Literature DB >> 25599175

Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors.

Xiaoling Wang1, Yebo Wang2, Xiwei Wu3, Jinhui Wang3, Yingjia Wang2, Zhaojun Qiu3, Tammy Chang1, He Huang4, Ren-Jang Lin3, Jiing-Kuan Yee1.   

Abstract

The utility of CRISPR-Cas9 and TALENs for genome editing may be compromised by their off-target activity. We show that integrase-defective lentiviral vectors (IDLVs) can detect such off-target cleavage with a frequency as low as 1%. In the case of Cas9, we find frequent off-target sites with a one-base bulge or up to 13 mismatches between the single guide RNA (sgRNA) and its genomic target, which refines sgRNA design.

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Year:  2015        PMID： 25599175     DOI： 10.1038/nbt.3127

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


  20 in total

1.  Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity.

Authors:  F Ann Ran; Patrick D Hsu; Chie-Yu Lin; Jonathan S Gootenberg; Silvana Konermann; Alexandro E Trevino; David A Scott; Azusa Inoue; Shogo Matoba; Yi Zhang; Feng Zhang
Journal:  Cell       Date:  2013-08-29       Impact factor: 41.582

2.  An unbiased genome-wide analysis of zinc-finger nuclease specificity.

Authors:  Richard Gabriel; Angelo Lombardo; Anne Arens; Jeffrey C Miller; Pietro Genovese; Christine Kaeppel; Ali Nowrouzi; Cynthia C Bartholomae; Jianbin Wang; Geoffrey Friedman; Michael C Holmes; Philip D Gregory; Hanno Glimm; Manfred Schmidt; Luigi Naldini; Christof von Kalle
Journal:  Nat Biotechnol       Date:  2011-08-07       Impact factor: 54.908

3.  Genetic screens in human cells using the CRISPR-Cas9 system.

Authors:  Tim Wang; Jenny J Wei; David M Sabatini; Eric S Lander
Journal:  Science       Date:  2013-12-12       Impact factor: 47.728

4.  TALEN-based gene correction for epidermolysis bullosa.

Authors:  Mark J Osborn; Colby G Starker; Amber N McElroy; Beau R Webber; Megan J Riddle; Lily Xia; Anthony P DeFeo; Richard Gabriel; Manfred Schmidt; Christof von Kalle; Daniel F Carlson; Morgan L Maeder; J Keith Joung; John E Wagner; Daniel F Voytas; Bruce R Blazar; Jakub Tolar
Journal:  Mol Ther       Date:  2013-04-02       Impact factor: 11.454

5.  Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish.

Authors:  An Xiao; Zhanxiang Wang; Yingying Hu; Yingdan Wu; Zhou Luo; Zhipeng Yang; Yao Zu; Wenyuan Li; Peng Huang; Xiangjun Tong; Zuoyan Zhu; Shuo Lin; Bo Zhang
Journal:  Nucleic Acids Res       Date:  2013-06-06       Impact factor: 16.971

6.  CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering.

Authors:  Prashant Mali; John Aach; P Benjamin Stranges; Kevin M Esvelt; Mark Moosburner; Sriram Kosuri; Luhan Yang; George M Church
Journal:  Nat Biotechnol       Date:  2013-08-01       Impact factor: 54.908

7.  Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases.

Authors:  Seung Woo Cho; Sojung Kim; Yongsub Kim; Jiyeon Kweon; Heon Seok Kim; Sangsu Bae; Jin-Soo Kim
Journal:  Genome Res       Date:  2013-11-19       Impact factor: 9.043

8.  Precise gene modification mediated by TALEN and single-stranded oligodeoxynucleotides in human cells.

Authors:  Xiaoling Wang; Yingjia Wang; He Huang; Buyuan Chen; Xinji Chen; Jianda Hu; Tammy Chang; Ren-Jang Lin; Jiing-Kuan Yee
Journal:  PLoS One       Date:  2014-04-01       Impact factor: 3.240

9.  RNA-guided gene activation by CRISPR-Cas9-based transcription factors.

Authors:  Pablo Perez-Pinera; D Dewran Kocak; Christopher M Vockley; Andrew F Adler; Ami M Kabadi; Lauren R Polstein; Pratiksha I Thakore; Katherine A Glass; David G Ousterout; Kam W Leong; Farshid Guilak; Gregory E Crawford; Timothy E Reddy; Charles A Gersbach
Journal:  Nat Methods       Date:  2013-07-25       Impact factor: 28.547

10.  PEAR: a fast and accurate Illumina Paired-End reAd mergeR.

Authors:  Jiajie Zhang; Kassian Kobert; Tomáš Flouri; Alexandros Stamatakis
Journal:  Bioinformatics       Date:  2013-10-18       Impact factor: 6.937
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  177 in total

Review 1.  Creating and evaluating accurate CRISPR-Cas9 scalpels for genomic surgery.

