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https://www.readbyqxmd.com/read/27918548/multiplex-gene-editing-by-crispr-cpf1-using-a-single-crrna-array
#1
Bernd Zetsche, Matthias Heidenreich, Prarthana Mohanraju, Iana Fedorova, Jeroen Kneppers, Ellen M DeGennaro, Nerges Winblad, Sourav R Choudhury, Omar O Abudayyeh, Jonathan S Gootenberg, Wen Y Wu, David A Scott, Konstantin Severinov, John van der Oost, Feng Zhang
Targeting of multiple genomic loci with Cas9 is limited by the need for multiple or large expression constructs. Here we show that the ability of Cpf1 to process its own CRISPR RNA (crRNA) can be used to simplify multiplexed genome editing. Using a single customized CRISPR array, we edit up to four genes in mammalian cells and three in the mouse brain, simultaneously.
December 5, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27905529/efficient-targeted-mutagenesis-of-rice-and-tobacco-genomes-using-cpf1-from-francisella-novicida
#2
Akira Endo, Mikami Masafumi, Hidetaka Kaya, Seiichi Toki
CRISPR/Cas9 systems are nowadays applied extensively to effect genome editing in various organisms including plants. CRISPR from Prevotella and Francisella 1 (Cpf1) is a newly characterized RNA-guided endonuclease that has two distinct features as compared to Cas9. First, Cpf1 utilizes a thymidine-rich protospacer adjacent motif (PAM) while Cas9 prefers a guanidine-rich PAM. Cpf1 could be used as a sequence-specific nuclease to target AT-rich regions of a genome that Cas9 had difficulty accessing. Second, Cpf1 generates DNA ends with a 5' overhang, whereas Cas9 creates blunt DNA ends after cleavage...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27895652/rapid-evolution-of-manifold-crispr-systems-for-plant-genome-editing
#3
REVIEW
Levi Lowder, Aimee Malzahn, Yiping Qi
Advanced CRISPR-Cas9 based technologies first validated in mammalian cell systems are quickly being adapted for use in plants. These new technologies increase CRISPR-Cas9's utility and effectiveness by diversifying cellular capabilities through expression construct system evolution and enzyme orthogonality, as well as enhanced efficiency through delivery and expression mechanisms. Here, we review the current state of advanced CRISPR-Cas9 and Cpf1 capabilities in plants and cover the rapid evolution of these tools from first generation inducers of double strand breaks for basic genetic manipulations to second and third generation multiplexed systems with myriad functionalities, capabilities, and specialized applications...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27875019/generation-of-targeted-mutant-rice-using-a-crispr-cpf1-system
#4
Rongfang Xu, Ruiying Qin, Hao Li, Dongdong Li, Li Li, Pengcheng Wei, Jianbo Yang
CRISPR-Cpf1 is a newly identified CRISPR-Cas system, and Cpf1 was recently engineered as a molecular tool for targeted genome editing in mammalian cells. To test whether the engineered CRISPR-Cpf1 system could induce the production of rice mutants, we selected two genome targets in the OsPDS and OsBEL genes. Our results show that both targets could be efficiently mutated in transgenic rice plants using CRISPR-Cpf1. We found that pre-crRNAs with a full-length direct repeat sequence exhibited considerably increased efficiencies compared with mature crRNAs...
November 22, 2016: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/27760213/inulin-supplementation-lowered-the-metabolic-defects-of-prolonged-exposure-to-chlorpyrifos-from-gestation-to-young-adult-stage-in-offspring-rats
#5
Julie Reygner, Lydia Lichtenberger, Ghada Elmhiri, Samir Dou, Narges Bahi-Jaber, Larbi Rhazi, Flore Depeint, Veronique Bach, Hafida Khorsi-Cauet, Latifa Abdennebi-Najar
Increasing evidence indicates that chlorpyrifos (CPF), an organophosphorus insecticide, is involved in metabolic disorders. We assess the hypothesis whether supplementation with prebiotics from gestation to adulthood, through a modulation of microbiota composition and fermentative activity, alleviates CPF induced metabolic disorders of 60 days old offspring. 5 groups of Wistar rats, from gestation until weaning, received two doses of CPF pesticide: 1 mg/kg/day (CPF1) or 3.5 mg/kg/day (CPF3.5) with free access to inulin (10g/L in drinking water)...
2016: PloS One
https://www.readbyqxmd.com/read/27669025/two-distinct-rnase-activities-of-crispr-c2c2-enable-guide-rna-processing-and-rna-detection
#6
Alexandra East-Seletsky, Mitchell R O'Connell, Spencer C Knight, David Burstein, Jamie H D Cate, Robert Tjian, Jennifer A Doudna
Bacterial adaptive immune systems use CRISPRs (clustered regularly interspaced short palindromic repeats) and CRISPR-associated (Cas) proteins for RNA-guided nucleic acid cleavage. Although most prokaryotic adaptive immune systems generally target DNA substrates, type III and VI CRISPR systems direct interference complexes against single-stranded RNA substrates. In type VI systems, the single-subunit C2c2 protein functions as an RNA-guided RNA endonuclease (RNase). How this enzyme acquires mature CRISPR RNAs (crRNAs) that are essential for immune surveillance and how it carries out crRNA-mediated RNA cleavage remain unclear...
