7SK-controlled RNA polymerase II pausing orchestrates gene transcription with splicing

RNA polymerase (Pol) II promoter-proximal pausing is a common regulatory step to initiate RNA synthesis and it is coordinated by a ribonucleoprotein complex scaffolded containing the noncoding RNA Rn7sk. However, how this transcriptional mechanism modulates gene expression programs in adult tissues is largely unknown. Here, we released paused RNA Pol II by depleting Rn7sk during mouse and human epidermal stem cell differentiation. Unexpectedly, the forced release of transcription robustly repressed RNA levels including numerous cell cycle regulators leading to cell cycle exit and differentiation. The repression of genes occurred in the absence of chromatin remodelling at promoters and enhancers. Instead, it was caused by splicing defects and co-transcriptional RNA degradation. However, rather than acting globally, Rn7sk modulated transcription gene-specifically. Genes that required Rn7sk for efficient transcription contained highly accessible promoters, lower guanosine and cytosine (GC) content, shorter introns, and weaker 3' splice sites. In the absence of a tightly controlled Pol II pause release complex, these intrinsic gene properties cumulated in impaired splicing leading to RNA decay. Thus, 7SK-regulated transcriptional pausing is an essential step to coordinate transcription with splicing to permit productive transcription of a distinct set of genes. Overall design: Total and 4SU RNA-Seq of wild type and Rn7sk-/- human keratinocytes; with or without Pladienolide B treatment (1h, 4h, no); 4 replicates per condition.