Literature DB >> 20683473

Nucleosome sequence preferences influence in vivo nucleosome organization.

Noam Kaplan, Irene Moore, Yvonne Fondufe-Mittendorf, Andrea J Gossett, Desiree Tillo, Yair Field, Timothy R Hughes, Jason D Lieb, Jonathan Widom, Eran Segal.   

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Year:  2010        PMID： 20683473      PMCID： PMC2969171          DOI： 10.1038/nsmb0810-918

Source DB:  PubMed          Journal:  Nat Struct Mol Biol        ISSN： 1545-9985            Impact factor:   15.369


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  18 in total

1.  High-resolution mapping of sequence-directed nucleosome positioning on genomic DNA.

Authors:  Ross M Fraser; David Keszenman-Pereyra; Martin W Simmen; James Allan
Journal:  J Mol Biol       Date:  2009-05-07       Impact factor: 5.469

2.  Identification and characterization of genomic nucleosome-positioning sequences.

Authors:  H R Widlund; H Cao; S Simonsson; E Magnusson; T Simonsson; P E Nielsen; J D Kahn; D M Crothers; M Kubista
Journal:  J Mol Biol       Date:  1997-04-11       Impact factor: 5.469

3.  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

4.  A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning.

Authors:  Anton Valouev; Jeffrey Ichikawa; Thaisan Tonthat; Jeremy Stuart; Swati Ranade; Heather Peckham; Kathy Zeng; Joel A Malek; Gina Costa; Kevin McKernan; Arend Sidow; Andrew Fire; Steven M Johnson
Journal:  Genome Res       Date:  2008-05-13       Impact factor: 9.043

Review 5.  From DNA sequence to transcriptional behaviour: a quantitative approach.

Authors:  Eran Segal; Jonathan Widom
Journal:  Nat Rev Genet       Date:  2009-07       Impact factor: 53.242

6.  Nucleosome positioning signals in genomic DNA.

Authors:  Heather E Peckham; Robert E Thurman; Yutao Fu; John A Stamatoyannopoulos; William Stafford Noble; Kevin Struhl; Zhiping Weng
Journal:  Genome Res       Date:  2007-07-09       Impact factor: 9.043

7.  Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization.

Authors:  Yair Field; Yvonne Fondufe-Mittendorf; Irene K Moore; Piotr Mieczkowski; Noam Kaplan; Yaniv Lubling; Jason D Lieb; Jonathan Widom; Eran Segal
Journal:  Nat Genet       Date:  2009-03-01       Impact factor: 38.330

8.  Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure.

Authors:  V Iyer; K Struhl
Journal:  EMBO J       Date:  1995-06-01       Impact factor: 11.598

9.  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

10.  Distinct modes of regulation by chromatin encoded through nucleosome positioning signals.

Authors:  Yair Field; Noam Kaplan; Yvonne Fondufe-Mittendorf; Irene K Moore; Eilon Sharon; Yaniv Lubling; Jonathan Widom; Eran Segal
Journal:  PLoS Comput Biol       Date:  2008-11-07       Impact factor: 4.475
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  59 in total

1.  A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast.

Authors:  Judith B Zaugg; Nicholas M Luscombe
Journal:  Genome Res       Date:  2011-09-19       Impact factor: 9.043

2.  A preoccupied position on nucleosomes.

Authors:  B Franklin Pugh
Journal:  Nat Struct Mol Biol       Date:  2010-08       Impact factor: 15.369

3.  Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation.

Authors:  Xiaochun Fan; Zarmik Moqtaderi; Yi Jin; Yong Zhang; X Shirley Liu; Kevin Struhl
Journal:  Proc Natl Acad Sci U S A       Date:  2010-10-04       Impact factor: 11.205

Review 4.  New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?

Authors:  Karolin Luger; Mekonnen L Dechassa; David J Tremethick
Journal:  Nat Rev Mol Cell Biol       Date:  2012-06-22       Impact factor: 94.444

5.  The divalent cations Ca2+ and Mg2+ play specific roles in stabilizing histone-DNA interactions within nucleosomes that are partially redundant with the core histone tail domains.

Authors:  Zungyoon Yang; Jeffrey J Hayes
Journal:  Biochemistry       Date:  2011-10-31       Impact factor: 3.162

Review 6.  Chromatin and DNA replication.

Authors:  David M MacAlpine; Geneviève Almouzni
Journal:  Cold Spring Harb Perspect Biol       Date:  2013-08-01       Impact factor: 10.005

Review 7.  Nucleosome positioning in Saccharomyces cerevisiae.

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

8.  Widespread signatures of recent selection linked to nucleosome positioning in the human lineage.

Authors:  James G D Prendergast; Colin A M Semple
Journal:  Genome Res       Date:  2011-09-08       Impact factor: 9.043

9.  An analysis and prediction of nucleosome positioning based on information content.

Authors:  Yong-qiang Xing; Guo-qing Liu; Xiu-juan Zhao; Lu Cai
Journal:  Chromosome Res       Date:  2013-02-22       Impact factor: 5.239

Review 10.  Nucleosome positioning: bringing order to the eukaryotic genome.

Authors:  Vishwanath R Iyer
Journal:  Trends Cell Biol       Date:  2012-03-14       Impact factor: 20.808
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