Literature DB >> 23200123

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

Joshua C Black1, Capucine Van Rechem, Johnathan R Whetstine.   

Abstract

Histone lysine methylation has emerged as a critical player in the regulation of gene expression, cell cycle, genome stability, and nuclear architecture. Over the past decade, a tremendous amount of progress has led to the characterization of methyl modifications and the lysine methyltransferases (KMTs) and lysine demethylases (KDMs) that regulate them. Here, we review the discovery and characterization of the KMTs and KDMs and the methyl modifications they regulate. We discuss the localization of the KMTs and KDMs as well as the distribution of lysine methylation throughout the genome. We highlight how these data have shaped our view of lysine methylation as a key determinant of complex chromatin states. Finally, we discuss the regulation of KMTs and KDMs by proteasomal degradation, posttranscriptional mechanisms, and metabolic status. We propose key questions for the field and highlight areas that we predict will yield exciting discoveries in the years to come.
Copyright © 2012 Elsevier Inc. All rights reserved.

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Year:  2012        PMID: 23200123      PMCID: PMC3861058          DOI: 10.1016/j.molcel.2012.11.006

Source DB:  PubMed          Journal:  Mol Cell        ISSN: 1097-2765            Impact factor:   17.970


  144 in total

1.  JmjC: cupin metalloenzyme-like domains in jumonji, hairless and phospholipase A2beta.

Authors:  P M Clissold; C P Ponting
Journal:  Trends Biochem Sci       Date:  2001-01       Impact factor: 13.807

2.  Partitioning and plasticity of repressive histone methylation states in mammalian chromatin.

Authors:  Antoine H F M Peters; Stefan Kubicek; Karl Mechtler; Roderick J O'Sullivan; Alwin A H A Derijck; Laura Perez-Burgos; Alexander Kohlmaier; Susanne Opravil; Makoto Tachibana; Yoichi Shinkai; Joost H A Martens; Thomas Jenuwein
Journal:  Mol Cell       Date:  2003-12       Impact factor: 17.970

3.  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

4.  LOX out, histones: a new enzyme is nipping at your tails.

Authors:  Joshua C Black; Johnathan R Whetstine
Journal:  Mol Cell       Date:  2012-05-11       Impact factor: 17.970

5.  Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Authors:  Mark B Gerstein; Zhi John Lu; Eric L Van Nostrand; Chao Cheng; Bradley I Arshinoff; Tao Liu; Kevin Y Yip; Rebecca Robilotto; Andreas Rechtsteiner; Kohta Ikegami; Pedro Alves; Aurelien Chateigner; Marc Perry; Mitzi Morris; Raymond K Auerbach; Xin Feng; Jing Leng; Anne Vielle; Wei Niu; Kahn Rhrissorrakrai; Ashish Agarwal; Roger P Alexander; Galt Barber; Cathleen M Brdlik; Jennifer Brennan; Jeremy Jean Brouillet; Adrian Carr; Ming-Sin Cheung; Hiram Clawson; Sergio Contrino; Luke O Dannenberg; Abby F Dernburg; Arshad Desai; Lindsay Dick; Andréa C Dosé; Jiang Du; Thea Egelhofer; Sevinc Ercan; Ghia Euskirchen; Brent Ewing; Elise A Feingold; Reto Gassmann; Peter J Good; Phil Green; Francois Gullier; Michelle Gutwein; Mark S Guyer; Lukas Habegger; Ting Han; Jorja G Henikoff; Stefan R Henz; Angie Hinrichs; Heather Holster; Tony Hyman; A Leo Iniguez; Judith Janette; Morten Jensen; Masaomi Kato; W James Kent; Ellen Kephart; Vishal Khivansara; Ekta Khurana; John K Kim; Paulina Kolasinska-Zwierz; Eric C Lai; Isabel Latorre; Amber Leahey; Suzanna Lewis; Paul Lloyd; Lucas Lochovsky; Rebecca F Lowdon; Yaniv Lubling; Rachel Lyne; Michael MacCoss; Sebastian D Mackowiak; Marco Mangone; Sheldon McKay; Desirea Mecenas; Gennifer Merrihew; David M Miller; Andrew Muroyama; John I Murray; Siew-Loon Ooi; Hoang Pham; Taryn Phippen; Elicia A Preston; Nikolaus Rajewsky; Gunnar Rätsch; Heidi Rosenbaum; Joel Rozowsky; Kim Rutherford; Peter Ruzanov; Mihail Sarov; Rajkumar Sasidharan; Andrea Sboner; Paul Scheid; Eran Segal; Hyunjin Shin; Chong Shou; Frank J Slack; Cindie Slightam; Richard Smith; William C Spencer; E O Stinson; Scott Taing; Teruaki Takasaki; Dionne Vafeados; Ksenia Voronina; Guilin Wang; Nicole L Washington; Christina M Whittle; Beijing Wu; Koon-Kiu Yan; Georg Zeller; Zheng Zha; Mei Zhong; Xingliang Zhou; Julie Ahringer; Susan Strome; Kristin C Gunsalus; Gos Micklem; X Shirley Liu; Valerie Reinke; Stuart K Kim; LaDeana W Hillier; Steven Henikoff; Fabio Piano; Michael Snyder; Lincoln Stein; Jason D Lieb; Robert H Waterston
Journal:  Science       Date:  2010-12-22       Impact factor: 47.728

6.  Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells.

