Cytoplasmic mRNA levels are regulated by a combination of chromatin retention and RNA stability

Abstract

Transcription and co-transcriptional processes, including pre-mRNA splicing and mRNA cleavage and polyadenylation, regulate the production of a mature mRNA. The carboxyl terminal domain (CTD) of RNA polymerase (pol) II, which comprises 52 repeats of the Tyr1Ser2Pro3Thr4Ser5Pro6Ser7 peptide, is involved in the coordination of transcription with co-transcriptional processes. The pol II CTD is dynamically modified by protein phosphorylation, which regulates recruitment of transcription and co-transcriptional factors. We have investigated whether cytoplasmic levels of mature mRNA from intron-containing protein-coding genes can be inferred from RNA processing efficiency, CTD phosphorylation, and/or association of proteins complexes regulating RNA production. Surprisingly, we found that genes associated with efficient RNA processing have relatively low phosphorylation of the pol II CTD. In contrast, protein-coding genes that produce a low level of mature mRNA are associated with high pol II CTD phosphorylation, poor RNA processing, and increased chromatin retention. Unexpectedly, the transcripts from this subset of genes are not actively degraded by the RNA exosome. RNA exosome-regulated genes are instead characterised by Tyr1 hyperphosphorylation and Integrator recruitment around the poly(A) site. Our results indicate that in addition to the transcription level, CTD phosphorylation and RNA processing efficiency play important roles in the regulation of chromatin retention of transcripts.