Paused RNA polymerase primes promoters via RNA-mediated stabilisation of transcription factor ERα

Rajat Mann, Deepanshu Soota, Ayan Das, Nitesh Kumar Podh, Gunjan Mehta and Dimple Notani ()
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Rajat Mann: Tata Institute of Fundamental Research
Deepanshu Soota: Tata Institute of Fundamental Research
Ayan Das: Indian Institute of Technology Hyderabad
Nitesh Kumar Podh: Indian Institute of Technology Hyderabad
Gunjan Mehta: Indian Institute of Technology Hyderabad
Dimple Notani: Tata Institute of Fundamental Research

Nature Communications, 2025, vol. 16, issue 1, 1-12

Abstract: Abstract Regulated pausing of RNA polymerase II (Pol II) is essential for enabling rapid and coordinated transcriptional responses to signalling cues. Pausing also contributes to the formation of nucleosome-free regions with the help of chromatin remodellers. However, if these nucleosome-free regions engage with transcription factors to stimulate the transcription potential of paused promoters is not known. In this study, we demonstrate that ligand-induced estrogen receptor-alpha (ERα) binding is stabilized at Pol II-paused sites. This stabilization results from an increased dwell time of ERα on chromatin, as revealed by single molecule tracking (SMT) experiments. Notably, short chromatin-associated RNAs generated by the paused Pol II contribute to enhancing ERα binding at paused promoters. We also observe that pausing increases H3K27ac levels, which primes paused promoters for robust transcriptional activation upon release. Collectively, these findings suggest that paused Pol II plays a central role in enhancing transcription factor binding through an RNA-dependent mechanism. This, in turn, results in a more vigorous transcriptional response following pausing release, thus contributing to the fine-tuning of ERα-mediated gene regulation.

Date: 2025
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DOI: 10.1038/s41467-025-64569-7

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