Literature DB >> 25311124

Purification of specific chromatin loci for proteomic analysis.

Stephanie D Byrum1, Sean D Taverna, Alan J Tackett.   

Abstract

Purification of small, native chromatin regions for proteomic identification of specifically bound proteins and histone posttranslational modifications is a powerful approach for studying mechanisms of chromosome metabolism. Here we detail a Chromatin Affinity Purification with Mass Spectrometry (ChAP-MS) approach for affinity purification of 1 kb regions of chromatin for targeted proteomic analysis. This approach utilizes quantitative, high resolution mass spectrometry to categorize proteins and histone posttranslational modifications co-enriched with the given chromatin region as either "specific" to the targeted chromatin or "nonspecific" contamination. In this way, the ChAP-MS approach can help define and redefine mechanisms of chromatin-templated activities.

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Year:  2015        PMID： 25311124      PMCID： PMC4324170          DOI： 10.1007/978-1-4939-1680-1_8

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


  10 in total

1.  Genome-wide location and function of DNA binding proteins.

Authors:  B Ren; F Robert; J J Wyrick; O Aparicio; E G Jennings; I Simon; J Zeitlinger; J Schreiber; N Hannett; E Kanin; T L Volkert; C J Wilson; S P Bell; R A Young
Journal:  Science       Date:  2000-12-22       Impact factor: 47.728

2.  Genome-wide map of nucleosome acetylation and methylation in yeast.

Authors:  Dmitry K Pokholok; Christopher T Harbison; Stuart Levine; Megan Cole; Nancy M Hannett; Tong Ihn Lee; George W Bell; Kimberly Walker; P Alex Rolfe; Elizabeth Herbolsheimer; Julia Zeitlinger; Fran Lewitter; David K Gifford; Richard A Young
Journal:  Cell       Date:  2005-08-26       Impact factor: 41.582

3.  High-resolution profiling of histone methylations in the human genome.

Authors:  Artem Barski; Suresh Cuddapah; Kairong Cui; Tae-Young Roh; Dustin E Schones; Zhibin Wang; Gang Wei; Iouri Chepelev; Keji Zhao
Journal:  Cell       Date:  2007-05-18       Impact factor: 41.582

4.  Formaldehyde cross-linking and immunoprecipitation demonstrate developmental changes in H1 association with transcriptionally active genes.

Authors:  P C Dedon; J A Soults; C D Allis; M A Gorovsky
Journal:  Mol Cell Biol       Date:  1991-03       Impact factor: 4.272

5.  Quantitative analysis of histone exchange for transcriptionally active chromatin.

Authors:  Sean D Taverna; Stephanie D Byrum; Alan J Tackett
Journal:  J Clin Bioinforma       Date:  2011-07-07

6.  Analysis of stable and transient protein-protein interactions.

Authors:  Stephanie Byrum; Sherri K Smart; Signe Larson; Alan J Tackett
Journal:  Methods Mol Biol       Date:  2012

7.  ChAP-MS: a method for identification of proteins and histone posttranslational modifications at a single genomic locus.

Authors:  Stephanie D Byrum; Ana Raman; Sean D Taverna; Alan J Tackett
Journal:  Cell Rep       Date:  2012-07-20       Impact factor: 9.423

8.  Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.

Authors:  Gordon Robertson; Martin Hirst; Matthew Bainbridge; Misha Bilenky; Yongjun Zhao; Thomas Zeng; Ghia Euskirchen; Bridget Bernier; Richard Varhol; Allen Delaney; Nina Thiessen; Obi L Griffith; Ann He; Marco Marra; Michael Snyder; Steven Jones
Journal:  Nat Methods       Date:  2007-06-11       Impact factor: 28.547

9.  Genome-wide mapping of in vivo protein-DNA interactions.

Authors:  David S Johnson; Ali Mortazavi; Richard M Myers; Barbara Wold
Journal:  Science       Date:  2007-05-31       Impact factor: 47.728

10.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.

Authors:  Tarjei S Mikkelsen; Manching Ku; David B Jaffe; Biju Issac; Erez Lieberman; Georgia Giannoukos; Pablo Alvarez; William Brockman; Tae-Kyung Kim; Richard P Koche; William Lee; Eric Mendenhall; Aisling O'Donovan; Aviva Presser; Carsten Russ; Xiaohui Xie; Alexander Meissner; Marius Wernig; Rudolf Jaenisch; Chad Nusbaum; Eric S Lander; Bradley E Bernstein
Journal:  Nature       Date:  2007-07-01       Impact factor: 49.962
  10 in total
  3 in total

Review 1.  Progesterone Receptor Regulation of Uterine Adaptation for Pregnancy.

Authors:  San-Pin Wu; Rong Li; Francesco J DeMayo
Journal:  Trends Endocrinol Metab       Date:  2018-04-25       Impact factor: 12.015

Review 2.  Formaldehyde crosslinking: a tool for the study of chromatin complexes.

Authors:  Elizabeth A Hoffman; Brian L Frey; Lloyd M Smith; David T Auble
Journal:  J Biol Chem       Date:  2015-09-09       Impact factor: 5.157

3.  Proteomic identification of histone post-translational modifications and proteins enriched at a DNA double-strand break.

Authors:  Pingping Wang; Stephanie Byrum; Faith C Fowler; Sangita Pal; Alan J Tackett; Jessica K Tyler
Journal:  Nucleic Acids Res       Date:  2017-11-02       Impact factor: 16.971
  3 in total

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