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The clustered regularly interspaced short palindromic repeat (CRISPR)–CRISPR-associated genes (Cas) adaptive immune system defends microbes against foreign genetic elements via DNA or RNA-DNA interference. We characterize the class 2 type VI CRISPR-Cas effector C2c2 and demonstrate its RNA-guided ribonuclease function. C2c2 from the bacterium Leptotrichia shahii provides interference against RNA phage. In vitro biochemical analysis shows that C2c2 is guided by a single CRISPR RNA and can be programmed to cleave single-stranded RNA targets carrying complementary protospacers. In bacteria, C2c2 can be programmed to knock down specific mRNAs. Cleavage is mediated by catalytic residues in the two conserved Higher Eukaryotes and Prokaryotes Nucleotide-binding (HEPN) domains, mutations of which generate catalytically inactive RNA-binding proteins. These results broaden our understanding of CRISPR-Cas systems and suggest that C2c2 can be used to develop new RNA-targeting tools.United States. Dept. of Energy (Computational Science Graduate Fellowship)Massachusetts Institute of Technology. Simons Center for the Social BrainNational Institute of General Medical Sciences (U.S.) (Award T32GM007753)National Institutes of Health (U.S.) (National Institute of Mental Health (U.S.) Grants 5DP1-MH100706 and 1R01-MH110049)National Science Foundation (U.S.)New York Stem Cell FoundationSimons FoundationPaul G. Allen Family FoundationVallee FoundationPoitras FoundationRobert MetcalfeDavid R. Chen

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector