One-carbon metabolism and epigenetics: Understanding the specificity

Annals of the New York Academy of Sciences

Volumn 1363, Issue 1, 2016, Pages 91-98

  Mentch, Samantha J ^a   Locasale, Jason W ^a,b,c  

^a Department of Molecular Biology and Genetics   (United States)

^b DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c DUKE CANCER INSTITUTE   (United States)

Author keywords

Epigenetics; Histone methylation; Histone methyltransferase; One carbon metabolism

Indexed keywords

HISTONE METHYLTRANSFERASE; METHIONINE; CHROMATIN; FOLIC ACID; HISTONE; HISTONE LYSINE METHYLTRANSFERASE; S ADENOSYLMETHIONINE;

ARTICLE; BIOCHEMICAL ANALYSIS; CARBON METABOLISM; CELL METABOLISM; EPIGENETICS; GENE CONTROL; GENE EXPRESSION; GENE TARGETING; HISTONE METHYLATION; HUMAN; ONE CARBON METABOLISM; ANIMAL; CHEMISTRY; CHROMATIN; ENZYME SPECIFICITY; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETICS; KINETICS; METABOLISM; METHYLATION;

ANIMALS; CHROMATIN; EPIGENESIS, GENETIC; EPIGENOMICS; FOLIC ACID; GENE EXPRESSION REGULATION; HISTONE-LYSINE N-METHYLTRANSFERASE; HISTONES; HUMANS; KINETICS; METABOLIC NETWORKS AND PATHWAYS; METHIONINE; METHYLATION; S-ADENOSYLMETHIONINE; SUBSTRATE SPECIFICITY;

EID: 84949655663     PISSN: 00778923     EISSN: 17496632     Source Type: Journal    
DOI: 10.1111/nyas.12956     Document Type: Article

References (73)

