Literature DB >> 20923397

Keeping it in the family: diverse histone recognition by conserved structural folds.

Kyoko L Yap1, Ming-Ming Zhou.   

Abstract

Epigenetic regulation of gene transcription relies on an array of recurring structural domains that have evolved to recognize post-translational modifications on histones. The roles of bromodomains, PHD fingers, and the Royal family domains in the recognition of histone modifications to direct transcription have been well characterized. However, only through recent structural studies has it been realized that these basic folds are capable of interacting with increasingly more complex histone modification landscapes, illuminating how nature has concocted a way to accomplish more with less. Here we review the recent biochemical and structural studies of several conserved folds that recognize modified as well as unmodified histone sequences, and discuss their implications on gene expression.

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Year:  2010        PMID: 20923397      PMCID: PMC2988946          DOI: 10.3109/10409238.2010.512001

Source DB:  PubMed          Journal:  Crit Rev Biochem Mol Biol        ISSN: 1040-9238            Impact factor:   8.250


  147 in total

1.  WDR5, a complexed protein.

Authors:  Raymond C Trievel; Ali Shilatifard
Journal:  Nat Struct Mol Biol       Date:  2009-07       Impact factor: 15.369

2.  Structure and site-specific recognition of histone H3 by the PHD finger of human autoimmune regulator.

Authors:  Suvobrata Chakravarty; Lei Zeng; Ming-Ming Zhou
Journal:  Structure       Date:  2009-05-13       Impact factor: 5.006

3.  Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression.

Authors:  Ahmad M Khalil; Mitchell Guttman; Maite Huarte; Manuel Garber; Arjun Raj; Dianali Rivea Morales; Kelly Thomas; Aviva Presser; Bradley E Bernstein; Alexander van Oudenaarden; Aviv Regev; Eric S Lander; John L Rinn
Journal:  Proc Natl Acad Sci U S A       Date:  2009-07-01       Impact factor: 11.205

Review 4.  The role of human bromodomains in chromatin biology and gene transcription.

Authors:  Roberto Sanchez; Ming-Ming Zhou
Journal:  Curr Opin Drug Discov Devel       Date:  2009-09

5.  Cooperative binding of two acetylation marks on a histone tail by a single bromodomain.

Authors:  Jeanne Morinière; Sophie Rousseaux; Ulrich Steuerwald; Montserrat Soler-López; Sandrine Curtet; Anne-Laure Vitte; Jérôme Govin; Jonathan Gaucher; Karin Sadoul; Darren J Hart; Jeroen Krijgsveld; Saadi Khochbin; Christoph W Müller; Carlo Petosa
Journal:  Nature       Date:  2009-10-01       Impact factor: 49.962

6.  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

7.  Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger.

Authors:  Gang G Wang; Jikui Song; Zhanxin Wang; Holger L Dormann; Fabio Casadio; Haitao Li; Jun-Li Luo; Dinshaw J Patel; C David Allis
Journal:  Nature       Date:  2009-06-11       Impact factor: 49.962

8.  The solution structure of the first PHD finger of autoimmune regulator in complex with non-modified histone H3 tail reveals the antagonistic role of H3R2 methylation.

Authors:  Francesca Chignola; Massimiliano Gaetani; Ana Rebane; Tõnis Org; Luca Mollica; Chiara Zucchelli; Andrea Spitaleri; Valeria Mannella; Pärt Peterson; Giovanna Musco
Journal:  Nucleic Acids Res       Date:  2009-03-17       Impact factor: 16.971

9.  Molecular recognition of histone lysine methylation by the Polycomb group repressor dSfmbt.

Authors:  Clemens Grimm; Raquel Matos; Nga Ly-Hartig; Ulrich Steuerwald; Doris Lindner; Vladimir Rybin; Jürg Müller; Christoph W Müller
Journal:  EMBO J       Date:  2009-06-04       Impact factor: 11.598

10.  Structural studies of a four-MBT repeat protein MBTD1.

Authors:  Jitka Eryilmaz; Patricia Pan; Maria F Amaya; Abdellah Allali-Hassani; Aiping Dong; Melanie A Adams-Cioaba; Farrell Mackenzie; Masoud Vedadi; Jinrong Min
Journal:  PLoS One       Date:  2009-10-20       Impact factor: 3.240

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  49 in total

1.  Druggability of methyl-lysine binding sites.

Authors:  C Santiago; K Nguyen; M Schapira
Journal:  J Comput Aided Mol Des       Date:  2011-12-07       Impact factor: 3.686

Review 2.  The PHD finger: a versatile epigenome reader.

Authors:  Roberto Sanchez; Ming-Ming Zhou
Journal:  Trends Biochem Sci       Date:  2011-04-21       Impact factor: 13.807

Review 3.  Molecular mechanisms and potential functions of histone demethylases.

Authors:  Susanne Marije Kooistra; Kristian Helin
Journal:  Nat Rev Mol Cell Biol       Date:  2012-04-04       Impact factor: 94.444

Review 4.  Structure and mechanisms of lysine methylation recognition by the chromodomain in gene transcription.

Authors:  Kyoko L Yap; Ming-Ming Zhou
Journal:  Biochemistry       Date:  2011-02-23       Impact factor: 3.162

Review 5.  Transcription-associated histone modifications and cryptic transcription.

Authors:  Michaela Smolle; Jerry L Workman
Journal:  Biochim Biophys Acta       Date:  2012-09-07

Review 6.  Writers and readers of histone acetylation: structure, mechanism, and inhibition.

Authors:  Ronen Marmorstein; Ming-Ming Zhou
Journal:  Cold Spring Harb Perspect Biol       Date:  2014-07-01       Impact factor: 10.005

Review 7.  Protein and DNA modifications: evolutionary imprints of bacterial biochemical diversification and geochemistry on the provenance of eukaryotic epigenetics.

Authors:  L Aravind; A Maxwell Burroughs; Dapeng Zhang; Lakshminarayan M Iyer
Journal:  Cold Spring Harb Perspect Biol       Date:  2014-07-01       Impact factor: 10.005

Review 8.  Regulation of histone methylation by noncoding RNAs.

Authors:  Richard I Joh; Christina M Palmieri; Ian T Hill; Mo Motamedi
Journal:  Biochim Biophys Acta       Date:  2014-06-17

Review 9.  Dynamic integration of splicing within gene regulatory pathways.

Authors:  Ulrich Braunschweig; Serge Gueroussov; Alex M Plocik; Brenton R Graveley; Benjamin J Blencowe
Journal:  Cell       Date:  2013-03-14       Impact factor: 41.582

10.  IRF5 regulates unique subset of genes in dendritic cells during West Nile virus infection.

Authors:  Kwan T Chow; Connor Driscoll; Yueh-Ming Loo; Megan Knoll; Michael Gale
Journal:  J Leukoc Biol       Date:  2018-11-20       Impact factor: 4.962

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