Literature DB >> 24120742

Structural insights into transcription initiation by RNA polymerase II.

Sebastian Grünberg1, Steven Hahn.   

Abstract

Transcriptional regulation is one of the most important steps in control of cell identity, growth, differentiation, and development. Many signaling pathways controlling these processes ultimately target the core transcription machinery that, for protein coding genes, consists of RNA polymerase II (Pol II) and the general transcription factors (GTFs). New studies on the structure and mechanism of the core assembly and how it interfaces with promoter DNA and coactivator complexes have given tremendous insight into early steps in the initiation process, genome-wide binding, and mechanisms conserved for all nuclear and archaeal Pols. Here, we review recent developments in dissecting the architecture of the Pol II core machinery with a focus on early and regulated steps in transcription initiation.
Copyright © 2013 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  RNA polymerase II; SAGA; TFIID; TFIIH; coactivators; mediator; open complex; preinitiation complex (PIC); transcription; translocase

Mesh:

Substances:

Year:  2013        PMID: 24120742      PMCID: PMC3843768          DOI: 10.1016/j.tibs.2013.09.002

Source DB:  PubMed          Journal:  Trends Biochem Sci        ISSN: 0968-0004            Impact factor:   13.807


  80 in total

1.  Subunit architecture of general transcription factor TFIIH.

Authors:  Brian J Gibbons; Edward J Brignole; Maia Azubel; Kenji Murakami; Neil R Voss; David A Bushnell; Francisco J Asturias; Roger D Kornberg
Journal:  Proc Natl Acad Sci U S A       Date:  2012-01-20       Impact factor: 11.205

2.  Mechanism of ATP-dependent promoter melting by transcription factor IIH.

Authors:  T K Kim; R H Ebright; D Reinberg
Journal:  Science       Date:  2000-05-26       Impact factor: 47.728

Review 3.  Conservation between the RNA polymerase I, II, and III transcription initiation machineries.

Authors:  Alessandro Vannini; Patrick Cramer
Journal:  Mol Cell       Date:  2012-02-24       Impact factor: 17.970

4.  Structure of a (Cys3His) zinc ribbon, a ubiquitous motif in archaeal and eucaryal transcription.

Authors:  H T Chen; P Legault; J Glushka; J G Omichinski; R A Scott
Journal:  Protein Sci       Date:  2000-09       Impact factor: 6.725

5.  Novel dimerization fold of RAP30/RAP74 in human TFIIF at 1.7 A resolution.

Authors:  F Gaiser; S Tan; T J Richmond
Journal:  J Mol Biol       Date:  2000-10-06       Impact factor: 5.469

6.  Architecture of the yeast RNA polymerase II open complex and regulation of activity by TFIIF.

Authors:  James Fishburn; Steven Hahn
Journal:  Mol Cell Biol       Date:  2011-10-24       Impact factor: 4.272

7.  Computational analysis of core promoters in the Drosophila genome.

Authors:  Uwe Ohler; Guo-chun Liao; Heinrich Niemann; Gerald M Rubin
Journal:  Genome Biol       Date:  2002-12-20       Impact factor: 13.583

8.  Opening and closing of the bacterial RNA polymerase clamp.

Authors:  Anirban Chakraborty; Dongye Wang; Yon W Ebright; You Korlann; Ekaterine Kortkhonjia; Taiho Kim; Saikat Chowdhury; Sivaramesh Wigneshweraraj; Herbert Irschik; Rolf Jansen; B Tracy Nixon; Jennifer Knight; Shimon Weiss; Richard H Ebright
Journal:  Science       Date:  2012-08-03       Impact factor: 47.728

9.  Architecture of the RNA polymerase II preinitiation complex and mechanism of ATP-dependent promoter opening.

Authors:  Sebastian Grünberg; Linda Warfield; Steven Hahn
Journal:  Nat Struct Mol Biol       Date:  2012-07-01       Impact factor: 15.369

10.  Genome-wide structure and organization of eukaryotic pre-initiation complexes.

Authors:  Ho Sung Rhee; B Franklin Pugh
Journal:  Nature       Date:  2012-01-18       Impact factor: 49.962

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  67 in total

1.  HIV Tat controls RNA Polymerase II and the epigenetic landscape to transcriptionally reprogram target immune cells.

Authors:  Jonathan E Reeder; Youn-Tae Kwak; Ryan P McNamara; Christian V Forst; Iván D'Orso
Journal:  Elife       Date:  2015-10-21       Impact factor: 8.140

2.  Double-stranded DNA translocase activity of transcription factor TFIIH and the mechanism of RNA polymerase II open complex formation.

Authors:  James Fishburn; Eric Tomko; Eric Galburt; Steven Hahn
Journal:  Proc Natl Acad Sci U S A       Date:  2015-03-16       Impact factor: 11.205

Review 3.  Structural basis of transcription initiation by RNA polymerase II.

Authors:  Sarah Sainsbury; Carrie Bernecky; Patrick Cramer
Journal:  Nat Rev Mol Cell Biol       Date:  2015-02-18       Impact factor: 94.444

4.  Chemical cross-linking and mass spectrometry to determine the subunit interaction network in a recombinant human SAGA HAT subcomplex.

Authors:  Nha-Thi Nguyen-Huynh; Grigory Sharov; Clément Potel; Pélagie Fichter; Simon Trowitzsch; Imre Berger; Valérie Lamour; Patrick Schultz; Noëlle Potier; Emmanuelle Leize-Wagner
Journal:  Protein Sci       Date:  2015-04-14       Impact factor: 6.725

5.  X-linked Dystonia-Parkinsonism patient cells exhibit altered signaling via nuclear factor-kappa B.

Authors:  Christine A Vaine; David Shin; Christina Liu; William T Hendriks; Jyotsna Dhakal; Kyle Shin; Nutan Sharma; D Cristopher Bragg
Journal:  Neurobiol Dis       Date:  2016-12-22       Impact factor: 5.996

6.  TFIID or not TFIID, a continuing transcriptional SAGA.

Authors:  Slawomir Kubik; Maria Jessica Bruzzone; David Shore
Journal:  EMBO J       Date:  2017-01-09       Impact factor: 11.598

Review 7.  Introduction to the Thematic Minireview Series: Chromatin and transcription.

Authors:  Joel M Gottesfeld; Michael F Carey
Journal:  J Biol Chem       Date:  2018-08-01       Impact factor: 5.157

8.  Human Trophoblast Differentiation Is Associated With Profound Gene Regulatory and Epigenetic Changes.

Authors:  Youn-Tae Kwak; Sribalasubashini Muralimanoharan; Aishwarya A Gogate; Carole R Mendelson
Journal:  Endocrinology       Date:  2019-09-01       Impact factor: 4.736

9.  Function of Conserved Topological Regions within the Saccharomyces cerevisiae Basal Transcription Factor TFIIH.

Authors:  Linda Warfield; Jie Luo; Jeffrey Ranish; Steven Hahn
Journal:  Mol Cell Biol       Date:  2016-09-12       Impact factor: 4.272

10.  Transcription initiation complex structures elucidate DNA opening.

Authors:  C Plaschka; M Hantsche; C Dienemann; C Burzinski; J Plitzko; P Cramer
Journal:  Nature       Date:  2016-05-11       Impact factor: 49.962

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