Literature DB >> 26647078

One-carbon metabolism and epigenetics: understanding the specificity.

Samantha J Mentch1, Jason W Locasale1,2,3,4.   

Abstract

One-carbon metabolism is a metabolic network that integrates nutrient status from the environment to yield multiple biological functions. The folate and methionine cycles generate S-adenosylmethionine (SAM), which is the universal methyl donor for methylation reactions, including histone and DNA methylation. Histone methylation is a crucial part of the epigenetic code and plays diverse roles in the establishment of chromatin states that mediate the regulation of gene expression. The activities of histone methyltransferases (HMTs) are dependent on intracellular levels of SAM, which fluctuate based on cellular nutrient availability, providing a link between cell metabolism and histone methylation. Here we discuss the biochemical properties of HMTs, their role in gene regulation, and the connection to cellular metabolism. Our emphasis is on understanding the specificity of this intriguing link.
© 2015 New York Academy of Sciences.

Entities:  

Keywords:  epigenetics; histone methylation; histone methyltransferase; one-carbon metabolism

Mesh:

Substances:

Year:  2015        PMID: 26647078      PMCID: PMC4801744          DOI: 10.1111/nyas.12956

Source DB:  PubMed          Journal:  Ann N Y Acad Sci        ISSN: 0077-8923            Impact factor:   5.691


  72 in total

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Journal:  Science       Date:  2001-03-15       Impact factor: 47.728

2.  Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity.

Authors:  Huck Hui Ng; François Robert; Richard A Young; Kevin Struhl
Journal:  Mol Cell       Date:  2003-03       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.  Enhancer-associated H3K4 monomethylation by Trithorax-related, the Drosophila homolog of mammalian Mll3/Mll4.

Authors:  Hans-Martin Herz; Man Mohan; Alexander S Garruss; Kaiwei Liang; Yoh-Hei Takahashi; Kristen Mickey; Olaf Voets; C Peter Verrijzer; Ali Shilatifard
Journal:  Genes Dev       Date:  2012-11-19       Impact factor: 11.361

