RNA polymerase II pausing regulates a quiescence-dependent transcriptional program, priming cells for cell cycle reentry

Abstract

Adult stem cells persist in mammalian tissues by entering a state of reversible arrest or quiescence associated with low transcription. Using cultured myoblasts and primary muscle stem cells, we show that RNA synthesis is strongly repressed in G₀, returning within minutes of activation. We investigate the underlying mechanism and reveal a role for promoter-proximal RNAPol II pausing: by mapping global Pol II occupancy using ChIP-seq, in conjunction with RNA-seq to identify repressed transcriptional networks unique to G₀. Strikingly, Pol II pausing is enhanced in G₀ on genes encoding regulators of RNA biogenesis (Ncl, Rps24, Ctdp1), and release of pausing is critical for cell cycle re-entry. Finally, we uncover a novel, unexpected repressive role of the super-elongation complex component Aff4 in G₀-specific stalling. We propose a model wherein Pol II pausing restrains transcription to maintain G₀, preconfigures gene networks required for the G₀-G₁ transition, and sets the timing of their transcriptional activation.