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Updated: May 11, 2026

Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events
Published on: May 13, 2019
Apical localization of RNA polymerases modulates transcription dynamics and supercoiling domains revealed by cryo-ET
Meng Zhang1, Cristhian Cañari-Chumpitaz2, Jianfang Liu3
1California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA; The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
Abstract:
Protein interactions with canonical B-form DNA are well characterized, yet the effect of torsionally constrained DNA on these interactions-ubiquitous in cells-remains underexplored. Using cryo-electron tomography (cryo-ET), we 3D-reconstructed entire negatively supercoiled DNA substrates bound to active RNA polymerase (RNAP), revealing diverse DNA supercoiling conformations and their interplay with transcription. RNAP preferentially localizes at plectoneme apices in a swiveled, pause-prone state. RNAP, along with other DNA-melting proteins such as dCas9, can act as torsional roadblocks that segregate "twin-supercoiling domains" during active transcription, independent of external DNA/RNAP tethering. Co-transcribing RNAPs further intensify this domain separation: tandem-oriented RNAPs relieve negative supercoiling more effectively than opposing ones and promote greater RNAP accumulation and enhanced elongation, both in vitro and in vivo. Topoisomerase I relieves torsional stress and facilitates RNAP escape from apical stalls, thereby supporting apical transcription regulation. Together, these findings support a load-and-release mechanism at plectoneme apices that may underlie supercoiling-dependent transcriptional bursting.
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