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Polymerase II pausing licenses cell-cycle progression (ChIP-Seq)

ABSTRACT: RNA polymerase II promoter-proximal pausing is orchestrated by a ribonucleoprotein complex scaffolded by the noncoding RNA Rn7sk. However, how this interruption of transcription is mechanistically linked to RNA production remains largely unknown. Here, we show that forcing the pause release by germ-line deletion of Rn7sk was embryonic lethal, yet conditional deletion of Rn7sk enhanced stem cell differentiation in skin. To explore the immediate transcriptional mechanisms underpinning enhanced differentiation, we metabolically labelled newly-synthesized RNAs after Rn7sk deletion. Unexpectedly, forced pause release robustly repressed transcription specifically at cell cycle regulators, in the absence of chromatin remodeling at promoters and enhancers. Our results indicate that polymerase pausing affords the core elongation machinery time to properly assemble, and forced elongation triggers splicing defects and nuclear RNA decay. Cell cycle regulators appear highly sensitive to mis-regulation of the elongation machinery due to unique genomic features of high promoter accessibility and low GC–content in the gene body. Transcriptional pausing thus serves as a rate-limiting step in controlling cell division.

ORGANISM(S): Homo sapiens

PROVIDER: GSE101215 | GEO | 2021/08/12

REPOSITORIES: GEO

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Polymerase II pausing licenses cell-cycle progression (RNA-Seq)

Project description:RNA polymerase II promoter-proximal pausing is orchestrated by a ribonucleoprotein complex scaffolded by the noncoding RNA Rn7sk. However, how this interruption of transcription is mechanistically linked to RNA production remains largely unknown. Here, we show that forcing the pause release by germ-line deletion of Rn7sk was embryonic lethal, yet conditional deletion of Rn7sk enhanced stem cell differentiation in skin. To explore the immediate transcriptional mechanisms underpinning enhanced differentiation, we metabolically labelled newly-synthesized RNAs after Rn7sk deletion. Unexpectedly, forced pause release robustly repressed transcription specifically at cell cycle regulators, in the absence of chromatin remodeling at promoters and enhancers. Our results indicate that polymerase pausing affords the core elongation machinery time to properly assemble, and forced elongation triggers splicing defects and nuclear RNA decay. Cell cycle regulators appear highly sensitive to mis-regulation of the elongation machinery due to unique genomic features of high promoter accessibility and low GC–content in the gene body. Transcriptional pausing thus serves as a rate-limiting step in controlling cell division.

2021-08-12 | GSE101216 | GEO

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

Project description: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.

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