Literature DB >> 23021224

Asymmetrically modified nucleosomes.

Philipp Voigt1, Gary LeRoy, William J Drury, Barry M Zee, Jinsook Son, David B Beck, Nicolas L Young, Benjamin A Garcia, Danny Reinberg.   

Abstract

Mononucleosomes, the basic building blocks of chromatin, contain two copies of each core histone. The associated posttranslational modifications regulate essential chromatin-dependent processes, yet whether each histone copy is identically modified in vivo is unclear. We demonstrate that nucleosomes in embryonic stem cells, fibroblasts, and cancer cells exist in both symmetrically and asymmetrically modified populations for histone H3 lysine 27 di/trimethylation (H3K27me2/3) and H4K20me1. Further, we obtained direct physical evidence for bivalent nucleosomes carrying H3K4me3 or H3K36me3 along with H3K27me3, albeit on opposite H3 tails. Bivalency at target genes was resolved upon differentiation of ES cells. Polycomb repressive complex 2-mediated methylation of H3K27 was inhibited when nucleosomes contain symmetrically, but not asymmetrically, placed H3K4me3 or H3K36me3. These findings uncover a potential mechanism for the incorporation of bivalent features into nucleosomes and demonstrate how asymmetry might set the stage to diversify functional nucleosome states.
Copyright © 2012 Elsevier Inc. All rights reserved.

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Year:  2012        PMID: 23021224      PMCID: PMC3498816          DOI: 10.1016/j.cell.2012.09.002

Source DB:  PubMed          Journal:  Cell        ISSN: 0092-8674            Impact factor:   41.582


  37 in total

1.  A bivalent chromatin structure marks key developmental genes in embryonic stem cells.

Authors:  Bradley E Bernstein; Tarjei S Mikkelsen; Xiaohui Xie; Michael Kamal; Dana J Huebert; James Cuff; Ben Fry; Alex Meissner; Marius Wernig; Kathrin Plath; Rudolf Jaenisch; Alexandre Wagschal; Robert Feil; Stuart L Schreiber; Eric S Lander
Journal:  Cell       Date:  2006-04-21       Impact factor: 41.582

Review 2.  How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers.

Authors:  Sean D Taverna; Haitao Li; Alexander J Ruthenburg; C David Allis; Dinshaw J Patel
Journal:  Nat Struct Mol Biol       Date:  2007-11-05       Impact factor: 15.369

3.  Pervasive combinatorial modification of histone H3 in human cells.

Authors:  Benjamin A Garcia; James J Pesavento; Craig A Mizzen; Neil L Kelleher
Journal:  Nat Methods       Date:  2007-05-21       Impact factor: 28.547

4.  Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4.

Authors:  Michiel Vermeulen; Klaas W Mulder; Sergei Denissov; W W M Pim Pijnappel; Frederik M A van Schaik; Radhika A Varier; Marijke P A Baltissen; Henk G Stunnenberg; Matthias Mann; H Th Marc Timmers
Journal:  Cell       Date:  2007-09-20       Impact factor: 41.582

5.  High throughput characterization of combinatorial histone codes.

Authors:  Nicolas L Young; Peter A DiMaggio; Mariana D Plazas-Mayorca; Richard C Baliban; Christodoulos A Floudas; Benjamin A Garcia
Journal:  Mol Cell Proteomics       Date:  2009-08-04       Impact factor: 5.911

6.  A mixed integer linear optimization framework for the identification and quantification of targeted post-translational modifications of highly modified proteins using multiplexed electron transfer dissociation tandem mass spectrometry.

Authors:  Peter A DiMaggio; Nicolas L Young; Richard C Baliban; Benjamin A Garcia; Christodoulos A Floudas
Journal:  Mol Cell Proteomics       Date:  2009-08-07       Impact factor: 5.911

7.  Crystal structure of the nucleosome core particle at 2.8 A resolution.

Authors:  K Luger; A W Mäder; R K Richmond; D F Sargent; T J Richmond
Journal:  Nature       Date:  1997-09-18       Impact factor: 49.962

Review 8.  Chromatin states in pluripotent, differentiated, and reprogrammed cells.

