions to unique chromosomal DNA while simultaneously measuring the (TTAGGG)n tract length at the end of each large telomere-terminal DNA segment...
October 12, 2017: Genome Research
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