SgRNAcas9: A software package for designing CRISPR sgRNA and evaluating potential off-target cleavage sites

PLoS ONE

Volumn 9, Issue 6, 2014, Pages

  Xie, Shengsong ^a   Shen, Bin ^b   Zhang, Chaobao ^a   Huang, Xingxu ^b   Zhang, Yonglian ^a,c  

^a INSTITUTE OF BIOCHEMISTRY AND CELL BIOLOGY   (China)

^b NANJING UNIVERSITY   (China)

^c SHANGHAI INSTITUTE OF PLANNED PARENTHOOD RESEARCH   (China)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; TRANSCRIPTION FACTOR EMX1; GUIDE RNA;

ARTICLE; BIOINFORMATICS; COMPUTER MODEL; COMPUTER PROGRAM; CRISPR SGRNA SYSTEM; EMX1 GENE; EXON; EXPRESSION VECTOR; GENE TARGETING; MUTATION; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PREDICTION; RNA CLEAVAGE; RNA EDITING; RNA SEQUENCE; SEQUENCE ALIGNMENT; ALGORITHM; BIOLOGY; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; DNA CLEAVAGE; GENETICS; HUMAN; MOLECULAR GENETICS; PROCEDURES; SEQUENCE HOMOLOGY;

ALGORITHMS; BASE SEQUENCE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; COMPUTATIONAL BIOLOGY; DNA CLEAVAGE; HUMANS; MOLECULAR SEQUENCE DATA; RNA EDITING; RNA, GUIDE; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOFTWARE;

EID: 84903549014     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0100448     Document Type: Article

References (40)

1. Cong L, Ran FA, Cox D, Lin S, Barretto R, et al. (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339: 819-23.
2. Mali P, Yang L, Esvelt KM, Aach J, Guell M, et al. (2013) RNA-guided human genome engineering via Cas9. Science 339: 823-6.
3. Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, et al. (2013) CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol 31: 833-8.
4. Cheng AW, Wang H, Yang H, Shi L, Katz Y, et al. (2013) Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cell Res 23: 1163-71.
5. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, et al. (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152: 1173-83.
6. Larson MH, Gilbert LA, Wang X, Lim WA, Weissman JS, et al. (2013) CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Nat Protoc 8: 2180-96.
7. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, et al. (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315: 1709-12. (Pubitemid 46515624)
8. Marraffini LA, Sontheimer EJ (2008) CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322: 1843-5.
9. Niu Y, Shen B, Cui Y, Chen Y, Wang J, et al. (2014) Generation of gene-modified cynomolgus monkey via Cas9/RNA-mediated gene targeting in one-cell embryos. Cell 156: 836-43.
10. Matsunaga T, Yamashita JK (2014) Single-step generation of gene knockout-rescue system in pluripotent stem cells by promoter insertion with CRISPR/Cas9. Biochem Biophys Res Commun\ 444: 158-63.
11. Yang H, Wang H, Shivalila CS, Cheng AW, Shi L, et al. (2013) One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell 154: 1370-9.
12. Zhou J, Shen B, Zhang W, Wang J, Yang J, et al. (2014) One-step generation of different immunodeficient mice with multiple gene modifications by CRISPR/Cas9 mediated genome engineering. Int J Biochem Cell Biol 46: 49-55.
13. Sung YH, Kim JM, Kim HT, Lee J, Jeon J, et al. (2014) Highly efficient gene knockout in mice and zebrafish with RNA-guided endonucleases. Genome Res 24: 125-31.
14. Fujii W, Kawasaki K, Sugiura K, Naito K (2013) Efficient generation of large-scale genome-modified mice using gRNA and CAS9 endonuclease. Nucleic Acids Res 41: e187.
15. Ma Y, Zhang X, Shen B, Lu Y, Chen W, et al. (2014) Generating rats with conditional alleles using CRISPR/Cas9. Cell Res 24: 122-5.
16. Auer TO, Duroure K, De Cian A, Concordet JP, Del Bene F (2014) Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair. Genome Res 24: 142-53.
17. Hisano Y, Ota S, Kawahara A (2014) Genome editing using artificial site-specific nucleases in zebrafish. Dev Growth Differ 56: 26-33.
18. Jao LE, Wente SR, Chen W (2013) Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc Natl Acad Sci U S A 110: 13904-9.
19. Chang N, Sun C, Gao L, Zhu D, Xu X, et al. (2013) Genome editing with RNA-guided Cas9 nuclease in zebrafish embryos. Cell Res 23: 465-72.
20. Ren X, Sun J, Housden BE, Hu Y, Roesel C, et al. (2013) Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9. Proc Natl Acad Sci U S A 110: 19012-7.
21. Bassett AR, Liu JL (2014) CRISPR/Cas9 and genome editing in Drosophila. J Genet Genomics 41: 7-19.
22. Dickinson DJ, Ward JD, Reiner DJ, Goldstein B (2013) Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination. Nat Methods 10: 1028-34.
23. Wu Y, Liang D, Wang Y, Bai M, Tang W, et al. (2013) Correction of a genetic disease in mouse via use of CRISPR-Cas9. Cell Stem Cell 13: 659-62.
24. Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, et al. (2013) DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 31: 827-32.
25. Pattanayak V, Lin S, Guilinger JP, Ma E, Doudna JA, et al. (2013) High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol 31: 839-43.
26. Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D, et al. (2013) High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol 31: 822-6.
27. Carroll D. (2013) Staying on target with CRISPR-Cas. Nat Biotechnol 3: 807-9.
28. Ran FA, Hsu PD, Lin CY, Gootenberg JS, Konermann S, et al. (2013) Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154: 1380-9.
29. Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK. (2014) Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol [Epub ahead of print].
30. Jiang H, Wong WH (2008) SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 24: 2395-6.
31. Wang T, Wei JJ, Sabatini DM, Lander ES (2014) Genetic screens in human cells using the CRISPR-Cas9 system. Science 343: 80-4.
32. Tsai SQ, Wyvekens N, Khayter C, Foden JA, Thapar V, et al. (2014) Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat Biotechnol. [Epub ahead of print]
33. Guilinger JP, Thompson DB, Liu DR (2014) Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat Biotechnol. [Epub ahead of print]
34. Jiang W, Zhou H, Bi H, Fromm M, Yang B, et al. (2013) Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Res 41: e188.
35. Bikard D, Marraffini LA (2013) Control of gene expression by CRISPR-Cas systems. F1000Prime Rep 5: 47.
36. Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA. (2013) RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 31: 233-9.
37. Ma M, Ye AY, Zheng W, Kong L (2013) A guide RNA sequence design platform for the CRISPR/Cas9 system for model organism genomes. Biomed Res Int 2013: 270805.
38. Bae S, Park J, Kim JS (2014) Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics [Epub ahead of print].
39. Xiao A, Cheng Z, Kong L, Zhu Z, Lin S, et al. (2014) CasOT: a genome-wide Cas9/gRNA off-target searching tool. Bioinformatics [Epub ahead of print].
40. Heigwer F, Kerr G, Boutros M (2014) E-CRISP: fast CRISPR target site identification. Nat Methods 11: 122-3.