Literature DB >> 18849650

Unraveling the histone's potential: a proteomics perspective.

Justin Brumbaugh1, Doug Phanstiel, Joshua J Coon.   

Abstract

Post translational modification (PTM) of histones has long been associated with epigenetic regulation. Although genomic approaches have established correlation between a handful of histone PTMs and transcriptional states, only recently have advancements in proteomics provided the tools necessary to study histone proteins and their relevant modifications in this context. Using mass spectrometry, researchers have demonstrated the ability to determine the full repertoire of histone PTMs, their residue specific location, the combinations in which they exist, and the proteins that interact with these combinations. Moving forward it will be imperative to develop novel approaches that combine proteomic and genomic technologies to determine the functional significance of these combinations of modifications. Assays with increased specificity will resolve more focused biological questions and determine to what extent, and by what mechanisms, histones influence transcription.

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Year:  2008        PMID: 18849650      PMCID: PMC2662511          DOI: 10.4161/epi.3.5.7005

Source DB:  PubMed          Journal:  Epigenetics        ISSN: 1559-2294            Impact factor:   4.528


  57 in total

1.  The language of covalent histone modifications.

Authors:  B D Strahl; C D Allis
Journal:  Nature       Date:  2000-01-06       Impact factor: 49.962

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.  WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development.

Authors:  Joanna Wysocka; Tomek Swigut; Thomas A Milne; Yali Dou; Xin Zhang; Alma L Burlingame; Robert G Roeder; Ali H Brivanlou; C David Allis
Journal:  Cell       Date:  2005-06-17       Impact factor: 41.582

4.  Protein identification using sequential ion/ion reactions and tandem mass spectrometry.

Authors:  Joshua J Coon; Beatrix Ueberheide; John E P Syka; Deanna D Dryhurst; Juan Ausio; Jeffrey Shabanowitz; Donald F Hunt
Journal:  Proc Natl Acad Sci U S A       Date:  2005-06-27       Impact factor: 11.205

5.  Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells.

Authors:  Guangjin Pan; Shulan Tian; Jeff Nie; Chuhu Yang; Victor Ruotti; Hairong Wei; Gudrun A Jonsdottir; Ron Stewart; James A Thomson
Journal:  Cell Stem Cell       Date:  2007-09-13       Impact factor: 24.633

6.  Quantitative analysis of complex protein mixtures using isotope-coded affinity tags.

Authors:  S P Gygi; B Rist; S A Gerber; F Turecek; M H Gelb; R Aebersold
Journal:  Nat Biotechnol       Date:  1999-10       Impact factor: 54.908

7.  Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer.

Authors:  Mario F Fraga; Esteban Ballestar; Ana Villar-Garea; Manuel Boix-Chornet; Jesus Espada; Gunnar Schotta; Tiziana Bonaldi; Claire Haydon; Santiago Ropero; Kevin Petrie; N Gopalakrishna Iyer; Alberto Pérez-Rosado; Enrique Calvo; Juan A Lopez; Amparo Cano; Maria J Calasanz; Dolors Colomer; Miguel Angel Piris; Natalie Ahn; Axel Imhof; Carlos Caldas; Thomas Jenuwein; Manel Esteller
Journal:  Nat Genet       Date:  2005-03-13       Impact factor: 38.330

8.  Global histone modification patterns predict risk of prostate cancer recurrence.

Authors:  David B Seligson; Steve Horvath; Tao Shi; Hong Yu; Sheila Tze; Michael Grunstein; Siavash K Kurdistani
Journal:  Nature       Date:  2005-06-30       Impact factor: 49.962

9.  Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation.

Authors:  Marilyn G Pray-Grant; Jeremy A Daniel; David Schieltz; John R Yates; Patrick A Grant
Journal:  Nature       Date:  2005-01-12       Impact factor: 49.962

10.  Proteomic and genomic characterization of chromatin complexes at a boundary.

Authors:  Alan J Tackett; David J Dilworth; Megan J Davey; Michael O'Donnell; John D Aitchison; Michael P Rout; Brian T Chait
Journal:  J Cell Biol       Date:  2005-04-11       Impact factor: 10.539

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  9 in total

Review 1.  Chemical and biochemical approaches in the study of histone methylation and demethylation.

Authors:  Keqin Kathy Li; Cheng Luo; Dongxia Wang; Hualiang Jiang; Y George Zheng
Journal:  Med Res Rev       Date:  2012-07       Impact factor: 12.944

2.  Effects of Histone Deacetylase Inhibitors on Modulating H3K4 Methylation Marks - A Novel Cross-Talk Mechanism between Histone-Modifying Enzymes.

Authors:  Po-Hsien Huang; Christoph Plass; Ching-Shih Chen
Journal:  Mol Cell Pharmacol       Date:  2011

Review 3.  Proteomics and pluripotency.

Authors:  Justin Brumbaugh; Christopher M Rose; Douglas H Phanstiel; James A Thomson; Joshua J Coon
Journal:  Crit Rev Biochem Mol Biol       Date:  2011-10-15       Impact factor: 8.250

Review 4.  Breaking the histone code with quantitative mass spectrometry.

Authors:  Laura-Mae P Britton; Michelle Gonzales-Cope; Barry M Zee; Benjamin A Garcia
Journal:  Expert Rev Proteomics       Date:  2011-10       Impact factor: 3.940

5.  Histone deacetylase inhibitors stimulate histone H3 lysine 4 methylation in part via transcriptional repression of histone H3 lysine 4 demethylases.

Authors:  Po-Hsien Huang; Chun-Han Chen; Chih-Chien Chou; Aaron M Sargeant; Samuel K Kulp; Che-Ming Teng; John C Byrd; Ching-Shih Chen
Journal:  Mol Pharmacol       Date:  2010-10-19       Impact factor: 4.436

Review 6.  Deciphering post-translational modification codes.

Authors:  Adam P Lothrop; Matthew P Torres; Stephen M Fuchs
Journal:  FEBS Lett       Date:  2013-02-10       Impact factor: 4.124

7.  H3 lysine 4 is acetylated at active gene promoters and is regulated by H3 lysine 4 methylation.

Authors:  Benoit Guillemette; Paul Drogaris; Hsiu-Hsu Sophia Lin; Harry Armstrong; Kyoko Hiragami-Hamada; Axel Imhof; Eric Bonneil; Pierre Thibault; Alain Verreault; Richard J Festenstein
Journal:  PLoS Genet       Date:  2011-03-31       Impact factor: 5.917

Review 8.  Transcriptional reprogramming in cellular quiescence.

Authors:  Benjamin Roche; Benoit Arcangioli; Robert Martienssen
Journal:  RNA Biol       Date:  2017-05-12       Impact factor: 4.652

9.  Finding one's way in proteomics: a protein species nomenclature.

Authors:  Hartmut Schlüter; Rolf Apweiler; Hermann-Georg Holzhütter; Peter R Jungblut
Journal:  Chem Cent J       Date:  2009-09-09       Impact factor: 4.215

  9 in total

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