Synthetically modified guide RNA and donor DNA are a versatile platform for CRISPR-Cas9 engineering

eLife

Volumn 6, Issue , 2017, Pages

  Lee, Kunwoo ^a   Mackley, Vanessa A ^a   Rao, Anirudh ^b   Chong, Anthony T ^b   Dewitt, Mark A ^c   Corn, Jacob E ^c   Murthy, Niren ^b  

^a GenEdit Inc   (United States)

^b University of California at Berkeley   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA; BACTERIAL PROTEIN; CAS9 ENDONUCLEASE STREPTOCOCCUS PYOGENES; CPF1 NUCLEASE, ACIDAMINOCOCCUS; ENDONUCLEASE; GUIDE RNA;

ARTICLE; CAS9 GENE; CELL SELECTION; CPF1 GENE; CRISPR CAS SYSTEM; CRISPR CAS9 SYSTEM; DENSITOMETRY; DNA DAMAGE; DNA EXTRACTION; DNA PURIFICATION; ENZYME ANALYSIS; FLOW CYTOMETRY; FLUORESCENCE MICROSCOPY; GEL ELECTROPHORESIS; GENE; GENE EDITING; GENE SEQUENCE; GENETIC ENGINEERING; HUMAN; HUMAN CELL; IMMUNOGENICITY; POLYMERASE CHAIN REACTION; PROTEIN EXPRESSION; RNA PURIFICATION; SEQUENCE ANALYSIS; CHEMISTRY; GENETICS; METABOLISM; PROCEDURES;

BACTERIAL PROTEINS; CRISPR-CAS SYSTEMS; DNA; ENDONUCLEASES; GENE EDITING; RNA, GUIDE;

EID: 85018933152     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.25312.001     Document Type: Article

References (37)

1. Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B. 2013. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155:1479–1491. doi: 10.1016/j.cell.2013.12.001, PMID: 24360272
2. Cho SW, Kim S, Kim JM, Kim JS. 2013. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nature Biotechnology 31:230–232. doi: 10.1038/nbt.2507, PMID: 23360966
3. Conboy MJ, Conboy IM. 2010. Preparation of adult muscle fiber-associated stem/precursor cells. Methods in Molecular Biology 621:149–163. doi: 10.1007/978-1-60761-063-2_10, PMID: 20405365
4. 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. doi: 10.1126/science.1231143, PMID: 23287718
5. De Witt MA, Magis W, Bray NL, Wang T, Berman JR, Urbinati F, Heo SJ, Mitros T, Muñoz DP, Boffelli D, Kohn DB, Walters MC, Carroll D, Martin DI, Corn JE. 2016. Selection-free genome editing of the sickle mutation in human adult hematopoietic stem/progenitor cells. Science Translational Medicine 8:360ra134. doi: 10.1126/scitranslmed.aaf9336, PMID: 27733558
6. Dever DP, Bak RO, Reinisch A, Camarena J, Washington G, Nicolas CE, Pavel-Dinu M, Saxena N, Wilkens AB, Mantri S, Uchida N, Hendel A, Narla A, Majeti R, Weinberg KI, Porteus MH. 2016. CRISPR/Cas9 b-globin gene targeting in human haematopoietic stem cells. Nature 539:384–389. doi: 10.1038/nature20134, PMID: 27820 943
7. Durai S, Mani M, Kandavelou K, Wu J, Porteus MH, Chandrasegaran S. 2005. Zinc finger nucleases: custom- designed molecular scissors for genome engineering of plant and mammalian cells. Nucleic Acids Research 33: 5978–5990. doi: 10.1093/nar/gki912, PMID: 16251401
8. Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK. 2014. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nature Biotechnology 32:279–284. doi: 10.1038/nbt.2808, PMID: 24463574
9. Güell M, Yang L, Church GM. 2014. Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA). Bioinformatics 30:2968–2970. doi: 10.1093/bioinformatics/btu427, PMID: 24990609
10. Hendel A, Bak RO, Clark JT, Kennedy AB, Ryan DE, Roy S, Steinfeld I, Lunstad BD, Kaiser RJ, Wilkens AB, Bacchetta R, Tsalenko A, Dellinger D, Bruhn L, Porteus MH. 2015. Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells. Nature Biotechnology 33:985–989. doi: 10.1038/nbt.3290, PMID: 26121415
11. Holloman WK. 2011. Unraveling the mechanism of BRCA2 in homologous recombination. Nature Structural & Molecular Biology 18:748–754. doi: 10.1038/nsmb.2096, PMID: 21731065
12. Jiang F, Zhou K, Ma L, Gressel S, Doudna JA. 2015. STRUCTURAL BIOLOGY. A Cas9-guide RNA complex preorganized for target DNA recognition. Science 348:1477–1481. doi: 10.1126/science.aab1452, PMID: 26113724
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. doi: 10.1126/science.1225829, PMID: 22745249
14. Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, Ma E, Anders C, Hauer M, Zhou K, Lin S, Kaplan M, Iavarone AT, Charpentier E, Nogales E, Doudna JA. 2014. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343:1247997. doi: 10.1126/science.1247997, PMID: 24505130
15. Kim HJ, Ishii A, Miyata K, Lee Y, Wu S, Oba M, Nishiyama N, Kataoka K. 2010. Introduction of stearoyl moieties into a biocompatible cationic polyaspartamide derivative, PAsp(DET), with endosomal escaping function for enhanced siRNA-mediated gene knockdown. Journal of Controlled Release 145:141–148. doi: 10.1016/j.jconrel.2010.03.019, PMID: 20359509
16. Kim H, Kim MS, Wee G, Lee CI, Kim H, Kim JS. 2013. Magnetic separation and antibiotics selection enable enrichment of cells with ZFN/TALEN-induced mutations. PLoS One 8:e56476. doi: 10.1371/journal.pone.0056476, PMID: 23441197
17. Kim HJ, Takemoto H, Yi Y, Zheng M, Maeda Y, Chaya H, Hayashi K, Mi P, Pittella F, Christie RJ, Toh K, Matsumoto Y, Nishiyama N, Miyata K, Kataoka K. 2014. Precise engineering of siRNA delivery vehicles to tumors using polyion complexes and gold nanoparticles. ACS Nano 8:8979–8991. doi: 10.1021/nn502125h, PMID: 25133608
18. Kleinstiver BP, Tsai SQ, Prew MS, Nguyen NT, Welch MM, Lopez JM, McCaw ZR, Aryee MJ, Joung JK, Kim D. 2016. Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells. Nature Biotechnology 34:869–874. doi: 10.1038/nbt.3620, PMID: 27347757
19. Lee JS, Grav LM, Pedersen LE, Lee GM, Kildegaard HF. 2016. Accelerated homology-directed targeted integration of transgenes in chinese hamster ovary cells via CRISPR/Cas9 and fluorescent enrichment. Biotechnology and Bioengineering 113:2518–2523. doi: 10.1002/bit.26002, PMID: 27159230
20. Lin S, Staahl BT, Alla RK, Doudna JA. 2014. Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. eLife 3:1–13. doi: 10.7554/eLife.04766, PMID: 25497837
