Exploring collateral RNA cleavage by LbuCas13a in human cells using nanopore cDNA sequencing

LbuCas13a exhibits widespread collateral RNA cleavage in human cells after activation by a specific target RNA. We wanted to know which transcripts get cleaved, and where they get cleaved. Therefore we performed nanopore cDNA sequencing. We isolated RNA at different timepoints after transduction of HAP1-dEGFP cells with LbuCas13a protein and either a dEGFP or a non-targeting guide RNA. These data reveal widespread unbiased collateral cleavage of cytoplasmic transcripts. Furthermore, putative cleavage sites occur in very specific position, often in U containing loops of predicted stem loop structures.