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clustered regularly interspaced short palindromic repeats

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https://www.readbyqxmd.com/read/29344851/the-evolution-of-crispr-cas9-and-their-cousins-hope-or-hype
#1
REVIEW
Kulbhushan Chaudhary, Anirudha Chattopadhyay, Dharmendra Pratap
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system allows biologists to edit genomic DNA of any cell in precise and specific way, entailing great potential for crop improvement, drug development and gene therapy. The system involves a nuclease (Cas9) and a designed guide RNA that are involved in wide range of applications such as genome modification, transcriptional modulation, genomic loci marking and RNA tracking. The limitation of the technique, in view of resistance of thymidine-rich genome to Cas9 cleavage, has now been overcome by the use of Cpf1 nuclease...
January 17, 2018: Biotechnology Letters
https://www.readbyqxmd.com/read/29343825/a-survey-of-validation-strategies-for-crispr-cas9-editing
#2
Monica F Sentmanat, Samuel T Peters, Colin P Florian, Jon P Connelly, Shondra M Pruett-Miller
The T7 endonuclease 1 (T7E1) mismatch detection assay is a widely used method for evaluating the activity of site-specific nucleases, such as the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system. To determine the accuracy and sensitivity of this assay, we compared the editing estimates derived by the T7E1 assay with that of targeted next-generation sequencing (NGS) in pools of edited mammalian cells. Here, we report that estimates of nuclease activity determined by T7E1 most often do not accurately reflect the activity observed in edited cells...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29337866/crispr-cas-targeting-of-host-genes-as-an-antiviral-strategy
#3
REVIEW
Shuliang Chen, Xiao Yu, Deyin Guo
Currently, a new gene editing tool-the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) associated (Cas) system-is becoming a promising approach for genetic manipulation at the genomic level. This simple method, originating from the adaptive immune defense system in prokaryotes, has been developed and applied to antiviral research in humans. Based on the characteristics of virus-host interactions and the basic rules of nucleic acid cleavage or gene activation of the CRISPR-Cas system, it can be used to target both the virus genome and host factors to clear viral reservoirs and prohibit virus infection or replication...
January 16, 2018: Viruses
https://www.readbyqxmd.com/read/29337376/crispr-cas9-mediated-genome-editing-in-epstein-barr-virus-transformed-lymphoblastoid-b-cell-lines
#4
Sizun Jiang, Liang Wei Wang, Michael J Walsh, Stephen J Trudeau, Catherine Gerdt, Bo Zhao, Benjamin E Gewurz
Epstein-Barr virus (EBV) efficiently transforms primary human B cells into immortalized lymphoblastoid cell lines (LCLs), which are extensively used in human genetic, immunological and virological studies. LCLs provide unlimited sources of DNA for genetic investigation, but can be difficult to manipulate, for instance because low retroviral or lentiviral transduction frequencies hinder experiments that require co-expression of multiple components. This unit details Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 engineering for robust LCL genome editing...
January 16, 2018: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/29337372/crispr-cas9-edited-site-sequencing-cres-seq-an-efficient-and-high-throughput-method-for-the-selection-of-crispr-cas9-edited-clones
#5
Yaligara Veeranagouda, Delphine Debono-Lagneaux, Hamida Fournet, Gilbert Thill, Michel Didier
The emergence of clustered regularly interspaced short palindromic repeats-Cas9 (CRISPR-Cas9) gene editing systems has enabled the creation of specific mutants at low cost, in a short time and with high efficiency, in eukaryotic cells. Since a CRISPR-Cas9 system typically creates an array of mutations in targeted sites, a successful gene editing project requires careful selection of edited clones. This process can be very challenging, especially when working with multiallelic genes and/or polyploid cells (such as cancer and plants cells)...
