Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control

Cell-based studies of human ribonucleases traditionally rely on methods that deplete proteins slowly. We engineered cells in which the 3′→5′ exoribonucleases of the exosome complex, DIS3 and EXOSC10, can be rapidly eliminated to assess their immediate roles in nuclear RNA biology. The loss of DIS3 has the greatest impact, causing the substantial accumulation of thousands of transcripts within 60 min. These transcripts include enhancer RNAs, promoter upstream transcripts (PROMPTs), and products of premature cleavage and polyadenylation (PCPA). These transcripts are unaffected by the rapid loss of EXOSC10, suggesting that they are rarely targeted to it. More direct detection of EXOSC10-bound transcripts revealed its substrates to prominently include short 3′ extended ribosomal and small nucleolar RNAs. Finally, the 5′→3′ exoribonuclease, XRN2, has little activity on exosome substrates, but its elimination uncovers different mechanisms for the early termination of transcription from protein-coding gene promoters. [Display omitted] •Engineered human cells for rapid inducible degradation of EXOSC10 and DIS3•DIS3 degrades the majority of nuclear exosome substrates•Direct targets of EXOSC10 include ribosomal and small nucleolar RNAs•XRN2 has little activity on exosome substrates Using a system allowing very rapid protein depletion, Davidson et al. characterize the acute targets of the nuclear RNA degradation machinery in human cells. The thousands of substrates uncovered reveal wide ranging and immediate roles for exoribonucleases in non-coding RNA degradation, RNA processing, and early transcriptional termination.