A transcriptionally repressed quiescence program is associated with paused RNAPII and is poised for cell cycle reentry.

Adult stem cells persist in mammalian tissues by entering a state of reversible quiescence/ G0, associated with low transcription. Using cultured myoblasts and muscle stem cells, we report that in G0, global RNA content and synthesis are substantially repressed, correlating with decreased RNA Polymerase II (RNAPII) expression and activation. Integrating RNAPII occupancy and transcriptome profiling, we identify repressed networks and a role for promoter-proximal RNAPII pausing in G0. Strikingly, RNAPII shows enhanced pausing in G0 on repressed genes encoding regulators of RNA biogenesis (Nucleolin, Rps24, Ctdp1); release of pausing is associated with their increased expression in G1. Knockdown of these transcripts in proliferating cells leads to induction of G0 markers, confirming the importance of their repression in establishment of G0. A targeted screen of RNAPII regulators revealed that knockdown of Aff4 (positive regulator of elongation) unexpectedly enhances expression of G0-stalled genes and hastens S phase; NELF, a regulator of pausing appears to be dispensable. We propose that RNAPII pausing contributes to transcriptional control of a subset of G0-repressed genes to maintain quiescence and impacts the timing of the G0-G1 transition.