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Release of promoter-proximally paused RNA Pol II into elongation is a tightly regulated and rate-limiting step in metazoan gene transcription. However, the biophysical mechanism underlying pause release remains unclear. Here, we demonstrate that the pausing and elongation regulator SPT5 undergoes phase transition during transcriptional pause release. SPT5 per se is prone to form clusters. The disordered domain in SPT5 is required for pause release and gene activation. During early elongation, the super elongation complex (SEC) induces SPT5 transition into elongation droplets. Depletion of SEC increases SPT5 pausing clusters. Furthermore, disease-associated SEC mutations impair phase properties of elongation droplets and transcription. Our study suggests that SEC-mediated SPT5 phase transition might be essential for pause release and early elongation and that aberrant phase properties could contribute to transcription abnormality in diseases.
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http://dx.doi.org/10.15252/embr.202255699 | DOI Listing |
Mol Cell
September 2025
The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia; Peter MacCallum Cancer Centre, Laboratory Research Division, Parkville, VIC 3052, Australia. Electronic address:
Controlled gene expression is achieved through the intricate regulation of RNA polymerase II (Pol II) progression through transcription-cycle checkpoints. While the contribution of CDK9 for Pol II pause-release is well established, the requirement for other cyclin-dependent kinases (CDKs) has not been fully elucidated. In this study, we propose a critical role for CDK11 in the Pol II pausing-to-elongation transition at a checkpoint that precedes and is independent from CDK9.
View Article and Find Full Text PDFNucleic Acids Res
August 2025
The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL, 33458, United States.
Eradicating HIV-1 is complicated by latently infected CD4+T cells harboring dormant proviruses capable of reactivation. Through a pooled shRNAmir screen targeting human chromatin regulators, we identified EP400, a member of the p400 chromatin remodeling complex, as a potent inhibitor of HIV-1 transcription in Jurkat and primary CD4+T cells. EP400 and its complex partner DMAP1 co-localize with paused RNA Polymerase II (RNAPII) at transcriptional start sites of protein-coding genes and their depletion modestly reduced RNAPII pausing.
View Article and Find Full Text PDFMol Cell
August 2025
University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Department of Human Genetics, 1501 NW 10(th) Avenue, Miami, FL 33136, USA. Electronic address:
The mechanisms by which the expression of pluripotency and Polycomb networks are harmonized to allow the transition from pluripotency to a differentiated state have not been fully elucidated. Integrator complex regulates transcription pause release and RNA processing in metazoans. We show that Integrator is required for stemness and plays a critical role as early as day 2 in embryonic development.
View Article and Find Full Text PDFJ Mol Cell Cardiol
September 2025
School of Biosciences, College of Biomedical and Life Sciences, Cardiff University, Cardiff CF10 3AX, UK. Electronic address:
Background: Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a malignant inherited heart disease characterised by stress-induced arrhythmias that are thought to be caused by delayed afterdepolarizations resulting from abnormal Ca cycling. Some patients exhibit unusually large ECG U-waves that could be associated with altered ventricular repolarization, but the possible link with dysfunctional RyR2 is unclear. We investigated whether increased Ca leak during systole disrupts repolarization in a transgenic mouse model of CPVT.
View Article and Find Full Text PDFNat Genet
August 2025
Institut de Génétique Moléculaire de Montpellier, CNRS-UMR 5535, University of Montpellier, Montpellier, France.
Despite their central role in transcription, it has been difficult to define universal sequences associated with eukaryotic promoters. Within the chromatin context, recruitment of transcriptional machinery requires promoter opening, but how DNA elements contribute to this process is unclear. Here we show that G-quadruplex (G4) secondary DNA structures are highly enriched at mammalian promoters.
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