Literature DB >> 22929772

Genome-wide mapping of nucleosome positions in yeast using high-resolution MNase ChIP-Seq.

Megha Wal1, B Franklin Pugh.   

Abstract

Eukaryotic DNA is packaged into chromatin where nucleosomes form the basic building unit. Knowing the precise positions of nucleosomes is important because they determine the accessibility of underlying regulatory DNA sequences. Here we describe a detailed method to map on a genomic scale the locations of nucleosomes with very high resolution. Micrococcal nuclease (MNase) digestion followed by chromatin immunoprecipitation and facilitated library construction for deep sequencing provides a simple and accurate map of nucleosome positions.
Copyright © 2012 Elsevier Inc. All rights reserved.

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Year:  2012        PMID： 22929772      PMCID： PMC4871120          DOI： 10.1016/B978-0-12-391938-0.00010-0

Source DB:  PubMed          Journal:  Methods Enzymol        ISSN： 0076-6879            Impact factor:   1.600


  15 in total

1.  The structure of DNA in the nucleosome core.

Authors:  Timothy J Richmond; Curt A Davey
Journal:  Nature       Date:  2003-05-08       Impact factor: 49.962

2.  Chromatin remodelling at promoters suppresses antisense transcription.

Authors:  Iestyn Whitehouse; Oliver J Rando; Jeff Delrow; Toshio Tsukiyama
Journal:  Nature       Date:  2007-12-13       Impact factor: 49.962

3.  Analysis of in vivo nucleosome positions by determination of nucleosome-linker boundaries in crosslinked chromatin.

Authors:  G Fragoso; G L Hager
Journal:  Methods       Date:  1997-02       Impact factor: 3.608

4.  Sequence periodicities in chicken nucleosome core DNA.

Authors:  S C Satchwell; H R Drew; A A Travers
Journal:  J Mol Biol       Date:  1986-10-20       Impact factor: 5.469

5.  Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites.

Authors:  J D Anderson; J Widom
Journal:  Mol Cell Biol       Date:  2001-06       Impact factor: 4.272

6.  Nucleosome core particles containing a poly(dA.dT) sequence element exhibit a locally distorted DNA structure.

Authors:  Yunhe Bao; Cindy L White; Karolin Luger
Journal:  J Mol Biol       Date:  2006-07-05       Impact factor: 5.469

Review 7.  What controls nucleosome positions?

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

8.  Mechanisms that specify promoter nucleosome location and identity.

Authors:  Paul D Hartley; Hiten D Madhani
Journal:  Cell       Date:  2009-05-01       Impact factor: 41.582

9.  A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization.

Authors:  Triantaffyllos Gkikopoulos; Pieta Schofield; Vijender Singh; Marina Pinskaya; Jane Mellor; Michaela Smolle; Jerry L Workman; Geoffrey J Barton; Tom Owen-Hughes
Journal:  Science       Date:  2011-09-23       Impact factor: 47.728

10.  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
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  30 in total

1.  The nucleosome acidic patch directly interacts with subunits of the Paf1 and FACT complexes and controls chromatin architecture in vivo.

Authors:  Christine E Cucinotta; A Elizabeth Hildreth; Brendan M McShane; Margaret K Shirra; Karen M Arndt
Journal:  Nucleic Acids Res       Date:  2019-09-19       Impact factor: 16.971

Review 2.  Nucleosome positioning in yeasts: methods, maps, and mechanisms.

Authors:  Corinna Lieleg; Nils Krietenstein; Maria Walker; Philipp Korber
Journal:  Chromosoma       Date:  2014-12-23       Impact factor: 4.316

Review 3.  Protein-DNA binding in high-resolution.

Authors:  Shaun Mahony; B Franklin Pugh
Journal:  Crit Rev Biochem Mol Biol       Date:  2015-06-03       Impact factor: 8.250

Review 4.  Understanding nucleosome dynamics and their links to gene expression and DNA replication.

Authors:  William K M Lai; B Franklin Pugh
Journal:  Nat Rev Mol Cell Biol       Date:  2017-05-24       Impact factor: 94.444

5.  Genomic Nucleosome Organization Reconstituted with Pure Proteins.

Authors:  Nils Krietenstein; Megha Wal; Shinya Watanabe; Bongsoo Park; Craig L Peterson; B Franklin Pugh; Philipp Korber
Journal:  Cell       Date:  2016-10-20       Impact factor: 41.582

6.  Distinct features of lamin A-interacting chromatin domains mapped by ChIP-sequencing from sonicated or micrococcal nuclease-digested chromatin.

Authors:  Eivind G Lund; Isabelle Duband-Goulet; Anja Oldenburg; Brigitte Buendia; Philippe Collas
Journal:  Nucleus       Date:  2015       Impact factor: 4.197

Review 7.  ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions.

Authors:  Terrence S Furey
Journal:  Nat Rev Genet       Date:  2012-10-23       Impact factor: 53.242

8.  The Modifier of Transcription 1 (Mot1) ATPase and Spt16 Histone Chaperone Co-regulate Transcription through Preinitiation Complex Assembly and Nucleosome Organization.

Authors:  Jason D True; Joseph J Muldoon; Melissa N Carver; Kunal Poorey; Savera J Shetty; Stefan Bekiranov; David T Auble
Journal:  J Biol Chem       Date:  2016-05-16       Impact factor: 5.157

9.  Second-generation method for analysis of chromatin binding with formaldehyde-cross-linking kinetics.

Authors:  Hussain Zaidi; Elizabeth A Hoffman; Savera J Shetty; Stefan Bekiranov; David T Auble
Journal:  J Biol Chem       Date:  2017-09-26       Impact factor: 5.157

10.  Histone H3 Threonine 11 Phosphorylation Is Catalyzed Directly by the Meiosis-Specific Kinase Mek1 and Provides a Molecular Readout of Mek1 Activity in Vivo.

Authors:  Ryan Kniewel; Hajime Murakami; Yan Liu; Masaru Ito; Kunihiro Ohta; Nancy M Hollingsworth; Scott Keeney
Journal:  Genetics       Date:  2017-10-06       Impact factor: 4.562
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