@article{04430ed9635945a2b594c54fe5851a6c,
title = "Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II",
abstract = "Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous to capture pol II in the initiating state. Here, we report multiple structures of initiation complexes converted de novo from a 33-subunit yeast pre-initiation complex (PIC) through catalytic activities and subsequently stalled at different template positions. We determine that PICs in the initially transcribing complex (ITC) can synthesize a transcript of ∼26 nucleotides before transitioning to an elongation complex (EC) as determined by the loss of general transcription factors (GTFs). Unexpectedly, transition to an EC was greatly accelerated when an ITC encountered a downstream EC stalled at promoter proximal regions and resulted in a collided head-to-end dimeric EC complex. Our structural analysis reveals a dynamic state of TFIIH, the largest of GTFs, in PIC/ITC with distinct functional consequences at multiple steps on the pathway to elongation.",
keywords = "RNA polymerase II, TFIIH, elongation complex, initially transcribing complex, pre-initiation complex, promoter escape, promoter opening, start-site scanning, transcription initiation, yeast",
author = "Chun Yang and Rina Fujiwara and Kim, {Hee Jong} and Pratik Basnet and Yunye Zhu and {Gorbea Col{\'o}n}, {Jose J.} and Stefan Steimle and Garcia, {Benjamin A.} and Kaplan, {Craig D.} and Kenji Murakami",
note = "Funding Information: We thank Dr. Sudheer Molugu for assistance with cryo-EM sample screening. We thank UMass cryo-EM Facility, Drs. Chen Xu, KangKang Song, and Kyounghwan Lee for their assistance in data collection of G-less 26 complexes. We thank NCI National Cryo-EM Facility, Drs. Thomas Edwards, Adam Wier under contract HSSN261200800001 for data collection of the G-less 49 complex (EC+EC). We thank Drs. Janette Myers, Nancy Meyer, and Harry Scott at PNCC for cryo-EM screening and data collection of G-less 49 complexes (EC+ITC). We thank members in the lab and Dr. Peter Geiduschek for helpful discussions. Funding: A portion of this research was supported by NIH grant U24GM129547 and performed at the PNCC at OHSU and accessed through EMSL (grid.436923.9), a DOE Office of Science User Facility sponsored by the Office of Biological and Environmental Research. This research was supported by NIH R01-GM123233 to K.M. NIH grants CA196539 and AG031862 to B.A.G. NIH R01-GM120450 to C.D.K. computational resources were supported by NIH project grant S10OD023592. C.Y. and R.F. conducted the experiments, C.Y. R.F. and H.J.K. performed cryo-EM image analysis, C.Y. R.F. S.S. J.J.G. H.J.K. and K.M. conducted model building, P.B. Y.Z. and C.D.K. performed genetic analyzes. C.Y. R.F. B.A.G. and K.M. prepared figures, designed the study, and wrote the manuscript. C.D.K. edited the manuscript. The authors declare no competing interests. Funding Information: Funding: A portion of this research was supported by NIH grant U24GM129547 and performed at the PNCC at OHSU and accessed through EMSL (grid.436923.9), a DOE Office of Science User Facility sponsored by the Office of Biological and Environmental Research. This research was supported by NIH R01-GM123233 to K.M., NIH grants CA196539 and AG031862 to B.A.G., NIH R01-GM120450 to C.D.K. computational resources were supported by NIH project grant S10OD023592 . Publisher Copyright: {\textcopyright} 2021",
year = "2022",
month = feb,
day = "3",
doi = "10.1016/j.molcel.2021.12.020",
language = "English",
volume = "82",
pages = "660--676.e9",
journal = "Molecular cell",
issn = "1097-2765",
number = "3",
}