Cell Reports
Volume 26, Issue 10, 5 March 2019, Pages 2779-2791.e5
Journal home page for Cell Reports

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

https://doi.org/10.1016/j.celrep.2019.02.012Get rights and content
Under a Creative Commons license
open access

Highlights

  • 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

Summary

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.

Keywords

exosome
EXOSC10/Rrp6
DIS3
transcription
XRN2
non-coding RNA
degradation

Cited by (0)

3

Present address: Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle, Bldg. 1130, 8000 Aarhus, Denmark

4

Present address: Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK

5

These authors contributed equally

6

Lead Contact