Literature DB >> 32908249

The evolving metabolic landscape of chromatin biology and epigenetics.

Ziwei Dai1, Vijyendra Ramesh1, Jason W Locasale2,3.   

Abstract

Molecular inputs to chromatin via cellular metabolism are modifiers of the epigenome. These inputs - which include both nutrient availability as a result of diet and growth factor signalling - are implicated in linking the environment to the maintenance of cellular homeostasis and cell identity. Recent studies have demonstrated that these inputs are much broader than had previously been known, encompassing metabolism from a wide variety of sources, including alcohol and microbiotal metabolism. These factors modify DNA and histones and exert specific effects on cell biology, systemic physiology and pathology. In this Review, we discuss the nature of these molecular networks, highlight their role in mediating cellular responses and explore their modifiability through dietary and pharmacological interventions.

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Year:  2020        PMID: 32908249      PMCID: PMC8059378          DOI: 10.1038/s41576-020-0270-8

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  268 in total

Review 1.  Chromatin modifications and their function.

Authors:  Tony Kouzarides
Journal:  Cell       Date:  2007-02-23       Impact factor: 41.582

2.  Targeted in situ genome-wide profiling with high efficiency for low cell numbers.

Authors:  Peter J Skene; Jorja G Henikoff; Steven Henikoff
Journal:  Nat Protoc       Date:  2018-04-12       Impact factor: 13.491

3.  The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes.

Authors:  Robert Huether; Li Dong; Xiang Chen; Gang Wu; Matthew Parker; Lei Wei; Jing Ma; Michael N Edmonson; Erin K Hedlund; Michael C Rusch; Sheila A Shurtleff; Heather L Mulder; Kristy Boggs; Bhavin Vadordaria; Jinjun Cheng; Donald Yergeau; Guangchun Song; Jared Becksfort; Gordon Lemmon; Catherine Weber; Zhongling Cai; Jinjun Dang; Michael Walsh; Amanda L Gedman; Zachary Faber; John Easton; Tanja Gruber; Richard W Kriwacki; Janet F Partridge; Li Ding; Richard K Wilson; Elaine R Mardis; Charles G Mullighan; Richard J Gilbertson; Suzanne J Baker; Gerard Zambetti; David W Ellison; Jinghui Zhang; James R Downing
Journal:  Nat Commun       Date:  2014-04-08       Impact factor: 14.919

4.  Engineering Epigenetic Regulation Using Synthetic Read-Write Modules.

Authors:  Minhee Park; Nikit Patel; Albert J Keung; Ahmad S Khalil
Journal:  Cell       Date:  2018-12-06       Impact factor: 41.582

5.  Modification of histones by sugar β-N-acetylglucosamine (GlcNAc) occurs on multiple residues, including histone H3 serine 10, and is cell cycle-regulated.

Authors:  Suisheng Zhang; Kevin Roche; Heinz-Peter Nasheuer; Noel Francis Lowndes
Journal:  J Biol Chem       Date:  2011-09-06       Impact factor: 5.157

6.  Next-generation characterization of the Cancer Cell Line Encyclopedia.

Authors:  Mahmoud Ghandi; Franklin W Huang; Judit Jané-Valbuena; Gregory V Kryukov; Christopher C Lo; E Robert McDonald; Jordi Barretina; Ellen T Gelfand; Craig M Bielski; Haoxin Li; Kevin Hu; Alexander Y Andreev-Drakhlin; Jaegil Kim; Julian M Hess; Brian J Haas; François Aguet; Barbara A Weir; Michael V Rothberg; Brenton R Paolella; Michael S Lawrence; Rehan Akbani; Yiling Lu; Hong L Tiv; Prafulla C Gokhale; Antoine de Weck; Ali Amin Mansour; Coyin Oh; Juliann Shih; Kevin Hadi; Yanay Rosen; Jonathan Bistline; Kavitha Venkatesan; Anupama Reddy; Dmitriy Sonkin; Manway Liu; Joseph Lehar; Joshua M Korn; Dale A Porter; Michael D Jones; Javad Golji; Giordano Caponigro; Jordan E Taylor; Caitlin M Dunning; Amanda L Creech; Allison C Warren; James M McFarland; Mahdi Zamanighomi; Audrey Kauffmann; Nicolas Stransky; Marcin Imielinski; Yosef E Maruvka; Andrew D Cherniack; Aviad Tsherniak; Francisca Vazquez; Jacob D Jaffe; Andrew A Lane; David M Weinstock; Cory M Johannessen; Michael P Morrissey; Frank Stegmeier; Robert Schlegel; William C Hahn; Gad Getz; Gordon B Mills; Jesse S Boehm; Todd R Golub; Levi A Garraway; William R Sellers
Journal:  Nature       Date:  2019-05-08       Impact factor: 49.962

