Examination of CRISPR/Cas9 design tools and the effect of target site accessibility on Cas9 activity

Experimental Physiology

Volumn 103, Issue 4, 2018, Pages 456-460

  Lee, Ciaran M ^a   Davis, Timothy H ^a   Bao, Gang ^a  

^a Rice University   (United States)

Author keywords

CRISPR; Gene Targeting; molecular biology

Indexed keywords

CRISPR ASSOCIATED PROTEIN; CRISPR ASSOCIATED PROTEIN 9; DNA; SINGLE STRANDED RNA; UNCLASSIFIED DRUG; GUIDE RNA;

ARTICLE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CRISPR CAS SYSTEM; DNA MODIFICATION; FRAMESHIFT MUTATION; GENE ACTIVITY; GENE EDITING; GENE LIBRARY; GENE LOCUS; GENE TARGETING; GENETIC ALGORITHM; GENETIC ENGINEERING; GENOME ANALYSIS; HUMAN; HUMAN GENOME; NONHUMAN; PREDICTION; PROCESS OPTIMIZATION; PROTEIN CLEAVAGE; PROTEIN FUNCTION; PROTEIN RNA BINDING; RNA ANALYSIS; RNA SEQUENCE; ANIMAL; GENETICS; GENOME; METABOLISM; PROCEDURES;

ANIMALS; CRISPR-ASSOCIATED PROTEIN 9; CRISPR-CAS SYSTEMS; DNA; GENE EDITING; GENOME; HUMANS; RNA, GUIDE;

EID: 85017587935     PISSN: 09580670     EISSN: 1469445X     Source Type: Journal    
DOI: 10.1113/EP086043     Document Type: Article

References (25)

1. Bae S, Kweon J, Kim HS & Kim JS (2014). Microhomology-based choice of Cas9 nuclease target sites. Nat Methods 11, 705–706.
2. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA & Horvath P (2007). CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709–1712.
3. Chari R, Mali P, Moosburner M & Church GM (2015). Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nat Methods 12, 823–826.
4. Clapier CR & Cairns BR (2009). The biology of chromatin remodeling complexes. Annu Rev Biochem 78, 273–304.
5. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA & Zhang F (2013). Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823.
6. Cradick TJ, Fine EJ, Antico CJ & Bao G (2013). CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity. Nucleic Acids Res 41, 9584–9592.
7. Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C, Orchard R, Virgin HW, Listgarten J & Root DE (2016). Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol 34, 184–191.
8. Doench JG, Hartenian E, Graham DB, Tothova Z, Hegde M, Smith I, Sullender M, Ebert BL, Xavier RJ & Root DE (2014). Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nat Biotechnol 32, 1262–1267.
9. Haeussler M, Schönig K, Eckert H, Eschstruth A, Mianné J, Renaud JB, Schneider-Maunoury S, Shkumatava A, Teboul L, Kent J, Joly JS & Concordet JP (2016). Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol 17, 148.
10. Hinz JM, Laughery MF & Wyrick JJ (2015). Nucleosomes inhibit Cas9 endonuclease activity in vitro. Biochemistry 54, 7063–7066.
11. Horlbeck MA, Witkowsky LB, Guglielmi B, Replogle JM, Gilbert LA, Villalta JE, Torigoe SE, Tjian R & Weissman JS (2016). Nucleosomes impede Cas9 access to DNA in vivo and in vitro. Elife 5, e12677.
12. Isaac RS, Jiang F, Doudna JA, Lim WA, Narlikar GJ & Almeida R (2016). Nucleosome breathing and remodeling constrain CRISPR-Cas9 function. Elife 5, e13450.
13. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA & Charpentier E (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821.
14. Kim YG, Cha J & Chandrasegaran S (1996). Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci USA 93, 1156–1160.
15. Lee CM, Zhu H, Davis TH, Deshmukh H & Bao G (2017). Design and validation of CRISPR/Cas9 systems for targeted gene modification in induced pluripotent stem cells. Methods Mol Biol 1498, 3–21.
16. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE & Church GM (2013). RNA-guided human genome engineering via Cas9. Science 339, 823–826.
17. Marraffini LA & Sontheimer EJ (2008). CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322, 1843–1845.
18. Miller JC, Tan S, Qiao G, Barlow KA, Wang J, Xia DF, Meng X, Paschon DE, Leung E, Hinkley SJ, Dulay GP, Hua KL, Ankoudinova I, Cost GJ, Urnov FD, Zhang HS, Holmes MC, Zhang L, Gregory PD & Rebar EJ (2011). A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29, 143–148.
19. Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK & Giraldez AJ (2015). CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat Methods 12, 982–988.
20. Mussolino C, Morbitzer R, Lütge F, Dannemann N, Lahaye T & Cathomen T (2011). A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity. Nucleic Acids Res 39, 9283–9293.
21. Narlikar GJ, Sundaramoorthy R & Owen-Hughes T (2013). Mechanisms and functions of ATP-dependent chromatin-remodeling enzymes. Cell 154, 490–503.
22. Ren X, Yang Z, Xu J, Sun J, Mao D, Hu Y, Yang SJ, Qiao HH, Wang X, Hu Q, Deng P, Liu LP, Ji JY, Li JB & Ni JQ (2014). Enhanced specificity and efficiency of the CRISPR/Cas9 system with optimized sgRNA parameters in Drosophila. Cell Rep 9, 1151–1162.
23. Urnov FD, Miller JC, Lee YL, Beausejour CM, Rock JM, Augustus S, Jamieson AC, Porteus MH, Gregory PD & Holmes MC (2005). Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435, 646–651.
24. Wong N, Liu W & Wang X (2015). WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system. Genome Biol 16, 218.
25. Xu H, Xiao T, Chen CH, Li W, Meyer CA, Wu Q, Wu D, Cong L, Zhang F, Liu JS, Brown M & Liu XS (2015). Sequence determinants of improved CRISPR sgRNA design. Genome Res 25, 1147–1157.