September 26, 2016: Nature
https://www.readbyqxmd.com/read/27630115/cpf1-nucleases-demonstrate-robust-activity-to-induce-dna-modification-by-exploiting-homology-directed-repair-pathways-in-mammalian-cells
#7
Eszter Tóth, Nóra Weinhardt, Petra Bencsura, Krisztina Huszár, Péter I Kulcsár, András Tálas, Elfrieda Fodor, Ervin Welker
BACKGROUND: Cpf1 nucleases have recently been repurposed for site-specific genome modification. Two members of the Cpf1 family, the AsCpf1 from Acidaminococcus sp. and the LbCpf1 from Lachnospiraceae bacterium were shown to induce higher indel frequencies than SpCas9 when examining four randomly-selected target sequences for each type of nuclease. Whether they are a real match for Cas9 nucleases, however, remains to be verified. RESULTS: Here, we used AsCpf1 and LbCpf1 to induce homology directed repair, either single strand annealing (SSA) or homologous recombination (HR), in N2a mouse neuroblastoma cells...
2016: Biology Direct
https://www.readbyqxmd.com/read/27595403/augmenting-crispr-applications-in-drosophila-with-trna-flanked-sgrnas
#8
Fillip Port, Simon L Bullock
We present tRNA-based vectors for producing multiple clustered regularly interspaced short palindromic repeats (CRISPR) single guide RNAs (sgRNAs) from a single RNA polymerase II or III transcript in Drosophila. The system, which is based on liberation of sgRNAs by processing flanking tRNAs, permits highly efficient multiplexing of Cas9-based mutagenesis. We also demonstrate that the tRNA-sgRNA system markedly increases the efficacy of conditional gene disruption by Cas9 and can promote editing by the recently discovered RNA-guided endonuclease Cpf1...
October 2016: Nature Methods
https://www.readbyqxmd.com/read/27545116/impact-of-prenatal-and-postnatal-exposure-to-the-pesticide-chlorpyrifos-on-the-contraction-of-rat-ileal-muscle-strips-involvement-of-an-inducible-nitric-oxide-synthase-dependent-pathway
#9
W Darwiche, S Delanaud, S Dupont, H Ghamlouch, W Ramadan, W Joumaa, V Bach, J Gay-Quéheillard
BACKGROUND: Prenatal/postnatal exposure to insecticides has been linked to developmental disorders in adulthood. Chlorpyrifos (CPF) is a widely used organophosphorus acetylcholinesterase (AChE)-inhibiting insecticide. The present study established whether prenatal and postnatal exposure to CPF is associated with intestinal motor dysfunction in adult rats. METHODS: Three groups of pregnant rats were exposed to either CPF (1 or 5 mg/kg/day; the CPF1 and CPF5 groups) or vehicle (the control group) by gavage from gestational day 1 until weaning...
August 21, 2016: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
https://www.readbyqxmd.com/read/27504781/erratum-genome-wide-analysis-reveals-specificities-of-cpf1-endonucleases-in-human-cells
#10
Daesik Kim, Jungeun Kim, Junho K Hur, Kyung Wook Been, Sun-Heui Yoon, Jin-Soo Kim
No abstract text is available yet for this article.
August 9, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27444870/type-v-crispr-cas-cpf1-endonuclease-employs-a-unique-mechanism-for-crrna-mediated-target-dna-recognition
#11
Pu Gao, Hui Yang, Kanagalaghatta R Rajashankar, Zhiwei Huang, Dinshaw J Patel
CRISPR-Cas9 and CRISPR-Cpf1 systems have been successfully harnessed for genome editing. In the CRISPR-Cas9 system, the preordered A-form RNA seed sequence and preformed protein PAM-interacting cleft are essential for Cas9 to form a DNA recognition-competent structure. Whether the CRISPR-Cpf1 system employs a similar mechanism for target DNA recognition remains unclear. Here, we have determined the crystal structure of Acidaminococcus sp. Cpf1 (AsCpf1) in complex with crRNA and target DNA. Structural comparison between the AsCpf1-crRNA-DNA ternary complex and the recently reported Lachnospiraceae bacterium Cpf1 (LbCpf1)-crRNA binary complex identifies a unique mechanism employed by Cpf1 for target recognition...