7.  Cigarette smoke component acrolein modulates chromatin assembly by inhibiting histone acetylation.

Authors:  Danqi Chen; Lei Fang; Hongjie Li; Moon-shong Tang; Chunyuan Jin
Journal:  J Biol Chem       Date:  2013-06-14       Impact factor: 5.157

8.  Histone Methylation Dynamics and Gene Regulation Occur through the Sensing of One-Carbon Metabolism.

Authors:  Samantha J Mentch; Mahya Mehrmohamadi; Lei Huang; Xiaojing Liu; Diwakar Gupta; Dwight Mattocks; Paola Gómez Padilla; Gene Ables; Marcas M Bamman; Anna E Thalacker-Mercer; Sailendra N Nichenametla; Jason W Locasale
Journal:  Cell Metab       Date:  2015-09-24       Impact factor: 27.287

Review 9.  Writing, erasing and reading histone lysine methylations.

Authors:  Kwangbeom Hyun; Jongcheol Jeon; Kihyun Park; Jaehoon Kim
Journal:  Exp Mol Med       Date:  2017-04-28       Impact factor: 8.718

10.  Amino acid levels determine metabolism and CYP450 function of hepatocytes and hepatoma cell lines.

Authors:  Manoj Kumar; Tine Tricot; Ruben Boon; Ilaria Elia; Laura Ordovas; Frank Jacobs; Jennifer One; Jonathan De Smedt; Guy Eelen; Matthew Bird; Philip Roelandt; Ginevra Doglioni; Kim Vriens; Matteo Rossi; Marta Aguirre Vazquez; Thomas Vanwelden; François Chesnais; Adil El Taghdouini; Mustapha Najimi; Etienne Sokal; David Cassiman; Jan Snoeys; Mario Monshouwer; Wei-Shou Hu; Christian Lange; Peter Carmeliet; Sarah-Maria Fendt; Catherine M Verfaillie
Journal:  Nat Commun       Date:  2020-03-13       Impact factor: 14.919

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  51 in total

Review 1.  Non-coding RNA in alcohol use disorder by affecting synaptic plasticity.

Authors:  Shuang Zhu; Jiaming Wu; Jian Hu
Journal:  Exp Brain Res       Date:  2022-01-13       Impact factor: 1.972

Review 2.  Regulation of energy metabolism in human pluripotent stem cells.

Authors:  Weiwei Liu; Guokai Chen
Journal:  Cell Mol Life Sci       Date:  2021-11-13       Impact factor: 9.261

Review 3.  Micro but mighty-Micronutrients in the epigenetic regulation of adaptive immune responses.

Authors:  Heng-Yi Chen; Michael Hsu; Chan-Wang Jerry Lio
Journal:  Immunol Rev       Date:  2021-11-24       Impact factor: 12.988

Review 4.  Comparison of SHANK3 deficiency in animal models: phenotypes, treatment strategies, and translational implications.

Authors:  Jan Philipp Delling; Tobias M Boeckers
Journal:  J Neurodev Disord       Date:  2021-11-16       Impact factor: 4.025

5.  Epigenetic and metabolic interplay in cutaneous squamous cell carcinoma.

Authors:  Gina Pacella; Brian C Capell
Journal:  Exp Dermatol       Date:  2021-04-22       Impact factor: 3.960

Review 6.  Acetyl-CoA and Metabolite Fluxes Regulate White Adipose Tissue Expansion.

Authors:  Jessica B Felix; Aaron R Cox; Sean M Hartig
Journal:  Trends Endocrinol Metab       Date:  2021-03-09       Impact factor: 12.015

Review 7.  Mitochondria as Signaling Organelles Control Mammalian Stem Cell Fate.

Authors:  Ram Prosad Chakrabarty; Navdeep S Chandel
Journal:  Cell Stem Cell       Date:  2021-03-04       Impact factor: 24.633

Review 8.  The language of chromatin modification in human cancers.

Authors:  Shuai Zhao; C David Allis; Gang Greg Wang
Journal:  Nat Rev Cancer       Date:  2021-05-17       Impact factor: 60.716

Review 9.  Metabolic barriers to cancer immunotherapy.

Authors:  Kristin DePeaux; Greg M Delgoffe
Journal:  Nat Rev Immunol       Date:  2021-04-29       Impact factor: 53.106

10.  The Genomic Architecture of Adaptation to Larval Malnutrition Points to a Trade-off with Adult Starvation Resistance in Drosophila.

Authors:  Tadeusz J Kawecki; Berra Erkosar; Cindy Dupuis; Brian Hollis; R Craig Stillwell; Martin Kapun
Journal:  Mol Biol Evol       Date:  2021-06-25       Impact factor: 16.240

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