Authors:  Cynthia L Fisher; Amanda G Fisher
Journal:  Curr Opin Genet Dev       Date:  2011-04       Impact factor: 5.578

9.  Monomethylation of histone H4-lysine 20 is involved in chromosome structure and stability and is essential for mouse development.

Authors:  Hisanobu Oda; Ikuhiro Okamoto; Niall Murphy; Jianhua Chu; Sandy M Price; Michael M Shen; Maria Elena Torres-Padilla; Edith Heard; Danny Reinberg
Journal:  Mol Cell Biol       Date:  2009-02-17       Impact factor: 4.272

10.  Role of the polycomb protein EED in the propagation of repressive histone marks.

Authors:  Raphael Margueron; Neil Justin; Katsuhito Ohno; Miriam L Sharpe; Jinsook Son; William J Drury; Philipp Voigt; Stephen R Martin; William R Taylor; Valeria De Marco; Vincenzo Pirrotta; Danny Reinberg; Steven J Gamblin
Journal:  Nature       Date:  2009-09-20       Impact factor: 49.962

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  197 in total

Review 1.  Breaking Symmetry - Asymmetric Histone Inheritance in Stem Cells.

Authors:  Jing Xie; Matthew Wooten; Vuong Tran; Xin Chen
Journal:  Trends Cell Biol       Date:  2017-03-06       Impact factor: 20.808

Review 2.  Signaling Over Distances.

Authors:  Atsushi Saito; Valeria Cavalli
Journal:  Mol Cell Proteomics       Date:  2015-08-21       Impact factor: 5.911

Review 3.  The Necessity of Chromatin: A View in Perspective.

Authors:  Vincenzo Pirrotta
Journal:  Cold Spring Harb Perspect Biol       Date:  2016-01-04       Impact factor: 10.005

4.  Streamlined discovery of cross-linked chromatin complexes and associated histone modifications by mass spectrometry.

Authors:  Barry M Zee; Artyom A Alekseyenko; Kyle A McElroy; Mitzi I Kuroda
Journal:  Proc Natl Acad Sci U S A       Date:  2016-02-01       Impact factor: 11.205

Review 5.  A double take on bivalent promoters.

Authors:  Philipp Voigt; Wee-Wei Tee; Danny Reinberg
Journal:  Genes Dev       Date:  2013-06-15       Impact factor: 11.361

Review 6.  SET for life: biochemical activities and biological functions of SET domain-containing proteins.

Authors:  Hans-Martin Herz; Alexander Garruss; Ali Shilatifard
Journal:  Trends Biochem Sci       Date:  2013-10-20       Impact factor: 13.807

7.  Histone H3K27 trimethylation inhibits H3 binding and function of SET1-like H3K4 methyltransferase complexes.

Authors:  Dae-Hwan Kim; Zhanyun Tang; Miho Shimada; Beat Fierz; Brian Houck-Loomis; Maya Bar-Dagen; Seunghee Lee; Soo-Kyung Lee; Tom W Muir; Robert G Roeder; Jae W Lee
Journal:  Mol Cell Biol       Date:  2013-10-14       Impact factor: 4.272

8.  Histone H2A ubiquitination inhibits the enzymatic activity of H3 lysine 36 methyltransferases.

Authors:  Gang Yuan; Ben Ma; Wen Yuan; Zhuqiang Zhang; Ping Chen; Xiaojun Ding; Li Feng; Xiaohua Shen; She Chen; Guohong Li; Bing Zhu
Journal:  J Biol Chem       Date:  2013-09-09       Impact factor: 5.157

9.  Distinct Cellular Assembly Stoichiometry of Polycomb Complexes on Chromatin Revealed by Single-molecule Chromatin Immunoprecipitation Imaging.

Authors:  Roubina Tatavosian; Chao Yu Zhen; Huy Nguyen Duc; Maggie M Balas; Aaron M Johnson; Xiaojun Ren
Journal:  J Biol Chem       Date:  2015-09-17       Impact factor: 5.157

10.  Proteomic approaches for cancer epigenetics research.

Authors:  Dylan M Marchione; Benjamin A Garcia; John Wojcik
Journal:  Expert Rev Proteomics       Date:  2018-11-27       Impact factor: 3.940

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