Abstract: RNA editing tools for use in systems designed to measure RNA in vivo and manipulate specific cell types are disclosed herein. An RNA sensor system comprising a) a single-stranded RNA (ssRNA) sensor comprising a stop codon and a payload; optionally wherein the ssRNA sensor further comprises a normalizing gene; and b) an adenosine deaminase acting on RNA (ADAR) deaminase; wherein the sensor is capable of binding to a ssRNA target to form a double-stranded RNA (dsRNA) duplex that becomes a substrate for the ADAR deaminase; wherein the substrate comprises a mispairing within the stop codon; and wherein the mispairing is editable by the ADAR deaminase, which editing can effectively remove the stop codon so as to enable translation and expression of the payload. A method of quantifying ribonucleic acid (RNA) levels using the RNA sensor system is also disclosed.

Abstract: RNA editing tools for use in systems designed to measure RNA in vivo and manipulate specific cell types are disclosed herein. An RNA sensor system comprising a) a single-stranded RNA (ssRNA) sensor comprising a stop codon and a payload; optionally wherein the ssRNA sensor further comprises a normalizing gene; and b) an adenosine deaminase acting on RNA (ADAR) deaminase; wherein the sensor is capable of binding to a ssRNA target to form a double-stranded RNA (dsRNA) duplex that becomes a substrate for the ADAR deaminase; wherein the substrate comprises a mispairing within the stop codon; and wherein the mispairing is editable by the ADAR deaminase, which editing can effectively remove the stop codon so as to enable translation and expression of the payload. A method of quantifying ribonucleic acid (RNA) levels using the RNA sensor system is also disclosed.

Abstract: This disclosure provides systems, methods, and compositions comprising miniature CRISPR. nucleases for gene editing and programmable gene activation and inhibition. The miniature CRISPR nuclease is a target specific nuclease having a compact structure with a small number of amino acids. The target specific nuclease targets DNA and is directed to a target nucleic acid sequence from the DNA by a guide RNA. In some embodiments, the target specific nuclease exhibits DNA cleavage activity and is directed by a gRNA to a target nucleic acid sequence from a DNA. In some embodiments, the target specific nuclease does not exhibit DNA cleavage activity and is directed by a gRNA to a target nucleic acid sequence from a DNA.

Abstract: The invention relates to compositions and methods for targeting polynucleotides with eukaryotic RNA-guided nucleases. In particular, programmable RNA-guided DNA endonucleases termed Fanzors, can be harnessed for genome editing.

Abstract: Disclosed are methods of RNA-triggered protein cleavage by the CRISPR Cas7-11-Csx29 complex. A guide RNA specifically hybridizes to a RNA target, and Csx29 cleaves Csx30 when Cas7-11:Csx29 complex binds to the target RNA.

Abstract: Disclosed are methods of RNA-triggered protein cleavage by the CRISPR Cas7-11-Csx29 complex. A guide RNA specifically hybridizes to a RNA target, and Csx29 cleaves Csx30 when Cas7-11:Csx29 complex binds to the target RNA.

Abstract: Provided herein are compositions comprising, inter alia, a ttRNAs comprising (i) a primer binding site, (ii) a reverse transcriptase template sequence, (iii) an aptamer, and (iv) an integration sequence comprising an integration site. Also described herein are method of use of the ttRNAs in methods of editing and integrating polynucleotide sequences.

Abstract: This disclosure provides complexes for prime editing comprising an RNA-guided nuclease, a fusion protein comprising a reverse transcriptase domain linked to a nucleic acid binding protein, and a guide RNA (gRNA) comprising at least one protein-recruiting stem-loop nucleic acid sequence, wherein the protein-recruiting stem-loop nucleic acid sequence binds to the nucleic acid binding protein. Also provided are systems, methods, and compositions for site-specific genetic engineering using Programmable Addition via Site-Specific Targeting Elements (PASTE) with integration enzymes paired with the prime editing complex.

Abstract: RNA editing tools for use in systems designed to measure RNA in vivo and manipulate specific cell types are disclosed herein. An RNA sensor system comprising a) a single-stranded RNA (ssRNA) sensor comprising a stop codon and a payload; optionally wherein the ssRNA sensor further comprises a normalizing gene; and b) an adenosine deaminase acting on RNA (ADAR) deaminase; wherein the sensor is capable of binding to a ssRNA target to form a double-stranded RNA (dsRNA) duplex that becomes a substrate for the ADAR deaminase; wherein the substrate comprises a mispairing within the stop codon; and wherein the mispairing is editable by the ADAR deaminase, which editing can effectively remove the stop codon so as to enable translation and expression of the payload. A method of quantifying ribonucleic acid (RNA) levels using the RNA sensor system is also disclosed.