Authors:  Mehmet Fatih Bolukbasi; Ankit Gupta; Scot A Wolfe
Journal:  Nat Methods       Date:  2016-01       Impact factor: 28.547

2.  STING Gain-of-Function Disrupts Lymph Node Organogenesis and Innate Lymphoid Cell Development in Mice.

Authors:  Brock G Bennion; Carys A Croft; Teresa L Ai; Wei Qian; Amber M Menos; Cathrine A Miner; Marie-Louis Frémond; Jean-Marc Doisne; Prabhakar S Andhey; Derek J Platt; Jennifer K Bando; Erin R Wang; Hella Luksch; Thierry J Molina; Elisha D O Roberson; Maxim N Artyomov; Angela Rösen-Wolff; Marco Colonna; Frédéric Rieux-Laucat; James P Di Santo; Bénédicte Neven; Jonathan J Miner
Journal:  Cell Rep       Date:  2020-06-16       Impact factor: 9.423

3.  Tracking and transforming neocortical progenitors by CRISPR/Cas9 gene targeting and piggyBac transposase lineage labeling.

Authors:  Fuyi Chen; Joel Rosiene; Alicia Che; Albert Becker; Joseph LoTurco
Journal:  Development       Date:  2015-09-23       Impact factor: 6.868

4.  A CRISPR/Cas9 library to map the HIV-1 provirus genetic fitness.

Authors:  K E Yoder
Journal:  Acta Virol       Date:  2019       Impact factor: 1.162

5.  Using CRISPR-Cas9 to Generate Gene-Corrected Autologous iPSCs for the Treatment of Inherited Retinal Degeneration.

Authors:  Erin R Burnight; Manav Gupta; Luke A Wiley; Kristin R Anfinson; Audrey Tran; Robinson Triboulet; Jeremy M Hoffmann; Darcey L Klaahsen; Jeaneen L Andorf; Chunhua Jiao; Elliott H Sohn; Malavika K Adur; Jason W Ross; Robert F Mullins; George Q Daley; Thorsten M Schlaeger; Edwin M Stone; Budd A Tucker
Journal:  Mol Ther       Date:  2017-06-12       Impact factor: 11.454

6.  Efficient CRISPR-Cas9-mediated generation of knockin human pluripotent stem cells lacking undesired mutations at the targeted locus.

Authors:  Florian T Merkle; Werner M Neuhausser; David Santos; Eivind Valen; James A Gagnon; Kristi Maas; Jackson Sandoe; Alexander F Schier; Kevin Eggan
Journal:  Cell Rep       Date:  2015-04-30       Impact factor: 9.423

7.  Re-engineered RNA-Guided FokI-Nucleases for Improved Genome Editing in Human Cells.

Authors:  Steven Havlicek; Yang Shen; Yunus Alpagu; Michaela B Bruntraeger; Nurdiana B M Zufir; Zhi Yi Phuah; Zhiyan Fu; Norris R Dunn; Lawrence W Stanton
Journal:  Mol Ther       Date:  2017-02-01       Impact factor: 11.454

8.  Directed evolution of a recombinase that excises the provirus of most HIV-1 primary isolates with high specificity.

Authors:  Janet Karpinski; Ilona Hauber; Jan Chemnitz; Carola Schäfer; Maciej Paszkowski-Rogacz; Deboyoti Chakraborty; Niklas Beschorner; Helga Hofmann-Sieber; Ulrike C Lange; Adam Grundhoff; Karl Hackmann; Evelin Schrock; Josephine Abi-Ghanem; M Teresa Pisabarro; Vineeth Surendranath; Axel Schambach; Christoph Lindner; Jan van Lunzen; Joachim Hauber; Frank Buchholz
Journal:  Nat Biotechnol       Date:  2016-02-22       Impact factor: 54.908

9.  Structure and specificity of the RNA-guided endonuclease Cas9 during DNA interrogation, target binding and cleavage.

Authors:  Eric A Josephs; D Dewran Kocak; Christopher J Fitzgibbon; Joshua McMenemy; Charles A Gersbach; Piotr E Marszalek
Journal:  Nucleic Acids Res       Date:  2015-09-17       Impact factor: 16.971

Review 10.  CRISPR-Cas9: A multifaceted therapeutic strategy for cancer treatment.

Authors:  Itishree Kaushik; Sharavan Ramachandran; Sanjay K Srivastava
Journal:  Semin Cell Dev Biol       Date:  2019-05-04       Impact factor: 7.727
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