Literature DB >> 20067596

Chromatin 'programming' by sequence--is there more to the nucleosome code than %GC?

Amanda Hughes1, Oliver J Rando.   

Abstract

The role of genomic sequence in directing the packaging of eukaryotic genomes into chromatin has been the subject of considerable recent debate. A new paper from Tillo and Hughes shows that the intrinsic thermodynamic preference of a given sequence in the yeast genome for the histone octamer can largely be captured with a simple model, and in fact is mostly explained by %GC. Thus, the rules for predicting nucleosome occupancy from genomic sequence are much less complicated than has been claimed. See research article http://www.biomedcentral.com/1471-2105/10/442.

Entities:  

Mesh:

Substances:

Year:  2009        PMID: 20067596      PMCID: PMC2804288          DOI: 10.1186/jbiol207

Source DB:  PubMed          Journal:  J Biol        ISSN: 1475-4924


  13 in total

1.  In vitro assembly of the characteristic chromatin organization at the yeast PHO5 promoter by a replication-independent extract system.

Authors:  Philipp Korber; Wolfram Hörz
Journal:  J Biol Chem       Date:  2004-06-10       Impact factor: 5.157

Review 2.  The biology of chromatin remodeling complexes.

Authors:  Cedric R Clapier; Bradley R Cairns
Journal:  Annu Rev Biochem       Date:  2009       Impact factor: 23.643

3.  High-resolution nucleosome mapping reveals transcription-dependent promoter packaging.

Authors:  Assaf Weiner; Amanda Hughes; Moran Yassour; Oliver J Rando; Nir Friedman
Journal:  Genome Res       Date:  2009-10-21       Impact factor: 9.043

4.  DNA bending and its relation to nucleosome positioning.

Authors:  H R Drew; A A Travers
Journal:  J Mol Biol       Date:  1985-12-20       Impact factor: 5.469

Review 5.  What controls nucleosome positions?

Authors:  Eran Segal; Jonathan Widom
Journal:  Trends Genet       Date:  2009-07-10       Impact factor: 11.639

6.  The DNA-encoded nucleosome organization of a eukaryotic genome.

Authors:  Noam Kaplan; Irene K Moore; Yvonne Fondufe-Mittendorf; Andrea J Gossett; Desiree Tillo; Yair Field; Emily M LeProust; Timothy R Hughes; Jason D Lieb; Jonathan Widom; Eran Segal
Journal:  Nature       Date:  2008-12-17       Impact factor: 49.962

7.  Naturally occurring poly(dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast.

Authors:  K Struhl
Journal:  Proc Natl Acad Sci U S A       Date:  1985-12       Impact factor: 11.205

Review 8.  Nucleosome positioning and gene regulation: advances through genomics.

Authors:  Cizhong Jiang; B Franklin Pugh
Journal:  Nat Rev Genet       Date:  2009-03       Impact factor: 53.242

Review 9.  Nucleosome positioning: how is it established, and why does it matter?

Authors:  Marta Radman-Livaja; Oliver J Rando
Journal:  Dev Biol       Date:  2009-06-13       Impact factor: 3.582

10.  Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.

Authors:  Yong Zhang; Zarmik Moqtaderi; Barbara P Rattner; Ghia Euskirchen; Michael Snyder; James T Kadonaga; X Shirley Liu; Kevin Struhl
Journal:  Nat Struct Mol Biol       Date:  2009-07-20       Impact factor: 15.369

View more
  24 in total

Review 1.  Nucleosome positioning in Saccharomyces cerevisiae.

Authors:  An Jansen; Kevin J Verstrepen
Journal:  Microbiol Mol Biol Rev       Date:  2011-06       Impact factor: 11.056

2.  High-density nucleosome occupancy map of human chromosome 9p21-22 reveals chromatin organization of the type I interferon gene cluster.

Authors:  Jonathan E Freaney; Quanwei Zhang; Erbay Yigit; Rebecca Kim; Jonathan Widom; Ji-Ping Wang; Curt M Horvath
Journal:  J Interferon Cytokine Res       Date:  2014-03-27       Impact factor: 2.607

3.  Human Enhancers Harboring Specific Sequence Composition, Activity, and Genome Organization Are Linked to the Immune Response.

Authors:  Charles-Henri Lecellier; Wyeth W Wasserman; Anthony Mathelier
Journal:  Genetics       Date:  2018-06-05       Impact factor: 4.562

4.  A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome.

Authors:  Zhenhai Zhang; Christian J Wippo; Megha Wal; Elissa Ward; Philipp Korber; B Franklin Pugh
Journal:  Science       Date:  2011-05-20       Impact factor: 47.728

Review 5.  DNA shape, genetic codes, and evolution.

Authors:  Stephen C J Parker; Thomas D Tullius
Journal:  Curr Opin Struct Biol       Date:  2011-03-23       Impact factor: 6.809

6.  High-resolution genome-wide mapping of the primary structure of chromatin.

Authors:  Zhenhai Zhang; B Franklin Pugh
Journal:  Cell       Date:  2011-01-21       Impact factor: 41.582

7.  Prediction of CpG-island function: CpG clustering vs. sliding-window methods.

Authors:  Michael Hackenberg; Guillermo Barturen; Pedro Carpena; Pedro L Luque-Escamilla; Christopher Previti; José L Oliver
Journal:  BMC Genomics       Date:  2010-05-26       Impact factor: 3.969

8.  Oligonucleotide sequence motifs as nucleosome positioning signals.

Authors:  Clayton K Collings; Alfonso G Fernandez; Chad G Pitschka; Troy B Hawkins; John N Anderson
Journal:  PLoS One       Date:  2010-06-03       Impact factor: 3.240

9.  Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes.

Authors:  Konstantinos Kritsas; Samuel E Wuest; Daniel Hupalo; Andrew D Kern; Thomas Wicker; Ueli Grossniklaus
Journal:  Genome Res       Date:  2012-09-17       Impact factor: 9.043

10.  A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription.

Authors:  Harm van Bakel; Kyle Tsui; Marinella Gebbia; Sanie Mnaimneh; Timothy R Hughes; Corey Nislow
Journal:  PLoS Genet       Date:  2013-05-02       Impact factor: 5.917

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.