The phosphatase PP1 sustains global transcription by promoting RNA polymerase II pause release [TT-seq]

RNA polymerase II progression from initiation to elongation is driven in part by a cascade of protein kinases acting on the core transcription machinery. Conversely, the corresponding phosphatases, notably PP2A and PP1—the most abundant serine-threonine phosphatases in cells—are thought to mainly impede polymerase progression, respectively restraining pause release at promoters and polymerase elongation at terminators. Here we reveal an unexpected role of PP1, within the PNUTS-PP1 complex, in sustaining global transcriptional activation. Acute disruption of PNUTS-PP1 leads to severe defects in the release of paused polymerase and subsequent downregulation for the majority of transcribed genes. Mechanistically, PNUTS-PP1 promotes pause release by dephosphorylating multiple substrates, including the 7SK snRNP subunit MEPCE, a known regulator of pause release. PNUTS-PP1 exhibits antagonistic functions compared to INTAC phosphatase, which generally inhibits pause release. Our research thus highlights the opposing roles of PP1 and PP2A in modulating genome-wide transcriptional pausing and gene expression. Overall design: We performed calibrated ChIP-seq, PRO-seq, TT-seq, or RNA-seq to investigate the role of protein phosphotase PNUTS-PP1 in regulating transcription. ChIP-seq, PRO-seq, TT-seq, or RNA-seq were normalizated by MEF as spike-in. The reads passed the quality check were aligned to the human hg19 and mouse mm10 genome. In this study, samples for each condition were collected in biological duplicates. Cells were treated with dTAG13 for 3,12h, the corresponding control cells were treated with vehicle only (DMSO) at the same vol/vol dilution.