BiologyTechnion

@biologytechnion.bsky.social

Faculty of Biology @ Technion https://biology.technion.ac.il/en/

🧵New preprint! How does an elongating RNA polymerase deal with a DNA-bound transcription factor in its path? We developed a label-free single-molecule assay that detects RNAP arrival by suppression of fluctuations in a partially unzipped DNA fork. biorxiv.org/cgi/content/... 1/

Tunable kinetic destabilization governs RNA polymerase passage through a DNA-bound transcription factor

Eukaryotic transcription factors recognize short motifs, creating abundant binding sites within gene bodies and potential collisions with elongating RNA polymerases, yet how such encounters are resolved remains unclear. Here, we use optical tweezers to monitor RNA polymerase transcription through DNA-bound Egr-1, a zinc-finger transcription factor. Using DNA-fluctuation suppression as a readout of polymerase arrival, we show that Egr-1 delays elongation in an orientation- and rNTP-dependent manner, whereas force measurements indicate that RNAP does not bypass the TF by mechanical eviction. Instead, RNAP destabilizes the Egr-1-DNA complex over a short, structured interaction zone, increasing TF dissociation non-monotonically with distance. Monte Carlo simulations incorporating these kinetic changes recapitulate passage-time distributions. CpG methylation shortens Egr-1 residence time and largely eliminates the TF-dependent delay, suggesting a role for gene-body methylation in reducing kinetic barriers to elongation. These results reveal DNA-bound TFs as tunable barriers that locally shape transcription elongation. ### Competing Interest Statement The authors have declared no competing interest. Israel Science Foundation, https://ror.org/04sazxf24

biorxiv.org

Congratulations to our faculty members on receiving prestigious research grants from the Israel Science Foundation (ISF). Personal Research Grants : Dan Zilberstein, Sagi Levy, Ayala Shiber Breakthrough Research Grants (BRG): Oded Beja, Debbie Lindell, Roy Kishony

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