August 2016: Cell Research
https://www.readbyqxmd.com/read/27347757/genome-wide-specificities-of-crispr-cas-cpf1-nucleases-in-human-cells
#12
Benjamin P Kleinstiver, Shengdar Q Tsai, Michelle S Prew, Nhu T Nguyen, Moira M Welch, Jose M Lopez, Zachary R McCaw, Martin J Aryee, J Keith Joung
The activities and genome-wide specificities of CRISPR-Cas Cpf1 nucleases are not well defined. We show that two Cpf1 nucleases from Acidaminococcus sp. BV3L6 and Lachnospiraceae bacterium ND2006 (AsCpf1 and LbCpf1, respectively) have on-target efficiencies in human cells comparable with those of the widely used Streptococcus pyogenes Cas9 (SpCas9). We also report that four to six bases at the 3' end of the short CRISPR RNA (crRNA) used to program Cpf1 nucleases are insensitive to single base mismatches, but that many of the other bases in this region of the crRNA are highly sensitive to single or double substitutions...
August 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27294364/c-brick-a-new-standard-for-assembly-of-biological-parts-using-cpf1
#13
Shi-Yuan Li, Guo-Ping Zhao, Jin Wang
So far, several DNA assembly standards have been developed, enabling scientists to conveniently share and modify characterized DNA parts. However, a majority of the restriction endonucleases used in these standards bear short recognition sites (e.g., 6 bps in BioBrick standard), which are widely distributed and need to be removed before further construction, causing much inconvenience. Although homing endonucleases, which recognize long DNA sequences, can be used for DNA assembly (e.g., iBrick standard), long scars will be left between parts, limiting their application...
June 17, 2016: ACS Synthetic Biology
https://www.readbyqxmd.com/read/27272387/generation-of-knockout-mice-by-cpf1-mediated-gene-targeting
#14
Yongsub Kim, Seung-A Cheong, Jong Geol Lee, Sang-Wook Lee, Myeong Sup Lee, In-Jeoung Baek, Young Hoon Sung
No abstract text is available yet for this article.
August 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27272385/targeted-mutagenesis-in-mice-by-electroporation-of-cpf1-ribonucleoproteins
#15
Junho K Hur, Kyoungmi Kim, Kyung Wook Been, Gayoung Baek, Sunghyeok Ye, Junseok W Hur, Seuk-Min Ryu, Youn Su Lee, Jin-Soo Kim
No abstract text is available yet for this article.
August 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27272384/genome-wide-analysis-reveals-specificities-of-cpf1-endonucleases-in-human-cells
#16
Daesik Kim, Jungeun Kim, Junho K Hur, Kyung Wook Been, Sun-Heui Yoon, Jin-Soo Kim
Programmable clustered regularly interspaced short palindromic repeats (CRISPR) Cpf1 endonucleases are single-RNA-guided (crRNA) enzymes that recognize thymidine-rich protospacer-adjacent motif (PAM) sequences and produce cohesive double-stranded breaks (DSBs). Genome editing with CRISPR-Cpf1 endonucleases could provide an alternative to CRISPR-Cas9 endonucleases, but the determinants of targeting specificity are not well understood. Using mismatched crRNAs we found that Cpf1 could tolerate single or double mismatches in the 3' PAM-distal region, but not in the 5' PAM-proximal region...
August 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27210042/genome-editing-with-crispr-cas9-can-it-get-any-better
#17
REVIEW
Maximilian Haeussler, Jean-Paul Concordet
The CRISPR-Cas revolution is taking place in virtually all fields of life sciences. Harnessing DNA cleavage with the CRISPR-Cas9 system of Streptococcus pyogenes has proven to be extraordinarily simple and efficient, relying only on the design of a synthetic single guide RNA (sgRNA) and its co-expression with Cas9. Here, we review the progress in the design of sgRNA from the original dual RNA guide for S. pyogenes and Staphylococcus aureus Cas9 (SpCas9 and SaCas9). New assays for genome-wide identification of off-targets have provided important insights into the issue of cleavage specificity in vivo...
May 20, 2016: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/27185894/chopchop-v2-a-web-tool-for-the-next-generation-of-crispr-genome-engineering
#18
Kornel Labun, Tessa G Montague, James A Gagnon, Summer B Thyme, Eivind Valen
In just 3 years CRISPR genome editing has transformed biology, and its popularity and potency continue to grow. New CRISPR effectors and rules for locating optimum targets continue to be reported, highlighting the need for computational CRISPR targeting tools to compile these rules and facilitate target selection and design. CHOPCHOP is one of the most widely used web tools for CRISPR- and TALEN-based genome editing. Its overarching principle is to provide an intuitive and powerful tool that can serve both novice and experienced users...
July 8, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27142322/cpf1-shape-shifts-for-streamlined-crispr-cleavage
#19
Malcolm F White
No abstract text is available yet for this article.
May 4, 2016: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/27140686/structural-biology-how-cpf1-cuts-its-crispr-targets
#20
Naomi Attar
No abstract text is available yet for this article.
June 2016: Nature Reviews. Microbiology
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