Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors

Class 2 CRISPR-Cas systems endow microbes with diverse mechanisms for adaptive immunity. Here, we analyzed prokaryotic genome and metagenome sequences to identify an uncharacterized family of RNA-guided, RNA-targeting CRISPR systems that we classify as type VI-D. Biochemical characterization and protein engineering of seven distinct orthologs generated a ribonuclease effector derived from Ruminococcus flavefaciens XPD3002 (CasRx) with robust activity in human cells. CasRx-mediated knockdown exhibits high efficiency and specificity relative to RNA interference across diverse endogenous transcripts. As one of the most compact single-effector Cas enzymes, CasRx can also be flexibly packaged into adeno-associated virus. We target virally encoded, catalytically inactive CasRx to cis elements of pre-mRNA to manipulate alternative splicing, alleviating dysregulated tau isoform ratios in a neuronal model of frontotemporal dementia. Our results present CasRx as a programmable RNA-binding module for efficient targeting of cellular RNA, enabling a general platform for transcriptome engineering and future therapeutic development. [Display omitted] •Computational pipeline identifies the RNA-targeting type VI-D CRISPR-Cas family•Ortholog screen and protein engineering yields the programmable ribonuclease CasRx•CasRx RNA knockdown exhibits favorable efficiency and specificity relative to RNAi•Neuronal AAV delivery of dCasRx splice effectors alleviates tau mis-splicing A new family of RNA-targeting CRISPR-Cas systems allows specific modulation of splicing events to reduce pathological tau isoforms in a neuronal model of frontotemporal dementia.