Literature DB >> 20855937

Chromatin landscape: methylation beyond transcription.

Joshua C Black1, Johnathan R Whetstine.   

Abstract

The nucleus is organized and compartmentalized into a highly ordered structure that contains DNA, RNA, chromosomal and histone proteins. The dynamics associated with these various components are responsible for making sure that the DNA is properly duplicated, genes are properly transcribed, and the genome is stabilized. It is no surprise that alterations in these various components are directly associated with pathologies like cancer. This Point of View focuses on the role the chromatin modification landscape, especially histone 3 lysine 9 methylation (H3K9me), and heterochromatin proteins (HP1) play in regulating DNA-templated processes, with a particular focus on their role at non-genic regions and effects on chromatin structure. These observations will be further extended to the role that alterations in chromatin landscape will contribute to diseases. This Point of View emphasizes that alterations in histone modification landscapes are not only relevant to transcription but have broad range implications in chromatin structure, nuclear architecture, cell cycle, genome stability and disease progression.

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Year:  2011        PMID: 20855937      PMCID: PMC3052912          DOI: 10.4161/epi.6.1.13331

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


  59 in total

1.  Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones.

Authors:  Roger B Deal; Jorja G Henikoff; Steven Henikoff
Journal:  Science       Date:  2010-05-28       Impact factor: 47.728

2.  Stability of histone modifications across mammalian genomes: implications for 'epigenetic' marking.

Authors:  Benjamin M Lee; Louis C Mahadevan
Journal:  J Cell Biochem       Date:  2009-09-01       Impact factor: 4.429

3.  Sequencing newly replicated DNA reveals widespread plasticity in human replication timing.

Authors:  R Scott Hansen; Sean Thomas; Richard Sandstrom; Theresa K Canfield; Robert E Thurman; Molly Weaver; Michael O Dorschner; Stanley M Gartler; John A Stamatoyannopoulos
Journal:  Proc Natl Acad Sci U S A       Date:  2009-12-04       Impact factor: 11.205

4.  Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading.

Authors:  Heather K MacAlpine; Raluca Gordân; Sara K Powell; Alexander J Hartemink; David M MacAlpine
Journal:  Genome Res       Date:  2009-12-07       Impact factor: 9.043

5.  Heterochromatin protein 1 (HP1) modulates replication timing of the Drosophila genome.

Authors:  Michaela Schwaiger; Hubertus Kohler; Edward J Oakeley; Michael B Stadler; Dirk Schübeler
Journal:  Genome Res       Date:  2010-04-30       Impact factor: 9.043

Review 6.  Temporal regulation of DNA replication in mammalian cells.

Authors:  Juan Méndez
Journal:  Crit Rev Biochem Mol Biol       Date:  2009 Sep-Oct       Impact factor: 8.250

7.  Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Authors:  Erez Lieberman-Aiden; Nynke L van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R Lajoie; Peter J Sabo; Michael O Dorschner; Richard Sandstrom; Bradley Bernstein; M A Bender; Mark Groudine; Andreas Gnirke; John Stamatoyannopoulos; Leonid A Mirny; Eric S Lander; Job Dekker
Journal:  Science       Date:  2009-10-09       Impact factor: 47.728

8.  Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer.

Authors:  Gijs van Haaften; Gillian L Dalgliesh; Helen Davies; Lina Chen; Graham Bignell; Chris Greenman; Sarah Edkins; Claire Hardy; Sarah O'Meara; Jon Teague; Adam Butler; Jonathan Hinton; Calli Latimer; Jenny Andrews; Syd Barthorpe; Dave Beare; Gemma Buck; Peter J Campbell; Jennifer Cole; Simon Forbes; Mingming Jia; David Jones; Chai Yin Kok; Catherine Leroy; Meng-Lay Lin; David J McBride; Mark Maddison; Simon Maquire; Kirsten McLay; Andrew Menzies; Tatiana Mironenko; Lee Mulderrig; Laura Mudie; Erin Pleasance; Rebecca Shepherd; Raffaella Smith; Lucy Stebbings; Philip Stephens; Gurpreet Tang; Patrick S Tarpey; Rachel Turner; Kelly Turrell; Jennifer Varian; Sofie West; Sara Widaa; Paul Wray; V Peter Collins; Koichi Ichimura; Simon Law; John Wong; Siu Tsan Yuen; Suet Yi Leung; Giovanni Tonon; Ronald A DePinho; Yu-Tzu Tai; Kenneth C Anderson; Richard J Kahnoski; Aaron Massie; Sok Kean Khoo; Bin Tean Teh; Michael R Stratton; P Andrew Futreal
Journal:  Nat Genet       Date:  2009-03-29       Impact factor: 38.330

9.  Genomic study of replication initiation in human chromosomes reveals the influence of transcription regulation and chromatin structure on origin selection.

