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bioRxiv · 10.64898/2026.04.06.716678

Structural principles of transcriptional collisions

Watters, J. W.·Mueller, A. U.·Ju, X.·Chuquimarca, S. J.·Ye, H. J.·Darst, S. A.·Alushin, G. M.·Liu, S.
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Abstract

RNA polymerase (RNAP) must navigate crowded genomic tracks to robustly produce transcripts. DNA-bound proteins act as transcription-impeding roadblocks, which are eventually overcome by RNAPs through unclear mechanisms. Here, we use cryo-electron microscopy to visualize actively transcribing E. coli RNAP upon collision with an inactivated restriction enzyme (EcoRI*) or with another converging RNAP. Both collisions induce RNAP backtracking into an inactive swiveled state. Swiveling is coupled to DNA deformation through a characteristic structural landscape, mediating RNAP pause stabilization across distinct collision geometries. EcoRI* roadblock bypass efficiency is impacted by factors that modulate RNAP swiveling, backtracking rescue, and roadblock stability. In comparison, head-on RNAP-RNAP collisions feature substantial heterogeneity suggestive of sustained dynamics, with variable inter-RNAP distances that are modulated by nascent transcript hairpins which position bidirectional termination sites. By resolving, to our knowledge, novel structures of actively transcribing RNAP undergoing collisions, we provide a mechanistic framework for interpreting mechanical conflicts during transcription.

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Watters, J. W., Mueller, A. U., Ju, X., Chuquimarca, S. J., Ye, H. J., Darst, S. A., Alushin, G. M., Liu, S.. 2026-04-06. Structural principles of transcriptional collisions. https://doi.org/10.64898/2026.04.06.716678

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