Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells

Nature Biotechnology

Volumn 34, Issue 8, 2016, Pages 869-874

  Kleinstiver, Benjamin P ^a,b   Tsai, Shengdar Q ^a,b   Prew, Michelle S ^a   Nguyen, Nhu T ^a   Welch, Moira M ^a   Lopez, Jose M ^a,b   McCaw, Zachary R ^a,c   Aryee, Martin J ^a,b,c   Joung, J Keith ^a,b  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOTECHNOLOGY;

DEEP SEQUENCING ANALYSIS; DOUBLE SUBSTITUTION; HUMAN CELLS; SINGLE-BASE MISMATCH; STREPTOCOCCUS PYOGENES;

GENES;

CASPASE 9; CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN; CRISPR CAS CPF1 NUCLEASE; NUCLEASE; RNA; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; ENDONUCLEASE; PROTEIN BINDING;

ACIDAMINOCOCCUS; ARTICLE; BACTERIAL STRAIN; BASE MISPAIRING; CELL SPECIFICITY; CONTROLLED STUDY; ENZYME ACTIVITY; GENOMICS; HUMAN; HUMAN CELL; HUMAN GENOME; LACHNOSPIRACEAE; NONHUMAN; PRIORITY JOURNAL; PROTEIN CLEAVAGE; PROTEIN TARGETING; SEQUENCE ANALYSIS; STREPTOCOCCUS PYOGENES; BINDING SITE; CHROMOSOMAL MAPPING; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CRISPR CAS SYSTEM; ENZYME ACTIVATION; ENZYME SPECIFICITY; GENETICS; METABOLISM; PHYSIOLOGY; PROCEDURES;

BACTERIAL PROTEINS; BASE PAIR MISMATCH; BINDING SITES; CHROMOSOME MAPPING; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CRISPR-CAS SYSTEMS; ENDONUCLEASES; ENZYME ACTIVATION; GENOME, HUMAN; HUMANS; PROTEIN BINDING; SUBSTRATE SPECIFICITY;

EID: 84981347695     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.3620     Document Type: Article

References (30)

1. Zetsche, B. et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163, 759-771 (2015).
2. Sander, J.D. & Joung, J.K. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat. Biotechnol. 32, 347-355 (2014).
3. Hsu, P.D., Lander, E.S. & Zhang, F. Development and applications of CRISPR-Cas9 for genome engineering. Cell 157, 1262-1278 (2014).
4. Doudna, J.A. & Charpentier, E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 346, 1258096 (2014).
5. Maeder, M.L. & Gersbach, C.A. Genome-editing technologies for gene and cell therapy. Mol. Ther. 24, 430-446 (2016).
6. Wright, A.V., Nuñez, J.K. & Doudna, J.A. Biology and applications of CRISPR systems: harnessing nature's toolbox for genome engineering. Cell 164, 29-44 (2016).
7. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821 (2012).
8. Deltcheva, E. et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471, 602-607 (2011).
9. Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823 (2013).
10. Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823-826 (2013).
11. Jinek, M. et al. RNA-programmed genome editing in human cells. eLife 2, e00471 (2013).
12. Tsai, S.Q. et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat. Biotechnol. 33, 187-197 (2015).
13. Frock, R.L. et al. Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nat. Biotechnol. 33, 179-186 (2015).
14. Wang, X. et al. Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors. Nat. Biotechnol. 33, 175-178 (2015).
15. Kim, D. et al. Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nat. Methods 12, 237-243, 1, 243 (2015).
16. Kleinstiver, B.P. et al. High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529, 490-495 (2016).
17. Slaymaker, I.M. et al. Rationally engineered Cas9 nucleases with improved specificity. Science 351, 84-88 (2016).
18. Schunder, E., Rydzewski, K., Grunow, R. & Heuner, K. First indication for a functional CRISPR/Cas system in Francisella tularensis. Int. J. Med. Microbiol. 303, 51-60 (2013).
19. Makarova, K.S. et al. An updated evolutionary classification of CRISPR-Cas systems. Nat. Rev. Microbiol. 13, 722-736 (2015).
20. Fagerlund, R.D., Staals, R.H. & Fineran, P.C. The Cpf1 CRISPR-Cas protein expands genome-editing tools. Genome Biol. 16, 251 (2015).
21. Bae, S., Park, J. & Kim, J.S. Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30, 1473-1475 (2014).
22. Fu, Y., Sander, J.D., Reyon, D., Cascio, V.M. & Joung, J.K. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat. Biotechnol. 32, 279-284 (2014).
23. Kleinstiver, B.P. et al. Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition. Nat. Biotechnol. 33, 1293-1298 (2015).
24. Kleinstiver, B.P. et al. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 523, 481-485 (2015).
25. Yin, H. et al. Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo. Nat. Biotechnol. 34, 328-333 (2016).
26. Bolukbasi, M.F. et al. DNA-binding-domain fusions enhance the targeting range and precision of Cas9. Nat. Methods 12, 1150-1156 (2015).
27. Friedland, A.E. et al. Characterization of Staphylococcus aureus Cas9: a smaller Cas9 for all-in-one adeno-associated virus delivery and paired nickase applications. Genome Biol. 16, 257 (2015).
28. Tsai, S.Q. et al. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat. Biotechnol. 32, 569-576 (2014).
29. Reyon, D. et al. FLASH assembly of TALENs for high-throughput genome editing. Nat. Biotechnol. 30, 460-465 (2012).
30. Tsai, S.Q., Topkar, V.V., Joung, J.K. & Aryee, M.J. Open-source guideseq software for analysis of GUIDE-seq data. Nat. Biotechnol. 34, 483 (2016).