Literature DB >> 21863480

Genome-wide measurement of histone H3 replacement dynamics in yeast.

Oliver J Rando1.   

Abstract

Chromatin plays critical roles in processes governed in different timescales - responses to environmental changes require rapid plasticity, while long-term stability through multiple cell generations requires epigenetically heritable chromatin. Understanding the dynamic behavior of chromatin is of great interest for fields ranging from transcriptional regulation through meiosis and gametogenesis. Here, we describe a protocol for measuring histone replacement rates genome wide in the budding yeast Saccharomyces cerevisiae. With suitable modifications, this protocol could be applied to other organisms, or to replacement dynamics of other DNA-associated proteins.

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Year:  2011        PMID: 21863480      PMCID: PMC3974389          DOI: 10.1007/978-1-61779-173-4_3

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  19 in total

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Authors:  Christophe Thiriet; Jeffrey J Hayes
Journal:  Genes Dev       Date:  2005-03-15       Impact factor: 11.361

2.  Transcriptional activation triggers deposition and removal of the histone variant H3.3.

Authors:  Brian E Schwartz; Kami Ahmad
Journal:  Genes Dev       Date:  2005-03-17       Impact factor: 11.361

3.  Histones are incorporated in trans during reassembly of the yeast PHO5 promoter.

Authors:  Ulrike J Schermer; Philipp Korber; Wolfram Hörz
Journal:  Mol Cell       Date:  2005-07-22       Impact factor: 17.970

4.  Continuous histone H2B and transcription-dependent histone H3 exchange in yeast cells outside of replication.

Authors:  Adil Jamai; Rachel Maria Imoberdorf; Michel Strubin
Journal:  Mol Cell       Date:  2007-02-09       Impact factor: 17.970

5.  Evidence for nucleosome depletion at active regulatory regions genome-wide.

Authors:  Cheol-Koo Lee; Yoichiro Shibata; Bhargavi Rao; Brian D Strahl; Jason D Lieb
Journal:  Nat Genet       Date:  2004-07-11       Impact factor: 38.330

6.  Evidence for eviction and rapid deposition of histones upon transcriptional elongation by RNA polymerase II.

Authors:  Marc A Schwabish; Kevin Struhl
Journal:  Mol Cell Biol       Date:  2004-12       Impact factor: 4.272

7.  Dynamics of replication-independent histone turnover in budding yeast.

Authors:  Michael F Dion; Tommy Kaplan; Minkyu Kim; Stephen Buratowski; Nir Friedman; Oliver J Rando
Journal:  Science       Date:  2007-03-09       Impact factor: 47.728

8.  Dynamic regulation of replication independent deposition of histone H3 in fission yeast.

Authors:  Eun Shik Choi; Jin A Shin; Hyun Soo Kim; Yeun Kyu Jang
Journal:  Nucleic Acids Res       Date:  2005-12-15       Impact factor: 16.971

9.  Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters.

Authors:  Gregory J Hogan; Cheol-Koo Lee; Jason D Lieb
Journal:  PLoS Genet       Date:  2006-08-08       Impact factor: 5.917

10.  Global nucleosome occupancy in yeast.

Authors:  Bradley E Bernstein; Chih Long Liu; Emily L Humphrey; Ethan O Perlstein; Stuart L Schreiber
Journal:  Genome Biol       Date:  2004-08-20       Impact factor: 13.583

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  5 in total

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Authors:  Jason M Rizzo; Jonathan E Bard; Michael J Buck
Journal:  BMC Mol Biol       Date:  2012-05-06       Impact factor: 2.946

2.  A unified phylogeny-based nomenclature for histone variants.

Authors:  Paul B Talbert; Kami Ahmad; Geneviève Almouzni; Juan Ausió; Frederic Berger; Prem L Bhalla; William M Bonner; W Zacheus Cande; Brian P Chadwick; Simon W L Chan; George A M Cross; Liwang Cui; Stefan I Dimitrov; Detlef Doenecke; José M Eirin-López; Martin A Gorovsky; Sandra B Hake; Barbara A Hamkalo; Sarah Holec; Steven E Jacobsen; Kinga Kamieniarz; Saadi Khochbin; Andreas G Ladurner; David Landsman; John A Latham; Benjamin Loppin; Harmit S Malik; William F Marzluff; John R Pehrson; Jan Postberg; Robert Schneider; Mohan B Singh; M Mitchell Smith; Eric Thompson; Maria-Elena Torres-Padilla; David John Tremethick; Bryan M Turner; Jakob Harm Waterborg; Heike Wollmann; Ramesh Yelagandula; Bing Zhu; Steven Henikoff
Journal:  Epigenetics Chromatin       Date:  2012-06-21       Impact factor: 4.954

3.  High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts.

Authors:  Minghao Chia; Cai Li; Sueli Marques; Vicente Pelechano; Nicholas M Luscombe; Folkert J van Werven
Journal:  Genome Biol       Date:  2021-01-14       Impact factor: 13.583

4.  Elucidating the molecular bases of epigenetic inheritance in non-model invertebrates: the case of the root-knot nematode Meloidogyne incognita.

Authors:  Laetitia Perfus-Barbeoch; Philippe Castagnone-Sereno; Michael Reichelt; Sara Fneich; David Roquis; Loris Pratx; Céline Cosseau; Christoph Grunau; Pierre Abad
Journal:  Front Physiol       Date:  2014-06-06       Impact factor: 4.566

5.  Transcription of a 5' extended mRNA isoform directs dynamic chromatin changes and interference of a downstream promoter.

Authors:  Minghao Chia; Amy Tresenrider; Jingxun Chen; Gianpiero Spedale; Victoria Jorgensen; Elçin Ünal; Folkert Jacobus van Werven
Journal:  Elife       Date:  2017-09-14       Impact factor: 8.140

  5 in total

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