January 16, 2018: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/29337370/modulating-gene-expression-in-epstein-barr-virus-ebv-positive-b-cell-lines-with-crispra-and-crispri
#6
Liang Wei Wang, Stephen J Trudeau, Chong Wang, Catherine Gerdt, Sizun Jiang, Bo Zhao, Benjamin E Gewurz
Epstein-Barr virus (EBV) transforms small resting primary B cells into large lymphoblastoid cells which are able to grow and survive in vitro indefinitely. These cells represent a model for oncogenesis. In this unit, variants of conventional clustered regularly interspaced short palindromic repeats (CRISPR), namely the CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) methods, are discussed in the context of gene regulation at genomic DNA promoter and enhancer elements. Lymphoblastoid B cell lines (LCLs) stably expressing nuclease-deficient Cas9 (dCas9)-VP64 (Cas9 associated with CRISPRa) or dCas9-KRAB (Cas9 associated with CRISPRi) are transduced with lentivirus that encodes a single guide RNA (sgRNA) that targets a specific gene locus...
January 16, 2018: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/29335550/the-peg-responding-desiccome-of-the-alder-microsymbiont-frankia-alni
#7
Kais Ghedira, Emna Harigua-Souiai, Cherif Ben Hamda, Pascale Fournier, Petar Pujic, Sihem Guesmi, Ikram Guizani, Guylaine Miotello, Jean Armengaud, Philippe Normand, Haïtham Sghaier
Actinorhizal plants are ecologically and economically important. Symbiosis with nitrogen-fixing bacteria allows these woody dicotyledonous plants to colonise soils under nitrogen deficiency, water-stress or other extreme conditions. However, proteins involved in xerotolerance of symbiotic microorganisms have yet to be identified. Here we characterise the polyethylene glycol (PEG)-responding desiccome from the most geographically widespread Gram-positive nitrogen-fixing plant symbiont, Frankia alni, by next-generation proteomics, taking advantage of a Q-Exactive HF tandem mass spectrometer equipped with an ultra-high-field Orbitrap analyser...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29333573/simultaneous-site-directed-mutagenesis-of-duplicated-loci-in-soybean-using-a-single-guide-rna
#8
Yuhei Kanazashi, Aya Hirose, Ippei Takahashi, Masafumi Mikami, Masaki Endo, Sakiko Hirose, Seiichi Toki, Akito Kaga, Ken Naito, Masao Ishimoto, Jun Abe, Tetsuya Yamada
Using a gRNA and Agrobacterium-mediated transformation, we performed simultaneous site-directed mutagenesis of two GmPPD loci in soybean. Mutations in GmPPD loci were confirmed in at least 33% of T2 seeds. The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated endonuclease 9 (Cas9) system is a powerful tool for site-directed mutagenesis in crops. Using a single guide RNA (gRNA) and Agrobacterium-mediated transformation, we performed simultaneous site-directed mutagenesis of two homoeologous loci in soybean (Glycine max), GmPPD1 and GmPPD2, which encode the orthologs of Arabidopsis thaliana PEAPOD (PPD)...
January 15, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29332168/efficient-crispr-cas9-based-genome-editing-in-carrot-cells
#9
Magdalena Klimek-Chodacka, Tomasz Oleszkiewicz, Levi G Lowder, Yiping Qi, Rafal Baranski
The first report presenting successful and efficient carrot genome editing using CRISPR/Cas9 system. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas9) is a powerful genome editing tool that has been widely adopted in model organisms recently, but has not been used in carrot-a model species for in vitro culture studies and an important health-promoting crop grown worldwide. In this study, for the first time, we report application of the CRISPR/Cas9 system for efficient targeted mutagenesis of the carrot genome...
January 13, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29331085/verification-of-dna-motifs-in-arabidopsis-using-crispr-cas9-mediated-mutagenesis
#10
Chenlong Li, Chen Chen, Huhui Chen, Suikang Wang, Xuemei Chen, Yuhai Cui
Transcription factors (TFs) and chromatin-modifying factors (CMFs) access chromatin by recognizing specific DNA motifs in their target genes. Chromatin Immunoprecipitation followed by next generation sequencing (ChIP-seq) has been widely used to discover the potential DNA binding motifs for both TFs and CMFs. Yet, an in vivo method for verifying DNA motifs captured by ChIP-seq is lacking in plants. Here, we describe the use of clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) to verify DNA motifs in their native genomic context in Arabidopsis...