Authors:  Neerja Karnani; Christopher M Taylor; Ankit Malhotra; Anindya Dutta
Journal:  Mol Biol Cell       Date:  2009-12-02       Impact factor: 4.138

10.  Determination of enriched histone modifications in non-genic portions of the human genome.

Authors:  Jeffrey A Rosenfeld; Zhibin Wang; Dustin E Schones; Keji Zhao; Rob DeSalle; Michael Q Zhang
Journal:  BMC Genomics       Date:  2009-03-31       Impact factor: 3.969

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  43 in total

1.  The endoglycosidase heparanase enters the nucleus of T lymphocytes and modulates H3 methylation at actively transcribed genes via the interplay with key chromatin modifying enzymes.

Authors:  Yi Qing He; Elissa L Sutcliffe; Karen L Bunting; Jasmine Li; Katharine J Goodall; Ivan K A Poon; Mark D Hulett; Craig Freeman; Anjum Zafar; Russell L McInnes; Toshiki Taya; Christopher R Parish; Sudha Rao
Journal:  Transcription       Date:  2012 May-Jun

2.  Endogenous nuclear RNAi mediates behavioral adaptation to odor.

Authors:  Bi-Tzen Juang; Chen Gu; Linda Starnes; Francesca Palladino; Andrei Goga; Scott Kennedy; Noelle D L'Etoile
Journal:  Cell       Date:  2013-08-29       Impact factor: 41.582

3.  Prolonged re-expression of the hypermethylated gene EPB41L3 using artificial transcription factors and epigenetic drugs.

Authors:  Christian Huisman; Monique G P van der Wijst; Fahimeh Falahi; Juul Overkamp; Gellért Karsten; Martijn M Terpstra; Klaas Kok; Ate G J van der Zee; Ed Schuuring; G Bea A Wisman; Marianne G Rots
Journal:  Epigenetics       Date:  2015-04-01       Impact factor: 4.528

4.  Pericentric heterochromatin generated by HP1 protein interaction-defective histone methyltransferase Suv39h1.

Authors:  Daisuke Muramatsu; Prim B Singh; Hiroshi Kimura; Makoto Tachibana; Yoichi Shinkai
Journal:  J Biol Chem       Date:  2013-07-07       Impact factor: 5.157

Review 5.  A drive in SUVs: From development to disease.

Authors:  Vinay Kumar Rao; Ananya Pal; Reshma Taneja
Journal:  Epigenetics       Date:  2017-01-20       Impact factor: 4.528

6.  Protein interactions, post-translational modifications and topologies in human cells.

Authors:  Juan D Chavez; Chad R Weisbrod; Chunxiang Zheng; Jimmy K Eng; James E Bruce
Journal:  Mol Cell Proteomics       Date:  2013-01-25       Impact factor: 5.911

7.  CRL4-like Clr4 complex in Schizosaccharomyces pombe depends on an exposed surface of Dos1 for heterochromatin silencing.

Authors:  Canan Kuscu; Mikel Zaratiegui; Hyun Soo Kim; David A Wah; Robert A Martienssen; Thomas Schalch; Leemor Joshua-Tor
Journal:  Proc Natl Acad Sci U S A       Date:  2014-01-21       Impact factor: 11.205

8.  A complex interplay between SAM synthetase and the epigenetic regulator SIN3 controls metabolism and transcription.

Authors:  Mengying Liu; Nirmalya Saha; Ambikai Gajan; Nadia Saadat; Smiti V Gupta; Lori A Pile
Journal:  J Biol Chem       Date:  2019-11-27       Impact factor: 5.157

9.  The Polycomb Repressive Complex 1 Protein BMI1 Is Required for Constitutive Heterochromatin Formation and Silencing in Mammalian Somatic Cells.

Authors:  Mohamed Abdouh; Roy Hanna; Jida El Hajjar; Anthony Flamier; Gilbert Bernier
Journal:  J Biol Chem       Date:  2015-10-14       Impact factor: 5.157

Review 10.  Histone lysine methylation dynamics: establishment, regulation, and biological impact.

Authors:  Joshua C Black; Capucine Van Rechem; Johnathan R Whetstine
Journal:  Mol Cell       Date:  2012-11-30       Impact factor: 17.970

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