Fast ribozyme cleavage releases transcripts from RNA polymerase II and aborts co-transcriptional pre-mRNA processing

We investigated whether a continuous transcript is necessary for co-transcriptional pre-mRNA processing. Cutting an intron with the fast-cleaving hepatitis δ ribozyme, but not the slower hammerhead, inhibited splicing. Exon tethering to RNA pol II therefore cannot rescue splicing of a transcript severed by a ribozyme that cleaves rapidly relative to splicing. Ribozyme cutting also released cap-binding complex (CBC) from the gene, suggesting that exon 1 is not tethered. Unexpectedly, cutting within exons inhibits splicing of distal introns where exon definition is not affected, probably due to disruption of interactions with CBC and the pol II CTD that facilitate splicing. Ribozyme cutting within the mRNA also inhibited 3’ processing and transcription termination. We propose that damaging the nascent transcript aborts pre-mRNA processing and this mechanism may help prevent association of processing factors with pol II that is not productively engaged in transcription.