January 13, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29330178/development-of-an-efficient-genome-editing-tool-in-bacillus-licheniformis-using-crispr-cas9-nickase
#11
Kaifeng Li, Dongbo Cai, Zhangqian Wang, Zhili He, Shouwen Chen
Bacillus strains are important industrial bacteria that can produce various biochemical products. However, low transformation efficiencies and a lack of effective genome editing tools have hindered its widespread application. Recently, clustered regularly interspaced short palindromic repeat (CRISPR)/cas9 techniques have been utilized in many organisms as genome editing tools because of their high efficiency and easy manipulation. In this study, an efficient genome editing method was developed for Bacillus licheniformis using a CRISPR-Cas9 nickase integrated into the genome of B...
January 12, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29327438/establishing-rna-virus-resistance-in-plants-by-harnessing-crispr-immune-system
#12
Tong Zhang, Qiufeng Zheng, Xin Yi, Hong An, Yaling Zhao, Siqi Ma, Guohui Zhou
Recently, CRISPR-Cas (clustered, regularly interspaced short palindromic repeats-CRISPR associated proteins) system has been used to produce plants resistant to DNA virus infections. However, there is no RNA virus control method in plants that uses CRISPR-Cas system to target the viral genome directly. Here we reprogrammed the CRISPR-Cas9 system from Francisella novicida to confer molecular immunity against RNA viruses in Nicotiana benthamiana and Arabidopsis plants. Plants expressing FnCas9 and sgRNA specific for the cucumber mosaic virus (CMV) or tobacco mosaic virus (TMV) exhibited significantly attenuated virus infection symptoms and reduced viral RNA accumulation...
January 11, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29326210/complete-genome-sequencing-of-acinetobacter-sp-strain-logew2-3-isolated-from-the-pellet-of-a-white-stork-reveals-a-novel-class-d-beta-lactamase-gene
#13
Ulrike Blaschke, Evelyn Skiebe, Michael Kaatz, Paul G Higgins, Yvonne Pfeifer, Gottfried Wilharm
Whole-genome sequencing of Acinetobacter sp. strain LoGeW2-3, isolated from the pellet of a white stork (Ciconia ciconia), reveals the presence of a plasmid of 179,399 bp encoding a CRISPR-Cas (clustered regularly interspaced short palindromic repeats and associated genes) system of the I-F type, and the chromosomally encoded novel class D beta-lactamase OXA-568.
January 11, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29326075/use-of-crispr-cas9-gene-editing-tools-for-developing-models-in-drug-discovery
#14
REVIEW
Gulzar Ahmad, Mansoor Amiji
Clustered regularly interspaced short palindromic repeat/CRISPR-associated 9 (CRISPR/Cas9) enables targeted genome engineering. The simplicity of this system, its facile engineering, and amenability to multiplex genes make it the system of choice for many applications. This system has revolutionized our ability to carry out gene editing, transcription regulation, genome imaging, and epigenetic modification. In this review, we discuss the discovery of CRISPR/Cas9, its mechanism of action, its application in medicine and animal model development, and its delivery...
January 8, 2018: Drug Discovery Today
https://www.readbyqxmd.com/read/29317080/effective-regeneration-of-dystrophic-muscle-using-autologous-ipsc-derived-progenitors-with-crispr-cas9-mediated-precise-correction
#15
Mackenzie Hagan, Muhammad Ashraf, Il-Man Kim, Neal L Weintraub, Yaoliang Tang
Duchenne muscular dystrophy (DMD) is a lethal muscle wasting disease caused by a lack of dystrophin, which eventually leads to apoptosis of muscle cells and impaired muscle contractility. Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9 (CRISPR/Cas9) gene editing of induced pluripotent stem cells (IPSC) offers the potential to correct the DMD gene defect and create healthy IPSC for autologous cell transplantation without causing immune activation. However, IPSC carry a risk of tumor formation, which can potentially be mitigated by differentiation of IPSC into myogenic progenitor cells (MPC)...
