Abstract: Provided herein is a programmable RNA-activated DNA endonuclease activity associated with a Cmr complex. In one embodiment, the enzyme is a general double-stranded DNA endonuclease. Also provided is a programmable RNA endonuclease activity associated with a Cmr complex. In one embodiment, a Cmr2 protein present in a Cmr complex includes a mutation that reduces RNA-activated DNAse activity of the Cmr complex. In one embodiment, a Cmr4 protein present in a Cmr complex includes a mutation that reduces the RNase activity of the Cmr complex. Compositions including components of a Cmr complex and a CRISPR-RNA, and an optional activating RNA, are provided. Also provided are methods for using the compositions, and genetically engineered cells that include components of a Cmr complex and a CRISPR-RNA, and an optional activating RNA.

Abstract: Provided herein is a programmable RNA-activated DNA endonuclease activity associated with a Cmr complex. In one embodiment, the enzyme is a general double-stranded DNA endonuclease. Also provided is a programmable RNA endonuclease activity associated with a Cmr complex. In one embodiment, a Cmr2 protein present in a Cmr complex includes a mutation that reduces RNA-activated DNAse activity of the Cmr complex. In one embodiment, a Cmr4 protein present in a Cmr complex includes a mutation that reduces the RNase activity of the Cmr complex. Compositions including components of a Cmr complex and a CRIS-PR-RNA, and an optional activating RNA, are provided. Also provided are methods for using the compositions, and genetically engineered cells that include components of a Cmr complex and a CRISPR-RNA, and an optional activating RNA.

Abstract: Provided herein are proteins having A-specific RNase activity. A protein having A-specific RNAse activity is referred to herein as a Csx1 protein. A Csx1 protein is an endoribonuclease, and has the activity of cleaving the phosphodiester bond in a single strand of a target RNA molecule on the 3? (downstream) side of an adenosine base to result in a first cleavage product having a 5? hydroxyl group and a second cleavage product having a 2?,3?-cyclic phosphate at the 3? end. Also provided herein are methods for using a Csx1 protein. In one embodiment, the method includes incubating a sample that includes an isolated Csx1 protein and a target RNA molecule under suitable conditions for cleavage of the target RNA molecule. Also provided is a genetically modified microbe that includes an exogenous polynucleotide including a nucleotide sequence encoding a Csx1 protein, and a method for making Cxsl protein.

Abstract: Provided herein are methods for inactivating a target polynucleotide. The methods use a psiRNA having a 5? region and a 3? region. The 5? region includes, but is not limited to, 5 to 10 nucleotides chosen from a repeat from a CRISPR locus immediately upstream of a spacer. The 3? region is substantially complementary to a portion of the target polynucleotide. The methods may be practiced in a prokaryotic microbe or in vitro. Also provided are polypeptides that have endonuclease activity in the presence of a psiRNA and a target polynucleotide, and methods for using the polypeptides.

Abstract: Provided herein are methods for inactivating a target polynucleotide. The methods use a psiRNA having a 5? region and a 3? region. The 5? region includes, but is not limited to, 5 to 10 nucleotides chosen from a repeat from a CRISPR locus immediately upstream of a spacer. The 3? region is substantially complementary to a portion of the target polynucleotide. The methods may be practiced in a prokaryotic microbe or in vitro. Also provided are polypeptides that have endonuclease activity in the presence of a psiRNA and a target polynucleotide, and methods for using the polypeptides.

Abstract: Provided herein are methods for cleaving a target RNA polynucleotide. The target RNA polynucleotide includes a Cas6 recognition domain and a cleavage site, and may be based on a repeat from a CRISPR locus. The methods may be practiced in vivo or in vitro. Also provided are polypeptides that have Cas6 endoribonuclease activity in the presence of a target RNA polynucleotide, and methods for using the polypeptides.

Abstract: Provided herein are methods for inactivating a target polynucleotide. The methods use a psiRNA having a 5? region and a 3? region. The 5? region includes, but is not limited to, 5 to 10 nucleotides chosen from a repeat from a CRISPR locus immediately upstream of a spacer. The 3? region is substantially complementary to a portion of the target polynucleotide. The methods may be practiced in a prokaryotic microbe or in vitro. Also provided are polypeptides that have endonuclease activity in the presence of a psiRNA and a target polynucleotide, and methods for using the polypeptides.

Abstract: Provided herein are methods for cleaving a target RNA polynucleotide. The target RNA polynucleotide includes a Cas6 recognition domain and a cleavage site, and may be based on a repeat from a CRISPR locus. The methods may be practiced in vivo or in vitro. Also provided are polypeptides that have Cas6 endoribonuclease activity in the presence of a target RNA polynucleotide, and methods for using the polypeptides.