CasOT: A genome-wide Cas9/gRNA off-target searching tool

Bioinformatics

Volumn 30, Issue 8, 2014, Pages 1180-1182

  Xiao, An ^a   Cheng, Zhenchao ^a   Kong, Lei ^b   Zhu, Zuoyan ^a   Lin, Shuo ^c   Gao, Ge ^b   Zhang, Bo ^a  

^a Peking University   (China)

^b PEKING UNIVERSITY   (China)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GUIDE RNA;

BIOLOGY; CRISPR CAS SYSTEM; GENE TARGETING; GENETICS; HUMAN; PROCEDURES; SOFTWARE;

COMPUTATIONAL BIOLOGY; CRISPR-CAS SYSTEMS; GENE TARGETING; HUMANS; RNA, GUIDE; SOFTWARE;

EID: 84898889321     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt764     Document Type: Article

References (17)

1. Cong, L. et al. (2013) Multiplex genome engineering using CRISPR/Cas systems. Science, 339, 819-823.
2. Cradick, T.J. et al. (2013) CRISPR/Cas9 systems targeting beta-globin and CCR5 genes have substantial off-target activity. Nucleic Acids Res., 41, 9584-9592.
3. Fu, Y. et al. (2013) High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat. Biotechnol., 31, 822-826.
4. Fujji, W. et al. (2013) Efficient generation of large-scale genome-modified mice using gRNA and CAS9 endonuclease. Nucleic Acids Res., 41, e187.
5. Hsu, P.D. et al. (2013) DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol., 31, 827-832.
6. Iseli, C. et al. (2007) Indexing strategies for rapid searches of short words in genome sequences. PLoS One, 2, e579.
7. Jiang, W. et al. (2013) RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotechnol., 31, 233-239.
8. Jinek, M. et al. (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 337, 816-821.
9. Li, W. et al. (2013) Simultaneous generation and germline transmission of multiple gene mutations in rat using CRISPR-Cas systems. Nat. Biotechnol., 31, 684-686.
10. Liu, D. et al. (2013) Efficient gene targeting in zebrafish mediated by a zebrafish-codon-optimized Cas9 and evaluation of off-targeting effect. J. Genet. Genomics, [Epub ahead of print, doi: 10.1016/j.jgg.2013.11.004].
11. Mali, P. et al. (2013a) RNA-guided human genome engineering via Cas9. Science, 339, 823-826.
12. Mali, P. et al. (2013b) CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol., 31, 833-838.
13. Pattanayak, V. et al. (2013) High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat. Biotechnol., 31, 839-843.
14. Pennisi, E. (2013) The CRISPR craze. Science, 341, 833-836.
15. Ran, F.A. et al. (2013) Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell, 154, 1380-1389.
16. Shan, Q. et al. (2013) Targeted genome modification of crop plants using a CRISPR-Cas system. Nat. Biotechnol., 31, 686-688.
17. Xiao, A. et al. (2013) EENdb: a database and knowledge base of ZFNs and TALENs for endonuclease engineering. Nucleic Acids Res., 41, D415-D422.