Literature DB >> 19741699

The logic of chromatin architecture and remodelling at promoters.

Bradley R Cairns1.   

Abstract

The regulation of gene transcription involves a dynamic balance between packaging regulatory sequences into chromatin and allowing transcriptional regulators access to these sequences. Access is restricted by the nucleosomes, but these can be repositioned or ejected by enzymes known as nucleosome remodellers. In addition, the DNA sequence can impart stiffness or curvature to the DNA, thereby affecting the position of nucleosomes on the DNA, influencing particular promoter 'architectures'. Recent genome-wide studies in yeast suggest that constitutive and regulated genes have architectures that differ in terms of nucleosome position, turnover, remodelling requirements and transcriptional noise.

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Year:  2009        PMID: 19741699     DOI: 10.1038/nature08450

Source DB:  PubMed          Journal:  Nature        ISSN: 0028-0836            Impact factor:   49.962


  63 in total

1.  Genome-scale identification of nucleosome positions in S. cerevisiae.

Authors:  Guo-Cheng Yuan; Yuen-Jong Liu; Michael F Dion; Michael D Slack; Lani F Wu; Steven J Altschuler; Oliver J Rando
Journal:  Science       Date:  2005-06-16       Impact factor: 47.728

2.  Nucleosome stability mediated by histone variants H3.3 and H2A.Z.

Authors:  Chunyuan Jin; Gary Felsenfeld
Journal:  Genes Dev       Date:  2007-06-15       Impact factor: 11.361

3.  Two strategies for gene regulation by promoter nucleosomes.

Authors:  Itay Tirosh; Naama Barkai
Journal:  Genome Res       Date:  2008-04-30       Impact factor: 9.043

4.  Transcription regulation through promoter-proximal pausing of RNA polymerase II.

Authors:  Leighton J Core; John T Lis
Journal:  Science       Date:  2008-03-28       Impact factor: 47.728

5.  Modulation of ISWI function by site-specific histone acetylation.

Authors:  Davide F V Corona; Cedric R Clapier; Peter B Becker; John W Tamkun
Journal:  EMBO Rep       Date:  2002-03       Impact factor: 8.807

6.  Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription.

Authors:  Michael J Carrozza; Bing Li; Laurence Florens; Tamaki Suganuma; Selene K Swanson; Kenneth K Lee; Wei-Jong Shia; Scott Anderson; John Yates; Michael P Washburn; Jerry L Workman
Journal:  Cell       Date:  2005-11-18       Impact factor: 41.582

7.  Nucleosome positions predicted through comparative genomics.

Authors:  Ilya P Ioshikhes; Istvan Albert; Sara J Zanton; B Franklin Pugh
Journal:  Nat Genet       Date:  2006-09-10       Impact factor: 38.330

8.  A high-resolution atlas of nucleosome occupancy in yeast.

Authors:  William Lee; Desiree Tillo; Nicolas Bray; Randall H Morse; Ronald W Davis; Timothy R Hughes; Corey Nislow
Journal:  Nat Genet       Date:  2007-09-16       Impact factor: 38.330

9.  Acetylation of H2AZ Lys 14 is associated with genome-wide gene activity in yeast.

Authors:  Catherine B Millar; Feng Xu; Kangling Zhang; Michael Grunstein
Journal:  Genes Dev       Date:  2006-03-15       Impact factor: 11.361

10.  Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning.

Authors:  Benoît Guillemette; Alain R Bataille; Nicolas Gévry; Maryse Adam; Mathieu Blanchette; François Robert; Luc Gaudreau
Journal:  PLoS Biol       Date:  2005-11-01       Impact factor: 8.029

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  219 in total

1.  Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize.

Authors:  Daniel L Vera; Thelma F Madzima; Jonathan D Labonne; Mohammad P Alam; Gregg G Hoffman; S B Girimurugan; Jinfeng Zhang; Karen M McGinnis; Jonathan H Dennis; Hank W Bass
Journal:  Plant Cell       Date:  2014-10-31       Impact factor: 11.277

2.  Control of B cell development by the histone H2A deubiquitinase MYSM1.

Authors:  Xiao-Xia Jiang; Quan Nguyen; YuChia Chou; Tao Wang; Vijayalakshmi Nandakumar; Peter Yates; Lindsey Jones; Lifeng Wang; Haejung Won; Hye-Ra Lee; Jae U Jung; Markus Müschen; Xue F Huang; Si-Yi Chen
Journal:  Immunity       Date:  2011-12-08       Impact factor: 31.745

Review 3.  Transcription goes digital.

Authors:  Timothée Lionnet; Robert H Singer
Journal:  EMBO Rep       Date:  2012-04-02       Impact factor: 8.807

4.  A conserved regulatory element in the mammalian β-globin promoters.

Authors:  Ryoiti Kiyama; Yuko Wada-Kiyama
Journal:  J Mol Evol       Date:  2011-09-24       Impact factor: 2.395

5.  Activator-dependent p300 acetylation of chromatin in vitro: enhancement of transcription by disruption of repressive nucleosome-nucleosome interactions.

Authors:  Heather J Szerlong; Jessica E Prenni; Jennifer K Nyborg; Jeffrey C Hansen
Journal:  J Biol Chem       Date:  2010-08-18       Impact factor: 5.157

Review 6.  Regulation of DNA replication by chromatin structures: accessibility and recruitment.

Authors:  Makoto T Hayashi; Hisao Masukata
Journal:  Chromosoma       Date:  2010-08-03       Impact factor: 4.316

Review 7.  Architectural epigenetics: mitotic retention of mammalian transcriptional regulatory information.

Authors:  Sayyed K Zaidi; Daniel W Young; Martin Montecino; Jane B Lian; Janet L Stein; Andre J van Wijnen; Gary S Stein
Journal:  Mol Cell Biol       Date:  2010-08-09       Impact factor: 4.272

Review 8.  Inducible gene expression: diverse regulatory mechanisms.

Authors:  Vikki M Weake; Jerry L Workman
Journal:  Nat Rev Genet       Date:  2010-04-27       Impact factor: 53.242

9.  Chromatin density and splicing destiny: on the cross-talk between chromatin structure and splicing.

Authors:  Schraga Schwartz; Gil Ast
Journal:  EMBO J       Date:  2010-04-20       Impact factor: 11.598

Review 10.  Achieving singularity in mammalian odorant receptor gene choice.

Authors:  Timothy S McClintock
Journal:  Chem Senses       Date:  2010-05-11       Impact factor: 3.160

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