Authors:  Jamy C Peng; Anton Valouev; Tomek Swigut; Junmei Zhang; Yingming Zhao; Arend Sidow; Joanna Wysocka
Journal:  Cell       Date:  2009-12-24       Impact factor: 41.582

7.  The C-terminal domain of RNA polymerase II is modified by site-specific methylation.

Authors:  Robert J Sims; Luis Alejandro Rojas; David B Beck; Roberto Bonasio; Roland Schüller; William J Drury; Dirk Eick; Danny Reinberg
Journal:  Science       Date:  2011-04-01       Impact factor: 47.728

8.  Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of α-ketoglutarate-dependent dioxygenases.

Authors:  Wei Xu; Hui Yang; Ying Liu; Ying Yang; Ping Wang; Se-Hee Kim; Shinsuke Ito; Chen Yang; Pu Wang; Meng-Tao Xiao; Li-xia Liu; Wen-qing Jiang; Jing Liu; Jin-ye Zhang; Bin Wang; Stephen Frye; Yi Zhang; Yan-hui Xu; Qun-ying Lei; Kun-Liang Guan; Shi-min Zhao; Yue Xiong
Journal:  Cancer Cell       Date:  2011-01-18       Impact factor: 38.585

9.  Trans-generational epigenetic regulation of C. elegans primordial germ cells.

Authors:  Hirofumi Furuhashi; Teruaki Takasaki; Andreas Rechtsteiner; Tengguo Li; Hiroshi Kimura; Paula M Checchi; Susan Strome; William G Kelly
Journal:  Epigenetics Chromatin       Date:  2010-08-12       Impact factor: 4.954

10.  Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.

Authors:  Kimberly R Blahnik; Lei Dou; Lorigail Echipare; Sushma Iyengar; Henriette O'Geen; Erica Sanchez; Yongjun Zhao; Marco A Marra; Martin Hirst; Joseph F Costello; Ian Korf; Peggy J Farnham
Journal:  PLoS One       Date:  2011-02-15       Impact factor: 3.240

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  415 in total

Review 1.  Functional Crosstalk Between Lysine Methyltransferases on Histone Substrates: The Case of G9A/GLP and Polycomb Repressive Complex 2.

Authors:  Chiara Mozzetta; Julien Pontis; Slimane Ait-Si-Ali
Journal:  Antioxid Redox Signal       Date:  2014-12-19       Impact factor: 8.401

2.  A Role for Widely Interspaced Zinc Finger (WIZ) in Retention of the G9a Methyltransferase on Chromatin.

Authors:  Jeremy M Simon; Joel S Parker; Feng Liu; Scott B Rothbart; Slimane Ait-Si-Ali; Brian D Strahl; Jian Jin; Ian J Davis; Amber L Mosley; Samantha G Pattenden
Journal:  J Biol Chem       Date:  2015-09-03       Impact factor: 5.157

Review 3.  Epigenetic plasticity and the hallmarks of cancer.

Authors:  William A Flavahan; Elizabeth Gaskell; Bradley E Bernstein
Journal:  Science       Date:  2017-07-21       Impact factor: 47.728

Review 4.  X- and Y-Linked Chromatin-Modifying Genes as Regulators of Sex-Specific Cancer Incidence and Prognosis.

Authors:  Rossella Tricarico; Emmanuelle Nicolas; Michael J Hall; Erica A Golemis
Journal:  Clin Cancer Res       Date:  2020-07-30       Impact factor: 12.531

5.  DZNep represses Bcl-2 expression and modulates apoptosis sensitivity in response to Nutlin-3a.

Authors:  Yalu Zhou; Ricardo E Perez; Lei Duan; Carl G Maki
Journal:  Cancer Biol Ther       Date:  2018-03-13       Impact factor: 4.742

Review 6.  Clinically Applicable Inhibitors Impacting Genome Stability.

Authors:  Anu Prakash; Juan F Garcia-Moreno; James A L Brown; Emer Bourke
Journal:  Molecules       Date:  2018-05-13       Impact factor: 4.411

7.  Maternal low-protein diet decreases brain-derived neurotrophic factor expression in the brains of the neonatal rat offspring.

Authors:  Gurdeep Marwarha; Kate Claycombe-Larson; Jared Schommer; Othman Ghribi
Journal:  J Nutr Biochem       Date:  2017-04-06       Impact factor: 6.048

8.  Prefrontal cortex expression of chromatin modifier genes in male WSP and WSR mice changes across ethanol dependence, withdrawal, and abstinence.

Authors:  Joel G Hashimoto; David P Gavin; Kristine M Wiren; John C Crabbe; Marina Guizzetti
Journal:  Alcohol       Date:  2017-03-14       Impact factor: 2.405

9.  Silencing of odorant receptor genes by G protein βγ signaling ensures the expression of one odorant receptor per olfactory sensory neuron.

Authors:  Todd Ferreira; Sarah R Wilson; Yoon Gi Choi; Davide Risso; Sandrine Dudoit; Terence P Speed; John Ngai
Journal:  Neuron       Date:  2014-02-19       Impact factor: 17.173

10.  Structural Insight into Recognition of Methylated Histone H3K4 by Set3.

Authors:  Jovylyn Gatchalian; Muzaffar Ali; Forest H Andrews; Yi Zhang; Alexander S Barrett; Tatiana G Kutateladze
Journal:  J Mol Biol       Date:  2016-09-30       Impact factor: 5.469

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