Literature DB >> 27066865

The Determinants of Directionality in Transcriptional Initiation.

Dia N Bagchi1, Vishwanath R Iyer2.   

Abstract

A new paradigm has emerged in recent years characterizing transcription initiation as a bidirectional process encompassing a larger proportion of the genome than previously thought. Past concepts of coding genes thinly scattered among a vast background of transcriptionally inert noncoding DNA have been abandoned. A richer picture has taken shape, integrating transcription of coding genes, enhancer RNAs (eRNAs), and various other noncoding transcriptional events. In this review we give an overview of recent studies detailing the mechanisms of RNA polymerase II (RNA Pol II)-based transcriptional initiation and discuss the ways in which transcriptional direction is established as well as its functional implications.
Copyright © 2016 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  directionality; eRNA; enhancer; nucleosome-depleted region; promoter; transcriptional initiation

Mesh：

Substances：

Year:  2016        PMID： 27066865      PMCID： PMC4874897          DOI： 10.1016/j.tig.2016.03.005

Source DB:  PubMed          Journal:  Trends Genet        ISSN： 0168-9525            Impact factor:   11.639


  93 in total

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Journal:  Cell       Date:  2007-11-16       Impact factor: 41.582

2.  Transcription factor binding and modified histones in human bidirectional promoters.

Authors:  Jane M Lin; Patrick J Collins; Nathan D Trinklein; Yutao Fu; Hualin Xi; Richard M Myers; Zhiping Weng
Journal:  Genome Res       Date:  2007-06       Impact factor: 9.043

3.  Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase.

Authors:  Christopher M Weber; Srinivas Ramachandran; Steven Henikoff
Journal:  Mol Cell       Date:  2014-03-06       Impact factor: 17.970

4.  Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.

Authors:  Leighton J Core; André L Martins; Charles G Danko; Colin T Waters; Adam Siepel; John T Lis
Journal:  Nat Genet       Date:  2014-11-10       Impact factor: 38.330

5.  PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters.

Authors:  Pascal Preker; Kristina Almvig; Marianne S Christensen; Eivind Valen; Christophe K Mapendano; Albin Sandelin; Torben Heick Jensen
Journal:  Nucleic Acids Res       Date:  2011-05-19       Impact factor: 16.971

6.  Proteogenomics analysis reveals specific genomic orientations of distal regulatory regions composed by non-canonical histone variants.

Authors:  Kyoung-Jae Won; Inchan Choi; Gary LeRoy; Barry M Zee; Simone Sidoli; Michelle Gonzales-Cope; Benjamin A Garcia
Journal:  Epigenetics Chromatin       Date:  2015-04-10       Impact factor: 4.954

7.  Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription.

Authors:  Susanne Bornelöv; Jan Komorowski; Claes Wadelius
Journal:  BMC Genomics       Date:  2015-04-15       Impact factor: 3.969

8.  Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements.

Authors:  Daechan Park; Adam R Morris; Anna Battenhouse; Vishwanath R Iyer
Journal:  Nucleic Acids Res       Date:  2014-01-10       Impact factor: 16.971

9.  Extensive transcriptional heterogeneity revealed by isoform profiling.

Authors:  Vicent Pelechano; Wu Wei; Lars M Steinmetz
Journal:  Nature       Date:  2013-04-24       Impact factor: 49.962

10.  H2A.Z marks antisense promoters and has positive effects on antisense transcript levels in budding yeast.

Authors:  Muxin Gu; Yanin Naiyachit; Thomas J Wood; Catherine B Millar
Journal:  BMC Genomics       Date:  2015-02-19       Impact factor: 3.969
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  12 in total

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Authors:  Jenna E Gallegos; Alan B Rose
Journal:  Plant Cell       Date:  2017-04-03       Impact factor: 11.277

2.  Identification of regulatory elements recapitulating early expression of L-plastin in the zebrafish enveloping layer and embryonic periderm.