January 2018: Medical Hypotheses
https://www.readbyqxmd.com/read/29305085/engineering-the-delivery-system-for-crispr-based-genome-editing
#16
REVIEW
Zachary Glass, Matthew Lee, Yamin Li, Qiaobing Xu
Clustered regularly interspaced short palindromic repeat-CRISPR-associated protein (CRISPR-Cas) systems, found in nature as microbial adaptive immune systems, have been repurposed into an important tool in biological engineering and genome editing, providing a programmable platform for precision gene targeting. These tools have immense promise as therapeutics that could potentially correct disease-causing mutations. However, CRISPR-Cas gene editing components must be transported directly to the nucleus of targeted cells to exert a therapeutic effect...
January 2, 2018: Trends in Biotechnology
https://www.readbyqxmd.com/read/29301949/new-role-for-an-old-protein-an-educational-primer-for-use-with-the-identification-of-a-novel-mutant-allele-of-topoisomerase-ii-in-caenorhabditis-elegans-reveals-a-unique-role-in-chromosome-segregation-during-spermatogenesis
#17
Ruby Boateng, Anna K Allen
Modern experimental techniques, such as whole-genome sequencing and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 endogenous genome editing, are enabling researchers to identify and further characterize the roles of proteins that were previously thought of as well defined. In the December 2016 issue of GENETICS, an article by Jaramillo-Lambert et al. identified a new role for the enzyme topoisomerase II in Caenorhabditis elegans male meiosis. This Primer article is designed to provide essential background information on C...
January 2018: Genetics
https://www.readbyqxmd.com/read/29300985/disruption-of-ossec3a-increases-the-content-of-salicylic-acid-and-induces-plant-defense-responses-in-rice
#18
Jin Ma, Jun Chen, Min Wang, Yulong Ren, Shuai Wang, Cailin Lei, Zhijun Cheng, Sodmergen
The exocyst, an evolutionarily conserved octameric protein complex involved in exocytosis, has been reported to be involved in diverse aspects of morphogenesis in Arabidopsis. However, the molecular functions of such exocytotic molecules in rice are poorly understood. Here, we examined the molecular function of OsSEC3A, an important subunit of the exocyst complex in rice. The OsSEC3A gene is expressed in various organs, and OsSEC3A has the potential ability to participate in the exocyst complex by interacting with several other exocyst subunits...
December 30, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29296870/a-knock-in-mouse-strain-facilitates-dynamic-tracking-and-enrichment-of-meis1
#19
Ping Xiang, Wei Wei, Nicole Hofs, Jack Clemans-Gibbon, Tobias Maetzig, Courteney K Lai, Ishpreet Dhillon, Christopher May, Jens Ruschmann, Edith Schneider, Patricia Rosten, Kaiji Hu, Florian Kuchenbauer, Pamela A Hoodless, R Keith Humphries
Myeloid ecotropic viral integration site 1 (MEIS1), a HOX transcription cofactor, is a critical regulator of normal hematopoiesis, and its overexpression is implicated in a wide range of leukemias. Using the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 (Cas9) gene-editing system, we generated a knock-in transgenic mouse line in which a green fluorescent protein (GFP) reporter and a hemagglutinin (HA) epitope tag are inserted near the translational start site of endogenous Meis1...
November 14, 2017: Blood Advances
https://www.readbyqxmd.com/read/29295784/targeted-knock-in-of-an-scfv-fc-antibody-gene-into-the-hprt-locus-of-chinese-hamster-ovary-cells-using-crispr-cas9-and-cris-pitch-systems
#20
Yoshinori Kawabe, Shinya Komatsu, Shodai Komatsu, Mai Murakami, Akira Ito, Tetsushi Sakuma, Takahiro Nakamura, Takashi Yamamoto, Masamichi Kamihira
Chinese hamster ovary (CHO) cells have been used as host cells for the production of pharmaceutical proteins. For the high and stable production of target proteins, the transgene should be integrated into a suitable genomic locus of host cells. Here, we generated knock-in CHO cells, in which transgene cassettes without a vector backbone sequence were integrated into the hprt locus of the CHO genome using clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 and CRISPR-mediated precise integration into target chromosome (CRIS-PITCh) systems...
December 30, 2017: Journal of Bioscience and Bioengineering
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