The immediate impact of exoribonucleolysis on nuclear RNA processing, turnover and transcriptional control revealed by rapid depletion of DIS3, EXOSC10 or XRN2 from human cells

Cell-based studies of human ribonucleases traditionally relies on methods that deplete proteins slowly. To assess their immediate roles in nuclear RNA biology, we engineered cells where the 3’->5’ exoribonucleases of the exosome complex, Dis3 and EXOSC10, can be eliminated within 60 minutes. Loss of Dis3 has the greatest impact, causing thousands of enhancer RNAs, intragenic transcripts, promoter upstream transcripts (PROMPTs) and products of premature cleavage and polyadenylation (PCPA) to accumulate. Interestingly, EXOSC10 only targets these substrates when Dis3 is absent, which is explained by its rapid mis-localization to the nucleoplasm following Dis3 loss. Direct detection of EXOSC10 substrates revealed a more specific role in trimming of short 3’ extensions on ribosomal and small nucleolar RNAs. Finally, the 5’-3’ exoribonuclease, Xrn2, has little activity on exosome substrates, but promotes termination following PCPA. Interestingly, Xrn2 is not rate limiting for PROMPT termination providing a distinction between sense and anti-sense transcriptional regulation.