Authors:  Emily A Baumgartner; Zachary J Compton; Spencer Evans; Jacek Topczewski; Elizabeth E LeClair
Journal:  Gene Expr Patterns       Date:  2019-03-30       Impact factor: 1.224

3.  Osmolality/salinity-responsive enhancers (OSREs) control induction of osmoprotective genes in euryhaline fish.

Authors:  Xiaodan Wang; Dietmar Kültz
Journal:  Proc Natl Acad Sci U S A       Date:  2017-03-13       Impact factor: 11.205

4.  A Role for the Mre11-Rad50-Xrs2 Complex in Gene Expression and Chromosome Organization.

Authors:  Romain Forey; Antoine Barthe; Mireille Tittel-Elmer; Maxime Wery; Marie-Bénédicte Barrault; Cécile Ducrot; Andrew Seeber; Nils Krietenstein; Ugo Szachnowski; Magdalena Skrzypczak; Krzysztof Ginalski; Maga Rowicka; Jennifer A Cobb; Oliver J Rando; Julie Soutourina; Michel Werner; Karine Dubrana; Susan M Gasser; Antonin Morillon; Philippe Pasero; Armelle Lengronne; Jérôme Poli
Journal:  Mol Cell       Date:  2020-12-04       Impact factor: 17.970

5.  Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP.

Authors:  Anthony C Chiu; Hiroshi I Suzuki; Xuebing Wu; Dig B Mahat; Andrea J Kriz; Phillip A Sharp
Journal:  Mol Cell       Date:  2018-02-01       Impact factor: 17.970

6.  Regulation of the cohesin-loading factor NIPBL: Role of the lncRNA NIPBL-AS1 and identification of a distal enhancer element.

Authors:  Jessica Zuin; Valentina Casa; Jelena Pozojevic; Petros Kolovos; Mirjam C G N van den Hout; Wilfred F J van Ijcken; Ilaria Parenti; Diana Braunholz; Yorann Baron; Erwan Watrin; Frank J Kaiser; Kerstin S Wendt
Journal:  PLoS Genet       Date:  2017-12-20       Impact factor: 5.917

7.  Chicken CCDC152 shares an NFYB-regulated bidirectional promoter with a growth hormone receptor antisense transcript and inhibits cells proliferation and migration.

Authors:  Shudai Lin; Wei Luo; Mingya Jiang; Wen Luo; Bahareldin Ali Abdalla; Qinghua Nie; Li Zhang; Xiquan Zhang
Journal:  Oncotarget       Date:  2017-09-20

8.  Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters.

Authors:  Fatemeh Behjati Ardakani; Kathrin Kattler; Karl Nordström; Nina Gasparoni; Gilles Gasparoni; Sarah Fuchs; Anupam Sinha; Matthias Barann; Peter Ebert; Jonas Fischer; Barbara Hutter; Gideon Zipprich; Charles D Imbusch; Bärbel Felder; Jürgen Eils; Benedikt Brors; Thomas Lengauer; Thomas Manke; Philip Rosenstiel; Jörn Walter; Marcel H Schulz
Journal:  Epigenetics Chromatin       Date:  2018-11-10       Impact factor: 4.954

9.  Regulatory Architecture of the Neuronal Cacng2/Tarpγ2 Gene Promoter: Multiple Repressive Domains, a Polymorphic Regulatory Short Tandem Repeat, and Bidirectional Organization with Co-regulated lncRNAs.

Authors:  B P A Corney; C L Widnall; D J Rees; J S Davies; V Crunelli; D A Carter
Journal:  J Mol Neurosci       Date:  2018-11-26       Impact factor: 3.444

10.  High-Resolution Mapping of Transcription Initiation in the Asexual Stages of Toxoplasma gondii.

Authors:  Benedikt M Markus; Benjamin S Waldman; Hernan A Lorenzi; Sebastian Lourido
Journal:  Front Cell Infect Microbiol       Date:  2021-01-20       Impact factor: 5.293
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