1. Grandison, R.C., M.D. Piper & L. Partridge. 2009. Amino-acid imbalance explains extension of lifespan by dietary restriction in Drosophila. Nature 462: 1061-1064.
2. Yun, J. et al. 2012. Interactions between epigenetics and metabolism in cancers. Front. Oncol. 2: 163.
3. Kraus, D. et al. 2014. Nicotinamide N-methyltransferase knockdown protects against diet-induced obesity. Nature 508: 258-262.
4. Cabreiro, F. et al. 2013. Metformin retards aging in C. elegans by altering microbial folate and methionine metabolism. Cell 153: 228-239.
5. Ordovas, J.M. & C.E. Smith. 2010. Epigenetics and cardiovascular disease. Nat. Rev. Cardiol. 7: 510-519.
6. Benayoun, B.A., E.A. Pollina & A. Brunet. 2015. Epigenetic regulation of ageing: linking environmental inputs to genomic stability. Nat. Rev. Mol. Cell Biol. 16: 593-610.
7. Wellen, K.E. & C.B. Thompson. 2010. Cellular metabolic stress: considering how cells respond to nutrient excess. Mol. Cell 40: 323-332.
8. Locasale, J.W. 2013. Serine, glycine and one-carbon units: cancer metabolism in full circle. Nat. Rev. Cancer 13: 572-583.
9. Murray, K. 1964. The occurrence of ε-N-methyl lysine in histones. Biochemistry 3: 10-15.
10. Chen, D.G. et al. 1999. Regulation of transcription by a protein methyltransferase. Science 284: 2174-2177.
11. Rea, S. et al. 2000. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406: 593-599.
12. Deguchi, T. & J. Barchas. 1971. Inhibition of transmethylations of biogenic amines by S-adenosylhomocysteine. Enhancement of transmethylation by adenosylhomocysteinase. J. Biol. Chem. 246: 3175-3181.
13. Hoffman, D.R., W.E. Cornatzer & J.A. Duerre. 1979. Relationship between tissue-levels of S-adenosylmethionine, S-adenosylhomocysteine, and transmethylation reactions. Can. J. Biochem. 57: 56-65.
14. Locasale, J.W. & L.C. Cantley. 2011. Metabolic flux and the regulation of mammalian cell growth. Cell Metab. 14: 443-451.
15. Teperino, R., K. Schoonjans & J. Auwerx. 2010. Histone methyl transferases and demethylases; can they link metabolism and transcription? Cell Metab. 12: 321-327.
16. Shiraki, N. et al. 2014. Methionine metabolism regulates maintenance and differentiation of human pluripotent stem cells. Cell Metab. 19: 780-794.
17. Ulanovskaya, O.A., A.M. Zuhl & B.F. Cravatt. 2013. NNMT promotes epigenetic remodeling in cancer by creating a metabolic methylation sink. Nat. Chem. Biol. 9: 300-306.
18. Tang, X. et al. 2015. Comprehensive profiling of amino acid response uncovers unique methionine-deprived response dependent on intact creatine biosynthesis. PLoS Genet. 11: e1005158.
19. Shyh-Chang, N. et al. 2013. Influence of threonine metabolism on S-adenosylmethionine and histone methylation. Science 339: 222-226.
20. Wang, J. et al. 2009. Dependence of mouse embryonic stem cells on threonine catabolism. Science 325: 435-439.
21. Finkelstein, J.D. 1990. Methionine metabolism in mammals. J. Nutr. Biochem. 1: 228-237.
22. Cantoni, G.L. 1953. S-adenosylmethionine; a new intermediate formed enzymatically from l-methionine and adenosinetriphosphate. J. Biol. Chem. 204: 403-416.
23. De La Haba, G. & G.L. Cantoni. 1959. The enzymatic synthesis of S-adenosyl-L-homocysteine from adenosine and homocysteine. J. Biol. Chem. 234: 603-608.
24. Cynober, L.A. 2002. Plasma amino acid levels with a note on membrane transport: characteristics, regulation, and metabolic significance. Nutrition 18: 761-766.
25. Psychogios, N. et al. 2011. The human serum metabolome. PLoS One 6: 1-23.
26. Mentch, S.J. et al. 2015. Histone methylation dynamics and gene regulation occur through the sensing of one-carbon metabolism. Cell Metab. 22: 861-873.
27. Melnyk, S. et al. 2000. Measurement of plasma and intracellular S-adenosylmethionine and S-adenosylhomocysteine utilizing coulometric electrochemical detection: alterations with plasma homocysteine and pyridoxal 5'-phosphate concentrations. Clin. Chem. 46: 265-272.
28. Duncan, T.M., M.C. Reed & H.F. Nijhout. 2013. The relationship between intracellular and plasma levels of folate and metabolites in the methionine cycle: a model. Mol. Nutr. Food Res. 57: 628-636.
29. Feng, Q. et al. 2002. Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain. Curr. Biol. 12: 1052-1058.
30. Xiao, B. et al. 2003. Structure and catalytic mechanism of the human histone methyltransferase SET7/9. Nature 421: 652-656.
31. Dolinsky, T.J. et al. 2004. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 32: W665-W667.
32. Musselman, C.A. et al. 2012. Perceiving the epigenetic landscape through histone readers. Nat. Struct. Mol. Biol. 19: 1218-1227.
33. Taverna, S.D. et al. 2007. How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat. Struct. Mol. Biol. 14: 1025-1040.
34. Pray-Grant, M.G. et al. 2005. Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation. Nature 433: 434-438.
35. Bannister, A.J. et al. 2001. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410: 120-124.
36. Cao, R. et al. 2002. Role of histone H3 lysine 27 methylation in polycomb-group silencing. Science 298: 1039-1043.
