Genome-wide detection and quantitation of RNA distribution by ChIRC13a-seq

Abstract Eukaryotic genome are transcribed extensively, but a majority of transcripts remain functionally uncharacterized. This is most ascribed to lacking of a potent RNA-centric technology that is capable of accurately quantitating putative genomic binding sites for endogenous RNAs. We describe here a detailed protocol for Chromatin Isolation by RNA-Cas13a Complex sequencing (ChIRC13a-seq), based on recently discovered CRISPR-Cas13a from Leptotrichia wadei (LwaCas13a), for profiling of RNA associated chromatin binding cites. ChIRC13a-seq employs biotinylated, enzymatically-dead Cas13a (dCas13a) that is still capable of binding target RNA and guide RNAs (gRNAs) specific for the RNA target of interest to enrich RNA and its chromatin binding sites. This assay can be performed in standard molecular biology laboratories with 2 d taken for ChIRC13a-seq library preparation.