RNA degradation by DIS3 is a necessary step in the resolution of backtracked transcription complexes

The contribution of the ribonuclease activities of the RNA exosome to transcription has remained unclear. We have investigated the role of DIS3, one of the catalytic subunits of the RNA exosome, in transcription by RNA polymerase II (RNAPII). Rapid depletion of DIS3 reduces RNA synthesis and induces RNAPII elongation defects that are exacerbated by UV irradiation, a treatment that generates transcription-blocking DNA lesions and promotes RNAPII backtracking. DIS3 itself redistributes following UV irradiation, mirroring RNAPII dynamics, which suggests that DIS3 acts in concert with the transcription machinery. We show that the 3'-5' exoribonucleolytic activity of DIS3, but not its endonucleolytic activity, is essential for efficient transcription elongation. More specifically, DIS3 degrades the 3' ends of backtracked RNA, as shown by sequencing of RNA fragments released by TFIIS-induced transcript cleavage in vitro. This DIS3-dependent degradation of backtracked RNA is critical for resolving stalled RNAPII complexes and enabling productive transcription elongation.