37. Huyen, Y. et al. 2004. Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks. Nature 432: 406-411.
38. Koch, C.M. et al. 2007. The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res. 17: 691-707.
39. Roadmap Epigenomics Consortium et al. 2015. Integrative analysis of 111 reference human epigenomes. Nature 518: 317-330.
40. Consortium, E.P. et al. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
41. Barski, A. et al. 2007. High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837.
42. Noma, K. & S.I. Grewal. 2002. Histone H3 lysine 4 methylation is mediated by Set1 and promotes maintenance of active chromatin states in fission yeast. Proc. Natl. Acad. Sci. U.S.A. 99(Suppl 4): 16438-16445.
43. Bernstein, B.E. et al. 2002. Methylation of histone H3 Lys 4 in coding regions of active genes. Proc. Natl. Acad. Sci. U.S.A. 99: 8695-8700.
44. Chen, K. et al. 2015. Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes. Nat. Genet. 47: 1149-1157.
45. Benayoun, B.A. et al. 2014. H3K4me3 breadth is linked to cell identity and transcriptional consistency. Cell 158: 673-688.
46. van Ingen, H. et al. 2008. Structural insight into the recognition of the H3K4me3 mark by the TFIID subunit TAF3. Structure 16: 1245-1256.
47. Herz, H.M. et al. 2012. Enhancer-associated H3K4 monomethylation by Trithorax-related, the Drosophila homolog of mammalian Mll3/Mll4. Genes Dev. 26: 2604-2620.
48. Nakayama, J. et al. 2001. Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292: 110-113.
49. Noma, K., C.D. Allis & S.I. Grewal. 2001. Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 293: 1150-1155.
50. Peters, A.H. et al. 2002. Histone H3 lysine 9 methylation is an epigenetic imprint of facultative heterochromatin. Nat. Genet. 30: 77-80.
51. Peters, A.H. et al. 2001. Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell 107: 323-337.
52. Stewart, M.D., L.J. & J. Wong. 2005. Relationship between histone H3 lysine 9 methylation, transcription repression, and heterochromatin protein 1 recruitment. Mol. Cell. Biol. 25: 2525-2538.
53. Lachner, M. et al. 2001. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410: 116-120.
54. Abel, K.J. et al. 1996. Characterization of EZH1, a human homolog of Drosophila Enhancer of zeste near BRCA1. Genomics 37: 161-171.
55. Wang, H. et al. 2004. Role of histone H2A ubiquitination in Polycomb silencing. Nature 431: 873-878.
56. Vire, E. et al. 2006. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 439: 871-874.
57. Francis, N.J., R.E. Kingston & C.L. Woodcock. 2004. Chromatin compaction by a polycomb group protein complex. Science 306: 1574-1577.
58. Stassen, M.J. et al. 1995. The Drosophila trithorax proteins contain a novel variant of the nuclear receptor type DNA binding domain and an ancient conserved motif found in other chromosomal proteins. Mech. Dev. 52: 209-223.
59. Tschiersch, B. et al. 1994. The protein encoded by the Drosophila position-effect variegation suppressor gene Su(var)3-9 combines domains of antagonistic regulators of homeotic gene complexes. EMBO J. 13: 3822-3831.
60. Miller, T. et al. 2001. COMPASS: a complex of proteins associated with a trithorax-related SET domain protein. Proc. Natl. Acad. Sci. U.S.A. 98: 15393-15394.
61. Krogan, N.J. et al. 2002. COMPASS, a histone H3 (lysine 4) methyltransferase required for telomeric silencing of gene expression. J. Biol. Chem. 277: 10753-10755.
62. Shilatifard, A. 2012. The COMPASS family of histone H3K4 methylases: mechanisms of regulation in development and disease pathogenesis. Ann. Rev. Biochem. 81: 65-95.
63. Ng, H.H. et al. 2003. Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol. Cell 11: 709-719.
64. Wu, M. et al. 2008. Molecular regulation of H3K4 trimethylation by Wdr82, a component of human Set1/COMPASS. Mol. Cell. Biol. 28: 7337-7344.
65. Lee, J.H. et al. 2007. Identification and characterization of the human Set1B histone H3-Lys4 methyltransferase complex. J. Biol. Chem. 282: 13419-13428.
66. Nguyen, P. et al. 2008. BAT3 and SET1A form a complex with CTCFL/BORIS to modulate H3K4 histone dimethylation and gene expression. Mol. Cell. Biol. 28: 6720-6729.
67. Krivtsov, A.V. & S.A. Armstrong. MLL translocations, histone modifications and leukaemia stem-cell development. Nat. Rev. Cancer 7: 823-833.
68. Guenther, M.G. et al. 2005. Global and Hox-specific roles for the MLL1 methyltransferase. Proc. Natl. Acad. Sci. U.S.A. 102: 8603-8608.
69. Hu, D. et al. 2013. The Mll2 branch of the COMPASS family regulates bivalent promoters in mouse embryonic stem cells. Nat. Struct. Mol. Biol. 20: 1093-1097.
70. Lee, J.-E. et al. 2013. H3K4 mono- and di-methyltransferase MLL4 is required for enhancer activation during cell differentiation. eLife 2: e01503.
71. Mozzetta, C. et al. 2014. The histone H3 lysine 9 methyltransferases G9a and GLP regulate polycomb repressive complex 2-mediated gene silencing. Mol. Cell 53: 277-289.
72. McCabe, M.T. et al. 2012. EZH2 inhibition as a therapeutic strategy for lymphoma with EZH2-activating mutations. Nature 492: 108-112.
73. Vermeulen, M. et al. 2007. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell 131: 58-69.