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Structural visualization of de novo initiation of RNA polymerase II transcription

View ORCID ProfileChun Yang, View ORCID ProfileRina Fujiwara, View ORCID ProfileHee Jong Kim, View ORCID ProfileJose J. Gorbea Colón, View ORCID ProfileStefan Steimle, View ORCID ProfileBenjamin A. Garcia, View ORCID ProfileKenji Murakami
doi: https://doi.org/10.1101/2021.05.03.442346
Chun Yang
1Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, U.S.A.
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Rina Fujiwara
1Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, U.S.A.
2Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Hee Jong Kim
1Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, U.S.A.
2Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
3Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Jose J. Gorbea Colón
1Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, U.S.A.
2Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Stefan Steimle
1Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, U.S.A.
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Benjamin A. Garcia
1Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, U.S.A.
3Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Kenji Murakami
1Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, U.S.A.
4Penn Center for Genome Integrity, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, U.S.A.
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  • For correspondence: kenjim@pennmedicine.upenn.edu
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Summary

Structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription were previously facilitated by the use of synthetic oligonucleotides. Here we report structures of initiation complexes de novo converted from pre-initiation complex (PIC) through catalytic activities and stalled at different template positions. Contrary to previous models, the closed-to-open promoter transition was accompanied by a large positional change of the general transcription factor TFIIH which became in closer proximity to TFIIE for the active delivery of the downstream DNA to the pol II active center. The initially-transcribing complex (ITC) reeled over 80 base pairs of the downstream DNA by scrunching, while retaining the fixed upstream contact, and underwent the transition to elongation when it encountered promoter-proximal pol II from a preceding round of transcription. TFIIH is therefore conducive to promoter melting, TSS scanning, and promoter escape, extending far beyond synthesis of a short transcript.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 04, 2021.
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Structural visualization of de novo initiation of RNA polymerase II transcription
Chun Yang, Rina Fujiwara, Hee Jong Kim, Jose J. Gorbea Colón, Stefan Steimle, Benjamin A. Garcia, Kenji Murakami
bioRxiv 2021.05.03.442346; doi: https://doi.org/10.1101/2021.05.03.442346
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Structural visualization of de novo initiation of RNA polymerase II transcription
Chun Yang, Rina Fujiwara, Hee Jong Kim, Jose J. Gorbea Colón, Stefan Steimle, Benjamin A. Garcia, Kenji Murakami
bioRxiv 2021.05.03.442346; doi: https://doi.org/10.1101/2021.05.03.442346

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