5.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:  Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas R Gingeras; Elliott H Margulies; Zhiping Weng; Michael Snyder; Emmanouil T Dermitzakis; Robert E Thurman; Michael S Kuehn; Christopher M Taylor; Shane Neph; Christoph M Koch; Saurabh Asthana; Ankit Malhotra; Ivan Adzhubei; Jason A Greenbaum; Robert M Andrews; Paul Flicek; Patrick J Boyle; Hua Cao; Nigel P Carter; Gayle K Clelland; Sean Davis; Nathan Day; Pawandeep Dhami; Shane C Dillon; Michael O Dorschner; Heike Fiegler; Paul G Giresi; Jeff Goldy; Michael Hawrylycz; Andrew Haydock; Richard Humbert; Keith D James; Brett E Johnson; Ericka M Johnson; Tristan T Frum; Elizabeth R Rosenzweig; Neerja Karnani; Kirsten Lee; Gregory C Lefebvre; Patrick A Navas; Fidencio Neri; Stephen C J Parker; Peter J Sabo; Richard Sandstrom; Anthony Shafer; David Vetrie; Molly Weaver; Sarah Wilcox; Man Yu; Francis S Collins; Job Dekker; Jason D Lieb; Thomas D Tullius; Gregory E Crawford; Shamil Sunyaev; William S Noble; Ian Dunham; France Denoeud; Alexandre Reymond; Philipp Kapranov; Joel Rozowsky; Deyou Zheng; Robert Castelo; Adam Frankish; Jennifer Harrow; Srinka Ghosh; Albin Sandelin; Ivo L Hofacker; Robert Baertsch; Damian Keefe; Sujit Dike; Jill Cheng; Heather A Hirsch; Edward A Sekinger; Julien Lagarde; Josep F Abril; Atif Shahab; Christoph Flamm; Claudia Fried; Jörg Hackermüller; Jana Hertel; Manja Lindemeyer; Kristin Missal; Andrea Tanzer; Stefan Washietl; Jan Korbel; Olof Emanuelsson; Jakob S Pedersen; Nancy Holroyd; Ruth Taylor; David Swarbreck; Nicholas Matthews; Mark C Dickson; Daryl J Thomas; Matthew T Weirauch; James Gilbert; Jorg Drenkow; Ian Bell; XiaoDong Zhao; K G Srinivasan; Wing-Kin Sung; Hong Sain Ooi; Kuo Ping Chiu; Sylvain Foissac; Tyler Alioto; Michael Brent; Lior Pachter; Michael L Tress; Alfonso Valencia; Siew Woh Choo; Chiou Yu Choo; Catherine Ucla; Caroline Manzano; Carine Wyss; Evelyn Cheung; Taane G Clark; James B Brown; Madhavan Ganesh; Sandeep Patel; Hari Tammana; Jacqueline Chrast; Charlotte N Henrichsen; Chikatoshi Kai; Jun Kawai; Ugrappa Nagalakshmi; Jiaqian Wu; Zheng Lian; Jin Lian; Peter Newburger; Xueqing Zhang; Peter Bickel; John S Mattick; Piero Carninci; Yoshihide Hayashizaki; Sherman Weissman; Tim Hubbard; Richard M Myers; Jane Rogers; Peter F Stadler; Todd M Lowe; Chia-Lin Wei; Yijun Ruan; Kevin Struhl; Mark Gerstein; Stylianos E Antonarakis; Yutao Fu; Eric D Green; Ulaş Karaöz; Adam Siepel; James Taylor; Laura A Liefer; Kris A Wetterstrand; Peter J Good; Elise A Feingold; Mark S Guyer; Gregory M Cooper; George Asimenos; Colin N Dewey; Minmei Hou; Sergey Nikolaev; Juan I Montoya-Burgos; Ari Löytynoja; Simon Whelan; Fabio Pardi; Tim Massingham; Haiyan Huang; Nancy R Zhang; Ian Holmes; James C Mullikin; Abel Ureta-Vidal; Benedict Paten; Michael Seringhaus; Deanna Church; Kate Rosenbloom; W James Kent; Eric A Stone; Serafim Batzoglou; Nick Goldman; Ross C Hardison; David Haussler; Webb Miller; Arend Sidow; Nathan D Trinklein; Zhengdong D Zhang; Leah Barrera; Rhona Stuart; David C King; Adam Ameur; Stefan Enroth; Mark C Bieda; Jonghwan Kim; Akshay A Bhinge; Nan Jiang; Jun Liu; Fei Yao; Vinsensius B Vega; Charlie W H Lee; Patrick Ng; Atif Shahab; Annie Yang; Zarmik Moqtaderi; Zhou Zhu; Xiaoqin Xu; Sharon Squazzo; Matthew J Oberley; David Inman; Michael A Singer; Todd A Richmond; Kyle J Munn; Alvaro Rada-Iglesias; Ola Wallerman; Jan Komorowski; Joanna C Fowler; Phillippe Couttet; Alexander W Bruce; Oliver M Dovey; Peter D Ellis; Cordelia F Langford; David A Nix; Ghia Euskirchen; Stephen Hartman; Alexander E Urban; Peter Kraus; Sara Van Calcar; Nate Heintzman; Tae Hoon Kim; Kun Wang; Chunxu Qu; Gary Hon; Rosa Luna; Christopher K Glass; M Geoff Rosenfeld; Shelley Force Aldred; Sara J Cooper; Anason Halees; Jane M Lin; Hennady P Shulha; Xiaoling Zhang; Mousheng Xu; Jaafar N S Haidar; Yong Yu; Yijun Ruan; Vishwanath R Iyer; Roland D Green; Claes Wadelius; Peggy J Farnham; Bing Ren; Rachel A Harte; Angie S Hinrichs; Heather Trumbower; Hiram Clawson; Jennifer Hillman-Jackson; Ann S Zweig; Kayla Smith; Archana Thakkapallayil; Galt Barber; Robert M Kuhn; Donna Karolchik; Lluis Armengol; Christine P Bird; Paul I W de Bakker; Andrew D Kern; Nuria Lopez-Bigas; Joel D Martin; Barbara E Stranger; Abigail Woodroffe; Eugene Davydov; Antigone Dimas; Eduardo Eyras; Ingileif B Hallgrímsdóttir; Julian Huppert; Michael C Zody; Gonçalo R Abecasis; Xavier Estivill; Gerard G Bouffard; Xiaobin Guan; Nancy F Hansen; Jacquelyn R Idol; Valerie V B Maduro; Baishali Maskeri; Jennifer C McDowell; Morgan Park; Pamela J Thomas; Alice C Young; Robert W Blakesley; Donna M Muzny; Erica Sodergren; David A Wheeler; Kim C Worley; Huaiyang Jiang; George M Weinstock; Richard A Gibbs; Tina Graves; Robert Fulton; Elaine R Mardis; Richard K Wilson; Michele Clamp; James Cuff; Sante Gnerre; David B Jaffe; Jean L Chang; Kerstin Lindblad-Toh; Eric S Lander; Maxim Koriabine; Mikhail Nefedov; Kazutoyo Osoegawa; Yuko Yoshinaga; Baoli Zhu; Pieter J de Jong
Journal:  Nature       Date:  2007-06-14       Impact factor: 49.962