21. Long C, McAnally JR, Shelton JM, Mireault AA, Bassel-Duby R, Olson EN. 2014. Prevention of muscular dystrophy in mice by CRISPR/Cas9-mediated editing of germline DNA. Science 345:1184–1188. doi: 10.1126/science.1254445, PMID: 25123483
22. Long C, Amoasii L, Mireault AA, McAnally JR, Li H, Sanchez-Ortiz E, Bhattacharyya S, Shelton JM, Bassel-Duby R, Olson EN. 2016. Postnatal genome editing partially restores dystrophin expression in a mouse model of muscular dystrophy. Science 351:400–403. doi: 10.1126/science.aad5725, PMID: 26721683
23. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. 2013a. RNA-guided human genome engineering via Cas9. Science 339:823–826. doi: 10.1126/science.1232033, PMID: 23287722
24. Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM. 2013b. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nature Biotechnology 31:833–838. doi: 10.1038/nbt.2675, PMID: 23907171
25. Miyata K, Oba M, Nakanishi M, Fukushima S, Yamasaki Y, Koyama H, Nishiyama N, Kataoka K. 2008. Polyplexes from poly(aspartamide) bearing 1,2-diaminoethane side chains induce pH-selective, endosomal membrane destabilization with amplified transfection and negligible cytotoxicity. Journal of the American Chemical Society 130:16287–16294. doi: 10.1021/ja804561g, PMID: 19006313
26. Nelson CE, Hakim CH, Ousterout DG, Thakore PI, Moreb EA, Castellanos Rivera RM, Madhavan S, Pan X, Ran FA, Yan WX, Asokan A, Zhang F, Duan D, Gersbach CA. 2016. In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy. Science 351:403–407. doi: 10.1126/science.aad5143, PMID: 26721684
27. Rahdar M, McMahon MA, Prakash TP, Swayze EE, Bennett CF, Cleveland DW. 2015. Synthetic CRISPR RNA- Cas9-guided genome editing in human cells. PNAS 112:E7110–7117. doi: 10.1073/pnas.1520883112, PMID: 26589814
28. Rando TA, Blau HM. 1994. Primary mouse myoblast purification, characterization, and transplantation for cell- mediated gene therapy. The Journal of Cell Biology 125:1275–1287. doi: 10.1083/jcb.125.6.1275, PMID: 8207057
29. Renaud JB, Boix C, Charpentier M, De Cian A, Cochennec J, Duvernois-Berthet E, Perrouault L, Tesson L, Edouard J, Thinard R, Cherifi Y, Menoret S, Fontanière S, de Crozé N, Fraichard A, Sohm F, Anegon I, Concordet JP, Giovannangeli C. 2016. Improved Genome Editing Efficiency and Flexibility using modified oligonucleotides with TALEN and CRISPR-Cas9 nucleases. Cell Reports 14:2263–2272. doi: 10.1016/j.celrep.2016.02.018, PMID: 26923600
30. Richardson CD, Ray GJ, DeWitt MA, Curie GL, Corn JE. 2016. Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nature Biotechnology 34:339–344. doi: 10.1038/nbt.3481, PMID: 26789497
31. Schumann K, Lin S, Boyer E, Simeonov DR, Subramaniam M, Gate RE, Haliburton GE, Ye CJ, Bluestone JA, Doudna JA, Marson A. 2015. Generation of knock-in primary human T cells using Cas9 ribonucleoproteins. PNAS 112:10437–10442. doi: 10.1073/pnas.1512503112
32. Tabebordbar M, Zhu K, Cheng JK, Chew WL, Widrick JJ, Yan WX, Maesner C, Wu EY, Xiao R, Ran FA, Cong L, Zhang F, Vandenberghe LH, Church GM, Wagers AJ. 2016. In vivo gene editing in dystrophic mouse muscle and muscle stem cells. Science 351:407–411. doi: 10.1126/science.aad5177, PMID: 26721686
33. Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Fedorova I, Nakane T, Makarova KS, Koonin EV, Ishitani R, Zhang F, Nureki O. 2016. Crystal structure of Cpf1 in complex with Guide RNA and target DNA. Cell 165:949–962. doi: 10.1016/j.cell.2016.04.003, PMID: 27114038
34. Yin H, Song CQ, Dorkin JR, Zhu LJ, Li Y, Wu Q, Park A, Yang J, Suresh S, Bizhanova A, Gupta A, Bolukbasi MF, Walsh S, Bogorad RL, Gao G, Weng Z, Dong Y, Koteliansky V, Wolfe SA, Langer R, et al. 2016. Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo. Nature Biotechnology 34:328–333. doi: 10.1038/nbt.3471, PMID: 26829318
35. Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F. 2015. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163:759–771. doi: 10.1016/j.cell.2015.09.038, PMID: 26422227
36. Zetsche B, Heidenreich M, Mohanraju P, Fedorova I, Kneppers J, DeGennaro EM, Winblad N, Choudhury SR, Abudayyeh OO, Gootenberg JS, Wu WY, Scott DA, Severinov K, van der Oost J, Zhang F. 2017. Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array. Nature Biotechnology 35:31–34. doi: 10.1038/nbt.3737, PMID: 27918548
37. Zuris JA, Thompson DB, Shu Y, Guilinger JP, Bessen JL, Hu JH, Maeder ML, Joung JK, Chen ZY, Liu DR. 2015. Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo. Nature Biotechnology 33:73–80. doi: 10.1038/nbt.3081, PMID: 25357182