Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs

Mol Cell. 2012 Feb 10;45(3):292-302. doi: 10.1016/j.molcel.2011.10.023. Epub 2012 Jan 5.


Small RNAs target invaders for silencing in the CRISPR-Cas pathways that protect bacteria and archaea from viruses and plasmids. The CRISPR RNAs (crRNAs) contain sequence elements acquired from invaders that guide CRISPR-associated (Cas) proteins back to the complementary invading DNA or RNA. Here, we have analyzed essential features of the crRNAs associated with the Cas RAMP module (Cmr) effector complex, which cleaves targeted RNAs. We show that Cmr crRNAs contain an 8 nucleotide 5' sequence tag (also found on crRNAs associated with other CRISPR-Cas pathways) that is critical for crRNA function and can be used to engineer crRNAs that direct cleavage of novel targets. We also present data that indicate that the Cmr complex cleaves an endogenous complementary RNA in Pyrococcus furiosus, providing direct in vivo evidence of RNA targeting by the CRISPR-Cas system. Our findings indicate that the CRISPR RNA-Cmr protein pathway may be exploited to cleave RNAs of interest.

Publication types

  • Research Support, American Recovery and Reinvestment Act
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Archaeal Proteins / isolation & purification
  • Base Sequence
  • Genetic Engineering
  • Genetic Loci
  • Immunoprecipitation
  • Inverted Repeat Sequences*
  • Macromolecular Substances / isolation & purification
  • Molecular Sequence Data
  • Pyrococcus furiosus / genetics*
  • Pyrococcus furiosus / metabolism
  • RNA Cleavage*
  • RNA, Antisense
  • RNA, Archaeal / isolation & purification*
  • Sequence Analysis, RNA


  • Archaeal Proteins
  • Macromolecular Substances
  • RNA, Antisense
  • RNA, Archaeal