6.  Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain.

Authors:  Qin Feng; Hengbin Wang; Huck Hui Ng; Hediye Erdjument-Bromage; Paul Tempst; Kevin Struhl; Yi Zhang
Journal:  Curr Biol       Date:  2002-06-25       Impact factor: 10.834

7.  Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes.

Authors:  Kaifu Chen; Zhong Chen; Dayong Wu; Lili Zhang; Xueqiu Lin; Jianzhong Su; Benjamin Rodriguez; Yuanxin Xi; Zheng Xia; Xi Chen; Xiaobing Shi; Qianben Wang; Wei Li
Journal:  Nat Genet       Date:  2015-08-24       Impact factor: 38.330

8.  Nicotinamide N-methyltransferase knockdown protects against diet-induced obesity.

Authors:  Daniel Kraus; Qin Yang; Dong Kong; Alexander S Banks; Lin Zhang; Joseph T Rodgers; Eija Pirinen; Thomas C Pulinilkunnil; Fengying Gong; Ya-chin Wang; Yana Cen; Anthony A Sauve; John M Asara; Odile D Peroni; Brett P Monia; Sanjay Bhanot; Leena Alhonen; Pere Puigserver; Barbara B Kahn
Journal:  Nature       Date:  2014-04-10       Impact factor: 49.962

9.  Amino-acid imbalance explains extension of lifespan by dietary restriction in Drosophila.

Authors:  Richard C Grandison; Matthew D W Piper; Linda Partridge
Journal:  Nature       Date:  2009-12-02       Impact factor: 49.962

10.  Integrative analysis of 111 reference human epigenomes.

Authors:  Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi-Moussavi; Pouya Kheradpour; Zhizhuo Zhang; Jianrong Wang; Michael J Ziller; Viren Amin; John W Whitaker; Matthew D Schultz; Lucas D Ward; Abhishek Sarkar; Gerald Quon; Richard S Sandstrom; Matthew L Eaton; Yi-Chieh Wu; Andreas R Pfenning; Xinchen Wang; Melina Claussnitzer; Yaping Liu; Cristian Coarfa; R Alan Harris; Noam Shoresh; Charles B Epstein; Elizabeta Gjoneska; Danny Leung; Wei Xie; R David Hawkins; Ryan Lister; Chibo Hong; Philippe Gascard; Andrew J Mungall; Richard Moore; Eric Chuah; Angela Tam; Theresa K Canfield; R Scott Hansen; Rajinder Kaul; Peter J Sabo; Mukul S Bansal; Annaick Carles; Jesse R Dixon; Kai-How Farh; Soheil Feizi; Rosa Karlic; Ah-Ram Kim; Ashwinikumar Kulkarni; Daofeng Li; Rebecca Lowdon; GiNell Elliott; Tim R Mercer; Shane J Neph; Vitor Onuchic; Paz Polak; Nisha Rajagopal; Pradipta Ray; Richard C Sallari; Kyle T Siebenthall; Nicholas A Sinnott-Armstrong; Michael Stevens; Robert E Thurman; Jie Wu; Bo Zhang; Xin Zhou; Arthur E Beaudet; Laurie A Boyer; Philip L De Jager; Peggy J Farnham; Susan J Fisher; David Haussler; Steven J M Jones; Wei Li; Marco A Marra; Michael T McManus; Shamil Sunyaev; James A Thomson; Thea D Tlsty; Li-Huei Tsai; Wei Wang; Robert A Waterland; Michael Q Zhang; Lisa H Chadwick; Bradley E Bernstein; Joseph F Costello; Joseph R Ecker; Martin Hirst; Alexander Meissner; Aleksandar Milosavljevic; Bing Ren; John A Stamatoyannopoulos; Ting Wang; Manolis Kellis
Journal:  Nature       Date:  2015-02-19       Impact factor: 69.504

