The NELF pausing checkpoint mediates the functional divergence of Cdk9

Promoter-proximal pausing by RNA Pol II is a key aspect of how gene expression is transcriptionally regulated in higher eukaryotes. Here the authors show that only NELF-mediated pausing enforces a strict early checkpoint for Cdk9 by efficiently shutting down gene transcription following loss of Cdk9. Promoter-proximal pausing by RNA Pol II is a rate-determining step in gene transcription that is hypothesized to be a prominent point at which regulatory factors act. The pausing factor NELF is known to induce and stabilize pausing, but not all kinds of pausing are NELF-mediated. Here, we find that NELF-depleted Drosophila melanogaster cells functionally recapitulate the NELF-independent pausing we previously observed in fission yeast (which lack NELF). Critically, only NELF-mediated pausing establishes a strict requirement for Cdk9 kinase activity for the release of paused Pol II into productive elongation. Upon inhibition of Cdk9, cells with NELF efficiently shutdown gene transcription, while in NELF-depleted cells, defective, non-productive transcription continues unabated. By introducing a strict checkpoint for Cdk9, the evolution of NELF was likely critical to enable increased regulation of Cdk9 in higher eukaryotes, as Cdk9 availability can be restricted to limit gene transcription without inducing wasteful, non-productive transcription.

Automated summary

Promoter-proximal pausing by RNA Pol II is a critical aspect of transcriptional regulation in higher eukaryotes. The study shows that only NELF-mediated pausing enforces a strict early checkpoint for Cdk9, shutting down gene transcription efficiently. NELF-depleted cells in Drosophila melanogaster recapitulate the NELF-independent pausing observed in fission yeast. Importantly, only NELF-mediated pausing requires Cdk9 kinase activity for the release of paused Pol II into productive elongation.