Exploiting the CRISPR/Cas9 PAM constraint for single-nucleotide resolution interventions

PLoS ONE

Volumn 11, Issue 1, 2016, Pages

  Li, Yi ^a,b   Mendiratta, Saurabh ^c   Ehrhardt, Kristina ^a,b   Kashyap, Neha ^a,b   White, Michael A ^c   Bleris, Leonidas ^a,b  

^a The University of Texas at Dallas   (United States)

^b UNIVERSITY OF TEXAS AT DALLAS   (United States)

^c UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BENZIMIDAZOLE DERIVATIVE; GUIDE RNA; KRAS PROTEIN, HUMAN; PROTEIN P21; RNA; SELUMETINIB;

CHEMISTRY; CRISPR CAS SYSTEM; DRUG RESISTANCE; GENETICS; HEK293 CELL LINE; HUMAN; METABOLISM; RNA EDITING; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR CELL LINE;

BENZIMIDAZOLES; CELL LINE, TUMOR; CRISPR-CAS SYSTEMS; DRUG RESISTANCE, NEOPLASM; HEK293 CELLS; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTO-ONCOGENE PROTEINS P21(RAS); RNA; RNA EDITING; RNA, GUIDE;

EID: 84958214080     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0144970     Document Type: Article

References (27)

1. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013 Feb 15; 339(6121): 819-823.doi: 10. 1126/science.1231143
2. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNAguided DNA endonuclease in adaptive bacterial immunity. Science. 2012 Aug 17; 337(6096): 816-821.doi: 10.1126/science.1225829
3. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, et al. RNA-guided human genome engineering via Cas9. Science. 2013 Feb 15; 339(6121): 823-826.doi: 10.1126/science. 1232033
4. Yang L, Mali P, Kim-Kiselak C, Church G. CRISPR-cas-mediated targeted genome editing in human cells. In: Gene Correction. Springer; 2014. p. 245-267.
5. Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, et al. CRISPR-mediated modular RNAguided regulation of transcription in eukaryotes. Cell. 2013; 154(2): 442-451.doi: 10.1016/j.cell.2013. 06.044
6. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013; 152(5): 1173-1183.doi: 10.1016/j.cell.2013.02.022
7. Moore R, Spinhirne A, Lai MJ, Preisser S, Li Y, Kang T, et al. CRISPR-based self-cleaving mechanism for controllable gene delivery in human cells. Nucleic Acids Res. 2015 Jan 30; 43(2): 1297-1303.doi: 10.1093/nar/gku1326
8. Kuscu C, Arslan S, Singh R, Thorpe J, Adli M. Genome-wide analysis reveals characteristics of off-Target sites bound by the Cas9 endonuclease. Nat Biotechnol. 2014.
9. Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, et al. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol. 2014; 32(7): 670-676.doi: 10.1038/nbt.2889
10. Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V, et al. GUIDE-seq enables genomewide profiling of off-Target cleavage by CRISPR-cas nucleases. Nat Biotechnol. 2015; 33(2): 187-197.doi: 10.1038/nbt.3117
11. Kim HS, Mendiratta S, Kim J, Pecot CV, Larsen JE, Zubovych I, et al. Systematic identification of molecular subtype-selective vulnerabilities in non-small-cell lung cancer. Cell. 2013; 155(3): 552-566.doi: 10.1016/j.cell.2013.09.041
12. Little AS, Balmanno K, Sale MJ, Newman S, Dry JR, Hampson M, et al. Amplification of the driving oncogene, KRAS or BRAF, underpins acquired resistance to MEK1/2 inhibitors in colorectal cancer cells. Sci Signal. 2011 Mar 29; 4(166): ra17.doi: 10.1126/scisignal.2001752
13. Liao J, Karnik R, Gu H, Ziller MJ, Clement K, Tsankov AM, et al. Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells. Nat Genet. 2015.
14. Xie F, Ye L, Chang JC, Beyer AI, Wang J, Muench MO, et al. Seamless gene correction of beta-Thalassemia mutations in patient-specific iPSCs using CRISPR/Cas9 and piggyBac. Genome Res. 2014 Sep; 24(9): 1526-1533.doi: 10.1101/gr.173427.114
15. Sanjana NE, Shalem O, Zhang F. Improved vectors and genome-wide libraries for CRISPR screening. Nature methods. 2014; 11(8): 783-784.doi: 10.1038/nmeth.3047
16. Li Y, Moore R, Guinn M, Bleris L. Transcription activator-like effector hybrids for conditional control and rewiring of chromosomal transgene expression. Scientific Reports. 2012; 2.
17. Li Y, Ehrhardt K, Zhang MQ, Bleris L. Assembly and validation of versatile transcription activator-like effector libraries. Scientific reports. 2014; 4.
18. Moore R, Chandrahas A, Bleris L. Transcription activator-like effectors: A toolkit for synthetic biology. ACS synthetic biology. 2014; 3(10): 708-716.doi: 10.1021/sb400137b
19. Schreiber T, Bonas U. Repeat 1 of TAL effectors affects target specificity for the base at position zero. Nucleic Acids Res. 2014 Jun; 42(11): 7160-7169.doi: 10.1093/nar/gku341
20. Yoshimi K, Kaneko T, Voigt B, Mashimo T. Allele-specific genome editing and correction of diseaseassociated phenotypes in rats using the CRISPR-Cas platform. Nature communications. 2014; 5.
21. Courtney D, Moore J, Atkinson S, Maurizi E, Allen E, Pedrioli D, et al. CRISPR/Cas9 DNA cleavage at SNP-derived PAM enables both in vitro and in vivo KRT12 mutation-specific targeting. Gene Ther. 2015.
22. Taylor DW, Zhu Y, Staals RH, Kornfeld JE, Shinkai A, van der Oost J, et al. Structures of the CRISPRcmr complex reveal mode of RNA target positioning. Science. 2015 Apr 2.
23. Jiang F, Doudna JA. The structural biology of CRISPR-cas systems. Curr Opin Struct Biol. 2015; 30: 100-111.doi: 10.1016/j.sbi.2015.02.002
24. Fonfara I, Le Rhun A, Chylinski K, Makarova KS, Lecrivain AL, Bzdrenga J, et al. Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-cas systems. Nucleic Acids Res. 2014 Feb; 42(4): 2577-2590.doi: 10.1093/nar/gkt1074
25. Doudna JA, Charpentier E. Genome editing.The new frontier of genome engineering with CRISPRCas9. Science. 2014 Nov 28; 346(6213): 1258096.doi: 10.1126/science.1258096
26. Hilton IB, D'Ippolito AM, Vockley CM, Thakore PI, Crawford GE, Reddy TE, et al. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat Biotechnol. 2015.
27. Kleinstiver BP, Prew MS, Tsai SQ, Topkar VV, Nguyen NT, Zheng Z, et al. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature. 2015.