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  97 in total

Review 1.  Mitostemness.

Authors:  Elisabet Cuyàs; Sara Verdura; Núria Folguera-Blasco; Cristian Bastidas-Velez; Ángel G Martin; Tomás Alarcón; Javier A Menendez
Journal:  Cell Cycle       Date:  2018-07-02       Impact factor: 4.534

Review 2.  DNA Methylation and Susceptibility to Autism Spectrum Disorder.

Authors:  Martine W Tremblay; Yong-Hui Jiang
Journal:  Annu Rev Med       Date:  2019-01-27       Impact factor: 13.739

3.  Structural Basis for Regulation of METTL16, an S-Adenosylmethionine Homeostasis Factor.

Authors:  Katelyn A Doxtader; Ping Wang; Anna M Scarborough; Dahee Seo; Nicholas K Conrad; Yunsun Nam
Journal:  Mol Cell       Date:  2018-09-06       Impact factor: 17.970

4.  Genotoxicity of tetrahydrofolic acid to hematopoietic stem and progenitor cells.

Authors:  Clara B García-Calderón; José Antonio Bejarano-García; Isabel Tinoco-Gago; María José Castro; Paula Moreno-Gordillo; José I Piruat; Teresa Caballero-Velázquez; José A Pérez-Simón; Iván V Rosado
Journal:  Cell Death Differ       Date:  2018-03-06       Impact factor: 15.828

5.  Polo-like kinase 1 (PLK1)-dependent phosphorylation of methylenetetrahydrofolate reductase (MTHFR) regulates replication via histone methylation.

Authors:  Xueyan Li; Shanshan Nai; Yuehe Ding; Qizhi Geng; Bingtao Zhu; Kai Yu; Wei-Guo Zhu; Meng-Qiu Dong; Xiao-Dong Su; Xingzhi Xu; Jing Li
Journal:  Cell Cycle       Date:  2017-08-18       Impact factor: 4.534

6.  Oncogenic PI3K promotes methionine dependency in breast cancer cells through the cystine-glutamate antiporter xCT.

Authors:  Evan C Lien; Laura Ghisolfi; Renee C Geck; John M Asara; Alex Toker
Journal:  Sci Signal       Date:  2017-12-19       Impact factor: 8.192

7.  Metformin targets histone acetylation in cancer-prone epithelial cells.

Authors:  Elisabet Cuyàs; Salvador Fernández-Arroyo; Jorge Joven; Javier A Menendez
Journal:  Cell Cycle       Date:  2016-10-28       Impact factor: 4.534

Review 8.  Metabolic interactions with cancer epigenetics.

Authors:  Xia Gao; Michael A Reid; Mei Kong; Jason W Locasale
Journal:  Mol Aspects Med       Date:  2016-09-09

9.  Methionine-Restricted Diet Increases miRNAs That Can Target RUNX2 Expression and Alters Bone Structure in Young Mice.

Authors:  Jason Plummer; Miri Park; Frantz Perodin; Mark C Horowitz; Julie R Hens
Journal:  J Cell Biochem       Date:  2016-06-22       Impact factor: 4.429

Review 10.  Mitochondrial-epigenetic crosstalk in environmental toxicology.

Authors:  Caren Weinhouse
Journal:  Toxicology       Date:  2017-09-05       Impact factor: 4.221

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