skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Structural visualization of RNA polymerase III transcription machineries

Abstract

Abstract RNA polymerase III (Pol III) transcription initiation requires the action of the transcription factor IIIB (TFIIIB) and is highly regulated. Here, we determine the structures of Pol III pre-initiation complexes (PICs) using single particle cryo-electron microscopy (cryo-EM). We observe stable Pol III–TFIIIB complexes using nucleic acid scaffolds mimicking various functional states, in which TFIIIB tightly encircles the upstream promoter DNA. There is an intricate interaction between TFIIIB and Pol III, which stabilizes the winged-helix domains of the C34 subunit of Pol III over the active site cleft. The architecture of Pol III PIC more resembles that of the Pol II PIC than the Pol I PIC. In addition, we also obtain a 3D reconstruction of Pol III in complex with TFIIIB using the elongation complex (EC) scaffold, shedding light on the mechanism of facilitated recycling of Pol III prior to transcription re-initiation.

Authors:
ORCiD logo; ; ; ORCiD logo; ORCiD logo
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1459999
Alternate Identifier(s):
OSTI ID: 1543739
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Published Article
Journal Name:
Cell Discovery
Additional Journal Information:
Journal Name: Cell Discovery Journal Volume: 4 Journal Issue: 1; Journal ID: ISSN 2056-5968
Publisher:
Nature Publishing Group
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Cell Biology

Citation Formats

Han, Yan, Yan, Chunli, Fishbain, Susan, Ivanov, Ivaylo, and He, Yuan. Structural visualization of RNA polymerase III transcription machineries. United Kingdom: N. p., 2018. Web. doi:10.1038/s41421-018-0044-z.
Han, Yan, Yan, Chunli, Fishbain, Susan, Ivanov, Ivaylo, & He, Yuan. Structural visualization of RNA polymerase III transcription machineries. United Kingdom. https://doi.org/10.1038/s41421-018-0044-z
Han, Yan, Yan, Chunli, Fishbain, Susan, Ivanov, Ivaylo, and He, Yuan. 2018. "Structural visualization of RNA polymerase III transcription machineries". United Kingdom. https://doi.org/10.1038/s41421-018-0044-z.
@article{osti_1459999,
title = {Structural visualization of RNA polymerase III transcription machineries},
author = {Han, Yan and Yan, Chunli and Fishbain, Susan and Ivanov, Ivaylo and He, Yuan},
abstractNote = {Abstract RNA polymerase III (Pol III) transcription initiation requires the action of the transcription factor IIIB (TFIIIB) and is highly regulated. Here, we determine the structures of Pol III pre-initiation complexes (PICs) using single particle cryo-electron microscopy (cryo-EM). We observe stable Pol III–TFIIIB complexes using nucleic acid scaffolds mimicking various functional states, in which TFIIIB tightly encircles the upstream promoter DNA. There is an intricate interaction between TFIIIB and Pol III, which stabilizes the winged-helix domains of the C34 subunit of Pol III over the active site cleft. The architecture of Pol III PIC more resembles that of the Pol II PIC than the Pol I PIC. In addition, we also obtain a 3D reconstruction of Pol III in complex with TFIIIB using the elongation complex (EC) scaffold, shedding light on the mechanism of facilitated recycling of Pol III prior to transcription re-initiation.},
doi = {10.1038/s41421-018-0044-z},
url = {https://www.osti.gov/biblio/1459999}, journal = {Cell Discovery},
issn = {2056-5968},
number = 1,
volume = 4,
place = {United Kingdom},
year = {Tue Jul 31 00:00:00 EDT 2018},
month = {Tue Jul 31 00:00:00 EDT 2018}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at https://doi.org/10.1038/s41421-018-0044-z

Citation Metrics:
Cited by: 38 works
Citation information provided by
Web of Science

Figures / Tables:

Fig. 1 Fig. 1: Cryo-EM structure of the Pol III ITC. a Nucleic acid scaffold used. The non-template (top) and template (bottom) strands are depicted in cyan. Mismatched sequence is shown as separate strands. RNA is shown in red. TATA box is depicted in yellow. TFIIIB binding region and transcription bubble positionmore » are also labeled. b Cryo-EM reconstruction of the Pol III ITC. Pol III is colored gray, and the nucleic acid template is colored cyan. The TFIIIB subunits are depicted in blue (Brf1), red (TBP), and orange (Bdp1). Two views, front (left) and bottom (right), are shown. c Two views of the Pol III ITC model. Components are colored the same as in b« less

Save / Share:

Works referenced in this record:

A post-recruitment function for the RNA polymerase III transcription–initiation factor IIIB
journal, August 1998


Transcribing RNA polymerase III observed by electron cryomicroscopy
journal, April 2016


Double-stranded DNA translocase activity of transcription factor TFIIH and the mechanism of RNA polymerase II open complex formation
journal, March 2015


Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2
journal, November 2016


Molecular mechanisms of Bdp1 in TFIIIB assembly and RNA polymerase III transcription initiation
journal, July 2017


Near-atomic resolution visualization of human transcription promoter opening
journal, May 2016


Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression
journal, June 2016


DoG Picker and TiltPicker: Software tools to facilitate particle selection in single particle electron microscopy
journal, May 2009


Crystal structure of a yeast TFIIA/TBP/DNA complex
journal, May 1996


A structural perspective on RNA polymerase I and RNA polymerase III transcription machineries
journal, March 2013


Appion: An integrated, database-driven pipeline to facilitate EM image processing
journal, April 2009


Automated molecular microscopy: The new Leginon system
journal, July 2005


Crystal Structure of the Yeast TFIIA/TBP/DNA Complex
journal, May 1996


Crystal structure of a transcription factor IIIB core interface ternary complex
journal, March 2003


Multiple Forms of DNA-dependent RNA Polymerase in Eukaryotic Organisms
journal, October 1969


Molecular mechanism of promoter opening by RNA polymerase III
journal, January 2018


The 2.1-A crystal structure of an archaeal preinitiation complex: TATA-box-binding protein/transcription factor (II)B core/TATA-box
journal, June 1997


RNA polymerase II–TFIIB structure and mechanism of transcription initiation
journal, October 2009


Structural basis of RNA polymerase III transcription initiation
journal, January 2018


CTFFIND4: Fast and accurate defocus estimation from electron micrographs
journal, November 2015


Distinct roles of transcription factors TFIIIB and TFIIIC in RNA polymerase III transcription reinitiation
journal, September 2004


Comparative overview of RNA polymerase II and III transcription cycles, with focus on RNA polymerase III termination and reinitiation
journal, December 2013


Structure and function of the initially transcribing RNA polymerase II–TFIIB complex
journal, November 2012


GeneSilico protein structure prediction meta-server
journal, July 2003


Structural Basis of RNA Polymerase I Transcription Initiation
journal, March 2017


Architecture of the RNA polymerase II preinitiation complex and mechanism of ATP-dependent promoter opening
journal, July 2012


Structural insights into transcription initiation by yeast RNA polymerase I
journal, July 2017


Outcome of the First Electron Microscopy Validation Task Force Meeting
journal, February 2012


Structural visualization of key steps in human transcription initiation
journal, February 2013


MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy
journal, February 2017


UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004


Reconfiguring the connectivity of a multiprotein complex: Fusions of yeast TATA-binding protein with Brf1, and the function of transcription factor IIIB
journal, October 2005


Gctf: Real-time CTF determination and correction
journal, January 2016


Comparative Protein Modelling by Satisfaction of Spatial Restraints
journal, December 1993


Structure of an RNA Polymerase II–TFIIB Complex and the Transcription Initiation Mechanism
journal, November 2009


A Composite Upstream Sequence Motif Potentiates tRNA Gene Transcription in Yeast
journal, October 2003


Formation of open and elongating transcription complexes by RNA polymerase III
journal, July 1992


The Phenix software for automated determination of macromolecular structures
journal, September 2011


Transcription initiation complex structures elucidate DNA opening
journal, May 2016


EMAN2: An extensible image processing suite for electron microscopy
journal, January 2007


Molecular structures of unbound and transcribing RNA polymerase III
journal, November 2015


Transcription reinitiation by RNA polymerase III
journal, March 2013


Visualizing density maps with UCSF Chimera
journal, January 2007


A New Generation of the IMAGIC Image Processing System
journal, January 1996


RNA polymerase III transcription and cancer
journal, April 2004


RELION: Implementation of a Bayesian approach to cryo-EM structure determination
journal, December 2012


Crystal structure of a TFIIB–TBP–TATA-element ternary complex
journal, September 1995


Conserved functional domains of the RNA polymerase III general transcription factor BRF.
journal, December 1994


Structure of an RNA polymerase II preinitiation complex
journal, October 2015


DNA melting on yeast RNA polymerase II promoters
journal, August 1993


RNA polymerase III subunit architecture and implications for open promoter complex formation
journal, November 2012


The structural basis for the oriented assembly of a TBP/TFB/promoter complex
journal, November 1999


The expanding RNA polymerase III transcriptome
journal, December 2007


Functions of the TFIIE-Related Tandem Winged-Helix Domain of Rpc34 in RNA Polymerase III Initiation and Elongation
journal, November 2017


RNA polymerases I and III, non-coding RNAs and cancer
journal, December 2008


Conservation between the RNA Polymerase I, II, and III Transcription Initiation Machineries
journal, February 2012


Redox Signaling by the RNA Polymerase III TFIIB-Related Factor Brf2
journal, December 2015


Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.