Programmable RNA recognition and cleavage by CRISPR/Cas9

Nature

Volumn 516, Issue 7530, 2014, Pages 263-266

  O'Connell, Mitchell R ^a   Oakes, Benjamin L ^a   Sternberg, Samuel H ^a   East Seletsky, Alexandra ^a   Kaplan, Matias ^a,c   Doudna, Jennifer A ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c J Crayton Pruitt Family Department of Biomedical Engineering   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CRISPR ASSOCIATED PROTEIN; CRISPR ASSOCIATED PROTEIN CAS9; GENOMIC DNA; GUIDE RNA; MESSENGER RNA; NUCLEASE; OLIGONUCLEOTIDE; SINGLE STRANDED RNA; UNCLASSIFIED DRUG; CELL EXTRACT; DNA; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; RNA;

DNA; ENZYME ACTIVITY; GENETIC ANALYSIS; GENOME; GERM CELL; PROKARYOTE; RNA; SUBSTRATE;

ARTICLE; BASE PAIRING; BINDING AFFINITY; CHEMICAL MODIFICATION; CONTROLLED STUDY; DISSOCIATION CONSTANT; DNA CLEAVAGE; DNA RNA HYBRIDIZATION; DNA SEQUENCE; ENZYME ACTIVATION; FEMALE; GEL MOBILITY SHIFT ASSAY; GENE CONTROL; GENETIC TRANSCRIPTION; HELA CELL LINE; HUMAN; HUMAN CELL; IN VITRO STUDY; MOLECULAR RECOGNITION; NONHUMAN; NORTHERN BLOTTING; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTOSPACER ADJACENT MOTIF; RNA CLEAVAGE; RNA ISOLATION; RNA SEQUENCE; STREPTOCOCCUS PYOGENES; CHEMISTRY; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CRISPR CAS SYSTEM; ENZYME SPECIFICITY; GENETIC ENGINEERING; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; NUCLEOTIDE MOTIF; PHYSIOLOGY; PROCEDURES;

EUKARYOTA; PROKARYOTA;

BASE SEQUENCE; CELL EXTRACTS; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CRISPR-ASSOCIATED PROTEINS; CRISPR-CAS SYSTEMS; DNA; GENETIC ENGINEERING; GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (PHOSPHORYLATING); HELA CELLS; HUMANS; NUCLEOTIDE MOTIFS; OLIGONUCLEOTIDES; RNA; RNA, GUIDE; RNA, MESSENGER; SUBSTRATE SPECIFICITY;

EID: 84913568580     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature13769     Document Type: Article

References (30)

1. Wiedenheft, B., Sternberg, S. H. &Doudna, J. A. RNA-guided genetic silencing systems in bacteria and archaea. Nature 482, 331-338 (2012).
2. Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709-1712 (2007).
3. Garneau, J. E. et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468, 67-71 (2010).
4. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821 (2012).
5. Gasiunas, G., Barrangou, R., Horvath, P. &Siksnys, V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc. Natl Acad. Sci. USA 109, E2579-E2586 (2012).
6. Mojica, F. J. M., Diez-Villasenor, C., Garcia-Martinez, J. &Almendros, C. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiol 155, 733-740 (2009).
7. Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C. &Doudna, J. A. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507, 62-67 (2014).
8. Mali, P., Esvelt, K. M.&Church, G. M.Cas9 as a versatile tool for engineering biology. Nature Methods 10, 957-963 (2013).
9. Marraffini, L. A. &Sontheimer, E. J. Self versus non-self discrimination during CRISPR RNA-directed immunity. Nature 463, 568-571 (2010).
10. Sashital, D. G., Wiedenheft, B. &Doudna, J. A. Mechanismof foreign DNA selection in a bacterial adaptive immune system. Mol. Cell 46, 606-615 (2012).
11. Pommer, A. J. et al. Mechanism and cleavage specificity of the H-N-H endonuclease colicin E9. J. Mol. Biol. 314, 735-749 (2001).
12. Hsia, K. C. et al. DNAbinding and degradation by the HNH protein ColE7. Structure 12, 205-214 (2004).
13. Nishimasu, H. et al. Crystal structure of Cas9 in complex with guideRNA and target DNA. Cell 156, 935-949 (2014).
14. Wu, H. J., Lima, W. F. &Crooke, S. T. Properties of cloned and expressed human RNase H1. J. Biol. Chem. 274, 28270-28278 (1999).
15. Engreitz, J. M. et al. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 341 (2013).
16. Chu, C., Qu, K., Zhong, F. L., Artandi, S. E. &Chang, H. Y. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol. Cell 44, 667-678 (2011).
17. Simon, M. D. et al. The genomic binding sites of a noncoding RNA. Proc. Natl Acad. Sci. USA 108, 20497-20502 (2011).
18. Mackay, J. P., Font, J. &Segal, D. J. The prospects for designer single-stranded RNA-binding proteins. Nature Struct. Mol. Biol. 18, 256-261 (2011).
19. Filipovska, A. &Rackham, O. Designer RNA-binding proteins: new tools for manipulating the transcriptome. RNA Biol. 8, 978-983 (2011).
20. Wang, Y., Wang, Z. &Tanaka Hall, T. M. Engineered proteins with Pumilio/fem-3 mRNA binding factor scaffold to manipulate RNA metabolism. FEBS J. 280, 3755-3767 (2013).
21. Yin, P. et al. Structural basis for themodular recognition of single-strandedRNA by PPR proteins. Nature 504, 168-171 (2013).
22. Yagi, Y., Nakamura, T. &Small, I. The potential for manipulating RNA with pentatricopeptide repeat proteins. Plant J. 78, 772-782 (2014).
23. Kim, D. H. &Rossi, J. J. RNAi mechanisms and applications. Biotechniques 44, 613-616 (2008).
24. Hale, C. R. et al.RNA-guidedRNA cleavage by a CRISPRRNA-Cas protein complex. Cell 139, 945-956 (2009).
25. Hale, C. R. et al. Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs. Mol. Cell 45, 292-302 (2012).
26. Staals, R. H. J. et al. Structure and activity of the RNA-targeting type III-B CRISPRCas complex of Thermus thermophilus. Mol. Cell 52, 135-145 (2013).
27. Spilman, M. et al. Structure of an RNA silencing complex of the CRISPR-Cas immune system. Mol. Cell 52, 146-152 (2013).
28. Terns, R. M. &Terns, M. P. CRISPR-based technologies: prokaryotic defense weapons repurposed. Trends Genet. 30, 111-118 (2014).
29. Sampson, T. R.,Saroj, S. D., Llewellyn,A. C., Tzeng, Y. L.&Weiss, D. S.A. CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature 497, 254-257 (2013).
30. Sampson, T. R. &Weiss, D. S. Exploiting CRISPR/Cas systems for biotechnology. Bioessays 36, 34-38 (2014).