Chromatin accessibility and guide sequence secondary structure affect CRISPR-Cas9 gene editing efficiency

FEBS Letters

Volumn 591, Issue 13, 2017, Pages 1892-1901

  Jensen, Kristopher Torp ^a,b   Fløe, Lasse ^a   Petersen, Trine Skov ^a   Huang, Jinrong ^c   Xu, Fengping ^c,d   Bolund, Lars ^a,c   Luo, Yonglun ^a   Lin, Lin ^a  

^a AARHUS UNIVERSITY   (Denmark)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c BGI SHENZHEN   (China)

^d UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

chromatin accessibility; CRISPR; efficiency; gRNA

Indexed keywords

CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS ASSOCIATED PROTEIN 9; CRISPR ASSOCIATED PROTEIN; GUIDE RNA; UNCLASSIFIED DRUG; CHROMATIN;

CHROMATIN STRUCTURE; CONTROLLED STUDY; CRISPR CAS SYSTEM; DOUBLE STRANDED DNA BREAK; EUCHROMATIN; FIBROBLAST; GENE EDITING; GENE LOCUS; HEK293 CELL LINE; HELA CELL LINE; HETEROCHROMATIN; HUMAN; HUMAN CELL; LETTER; POINT MUTATION; PRIORITY JOURNAL; RNA SECONDARY STRUCTURE; RNA SEQUENCE; RNA STRUCTURE; CHROMATIN; DNA CLEAVAGE; GENETICS; GENOMICS; PROCEDURES;

CHROMATIN; CRISPR-CAS SYSTEMS; DNA CLEAVAGE; GENE EDITING; GENETIC LOCI; GENOMICS; HEK293 CELLS; HELA CELLS; HUMANS; POINT MUTATION;

EID: 85021257840     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1002/1873-3468.12707     Document Type: Article

References (25)

1. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA and Charpentier E (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821.
2. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA et al. (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823.
3. Mali P, Yang L, Esvelt KM, Aach J, Guell M, Dicarlo JE, Norville JE and Church GM (2013) RNA-guided human genome engineering via Cas9. Science 339, 823–826.
4. Li W, Teng F, Li T and Zhou Q (2013) Simultaneous generation and germline transmission of multiple gene mutations in rat using CRISPR-Cas systems. Nat Biotechnol 31, 684–686.
5. Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK and Giraldez AJ (2015) CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat Methods 12, 982–988.
6. Doench JG, Hartenian E, Graham DB, Tothova Z, Hegde M, Smith I, Sullender M, Ebert BL, Xavier RJ and Root DE (2014) Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nat Biotechnol 32, 1262–1267.
7. Xu H, Xiao T, Chen CH, Li W, Meyer CA, Wu Q, Wu D, Cong L, Zhang F, Liu JS et al. (2015) Sequence determinants of improved CRISPR sgRNA design. Genome Res 25, 1147–1157.
8. Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D, Joung JK and Sander JD (2013) High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol 31, 822–826.
9. Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX and Zhang F (2016) Rationally engineered Cas9 nucleases with improved specificity. Science 351, 84–88.
10. Kleinstiver BP, Pattanayak V, Prew MS, Tsai SQ, Nguyen NT, Zheng Z and Joung JK (2016) High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529, 490–495.
11. Fu Y, Sander JD, Reyon D, Cascio VM and Joung JK (2014) Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol 32, 279–284.
12. Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S et al. (2014) Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol 32, 670–676.
13. Daer RM, Cutts JP, Brafman DA and Haynes KA (2017) The impact of chromatin dynamics on Cas9-mediated genome editing in human cells. ACS Synth Biol 6, 428–438.
14. Chen X, Rinsma M, Janssen JM, Liu J, Maggio I and Goncalves MA (2016) Probing the impact of chromatin conformation on genome editing tools. Nucleic Acids Res 44, 6482–6492.
15. Chari R, Mali P, Moosburner M and Church GM (2015) Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nat Methods 12, 823–826.
16. Thyme SB, Akhmetova L, Montague TG, Valen E and Schier AF (2016) Internal guide RNA interactions interfere with Cas9-mediated cleavage. Nat Commun 7, 11750.
17. Wong N, Liu W and Wang X (2015) WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system. Genome Biol 16, 218.
18. Brinkman EK, Chen T, Amendola M and van Steensel B (2014) Easy quantitative assessment of genome editing by sequence trace decomposition. Nucleic Acids Res 42, e168.
19. Zhou Y, Liu Y, Hussmann D, Brøgger P, Al-Saaidi RA, Tan S, Lin L, Petersen TS, Zhou GQ, Bross P et al. (2016) Enhanced genome editing in mammalian cells with a modified dual-fluorescent surrogate system. Cell Mol Life Sci 73, 2543–2563.
20. Sugimoto N, Nakano S, Yoneyama M and Honda K (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res 24, 4501–4505.
21. Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA and Zhang F (2013) Genome engineering using the CRISPR-Cas9 system. Nat Protoc 8, 2281–2308.
22. Ren C, Xu K, Liu Z, Shen J, Han F, Chen Z and Zhang Z (2015) Dual-reporter surrogate systems for efficient enrichment of genetically modified cells. Cell Mol Life Sci 72, 2763–2772.
23. Kim H, Um E, Cho SR, Jung C, Kim H and Kim JS (2011) Surrogate reporters for enrichment of cells with nuclease-induced mutations. Nat Methods 8, 941–943.
24. Horlbeck MA, Witkowsky LB, Guglielmi B, Replogle JM, Gilbert LA, Villalta JE, Torigoe SE, Tjian R and Weissman JS (2016) Nucleosomes impede Cas9 access to DNA in vivo and in vitro. eLife. pii: e12677.
25. Wolfsheimer S and Hartmann AK (2010) Minimum-free-energy distribution of RNA secondary structures: entropic and thermodynamic properties of rare events. Phys Rev E Stat Nonlin Soft Matter Phys 82, 021902.