Howard, B. C. | Search bioRxiv

bioRxiv2025

BRD2 bridges TFIID and histone acetylation to promote transcriptional initiation

Members of the bromodomain and extraterminal domain (BET) protein family play a central role in transcription by RNA Polymerase II (Pol II). Small-molecule inhibitors that block interaction between BET bromodomains and acetylated histones have been developed to achieve therapeutic benefit. However, the BET protein BRD4 does not require bromodomains to perform its major transcriptional elongation function, and the mechanisms by which other BET proteins regulate transcription remain incompletely understood. Addressing the disparity between pan-BET degraders and BRD4-specific depletion, we report that the BET protein BRD2 generally functions to promote transcriptional initiation in a bromodomain-dependent manner at both promoters and enhancers in human cells. We demonstrate that BRD2 bromodomains preferentially bind to tetra-acetylated histones harboring MOF-mediated H4K16ac, while the BRD2 C terminal domain facilitates recruitment of TFIID. Our studies provide mechanistic insight into the distinct roles of BRD2 in transcriptional initiation through the recruitment of TFIID and BRD4 in transcriptional elongation through the recruitment of CDK9 and controlling proper regulation of gene expression.

biochemistry↗

bioRxiv2025

Transcriptional Elongation-Associated RNA Processing Errors in Induced Cellular Growth Arrest

Summary ParagraphTranscription elongation factors control post-initiation steps of gene expression by RNA polymerase II (RNAPII). We have established distinct mechanistic roles for the essential elongation factors PAF1, NELF, SPT5, SPT6, and the Super Elongaiton Complex (SEC) via acute depletion of each individually in auxin-inducible degron lines. Here, we leverage these degron lines to explore the regulatory intersection of transcription elongation control and pre-mRNA processing. Integrating long- and short-read RNA-seq data to quantify transcript isoform usage at single-molecule resolution, we identify elongation factor-specific RNA processing regulons including a cellular senescence-enriched regulon shared by NELF and SPT6. We then show that long-term depletion of NELF or SPT6 results in reversible growth arrest following early upregulation of a small group of genes, which include the senescence-associated genes CDKN1A (p21) and CCN2. We perform genetic suppressor screens that implicate the elongation factor Elongin A (ELOA) in NELF or SPT6 depletion-induced growth arrest. ELOA loss suppresses NELF depletion-induced pre-mRNA processing defects and the 3 extension of RNAPII occupancy past transcription end sites (TES) at genes induced by NELF depletion. ELOA also occupies TES-proximal regions under normal conditions, and acute ELOA depletion results in a loss of RNAPII processivity at the 3 end of genes, opposing the effects of NELF or SPT6 depletion. Finally, we demonstrate that genetic loss of ELOA confers a growth advantage to aging human primary dermal fibroblasts. These findings establish the existence of novel ELOA-dependent mechanisms regulating transcription maturation, and links these mechanisms to the complex phenomena of cellular senescence and aging.

molecular biology↗