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Methyl-Metabolite Depletion Elicits Adaptive Responses to Support Heterochromatin Stability and Epigenetic Persistence

Haws, Spencer A., Yu, Deyang, Ye, Cunqi, Wille, Coral K., Nguyen, Long C., Krautkramer, Kimberly A., Tomasiewicz, Jay L., Yang, Shany E., Miller, Blake R., Liu, Wallace H., Igarashi, Kazuhiko, Sridharan, Rupa, Tu, Benjamin P., Cryns, Vincent L., Lamming, Dudley W., Denu, John M.·2020·Molecular Cell

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Research works printed but not linked: 59

  1. Bannister, 2001, Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain, Nature, 410, 120, 10.1038/35065138 · DOI · Paper page
  2. Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170 · DOI · Paper page
  3. Bröer, 2001, Association of 4F2hc with light chains LAT1, LAT2 or y+LAT2 requires different domains, Biochem. J., 355, 725, 10.1042/bj3550725 · DOI
  4. Brown-Borg, 2018, Metabolic adaptation of short-living growth hormone transgenic mice to methionine restriction and supplementation, Ann. N Y Acad. Sci., 1418, 118, 10.1111/nyas.13687 · DOI
  5. Clasquin, 2012, LC-MS data processing with MAVEN: a metabolomic analysis and visualization engine, Curr. Protoc. Bioinforma, Chapter 14
  6. Ding, 2015, s-Adenosylmethionine levels govern innate immunity through distinct methylation-dependent pathways, Cell Metab., 22, 633, 10.1016/j.cmet.2015.07.013 · DOI
  7. Fan, 2015, Metabolic regulation of histone post-translational modifications, ACS Chem. Biol., 10, 95, 10.1021/cb500846u · DOI
  8. Farmer, 2014, Nutritional adequacy of plant-based diets for weight management: observations from the NHANES, Am. J. Clin. Nutr., 100, 365S, 10.3945/ajcn.113.071308 · DOI
  9. Fei, 2015, Histone methyltransferase SETDB1 regulates liver cancer cell growth through methylation of p53, Nat. Commun., 6, 8651, 10.1038/ncomms9651 · DOI
  10. Green, 2019, Regulation of metabolic health by essential dietary amino acids, Mech. Ageing Dev., 177, 186, 10.1016/j.mad.2018.07.004 · DOI
  11. Hardies, 2000, LINE-1 (L1) lineages in the mouse, Mol. Biol. Evol., 17, 616, 10.1093/oxfordjournals.molbev.a026340 · DOI
  12. Hayashi, 2018, S-Adenosylmethionine synthetase is required for cell growth, maintenance of G0 phase, and termination of quiescence in fission yeast, iScience, 5, 38, 10.1016/j.isci.2018.06.011 · DOI
  13. Heinz, 2010, Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities, Mol. Cell, 38, 576, 10.1016/j.molcel.2010.05.004 · DOI · Paper page
  14. Kang, 1999, Efficient integration of short interspersed element-flanked foreign DNA via homologous recombination, J. Biol. Chem., 274, 36585, 10.1074/jbc.274.51.36585 · DOI
  15. Katoh, 2011, Methionine adenosyltransferase II serves as a transcriptional corepressor of Maf oncoprotein, Mol. Cell, 41, 554, 10.1016/j.molcel.2011.02.018 · DOI · Paper page
  16. Kera, 2013, Methionine adenosyltransferase II-dependent histone H3K9 methylation at the COX-2 gene locus, J. Biol. Chem., 288, 13592, 10.1074/jbc.M112.429738 · DOI
  17. Klawitter, 2016, Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells, Nat. Commun., 7, 10286, 10.1038/ncomms10286 · DOI
  18. Krishnaiah, 2017, Clock regulation of metabolites reveals coupling between transcription and metabolism, Cell Metab., 25, 961, 10.1016/j.cmet.2017.03.019 · DOI
  19. Lachner, 2001, Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins, Nature, 410, 116, 10.1038/35065132 · DOI · Paper page
  20. Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat. Methods, 9, 357, 10.1038/nmeth.1923 · DOI · Paper page
  21. Larson, 2012, Heterochromatin formation promotes longevity and represses ribosomal RNA synthesis, PLoS Genet., 8, e1002473, 10.1371/journal.pgen.1002473 · DOI · Paper page
  22. Lees, 2014, Methionine restriction restores a younger metabolic phenotype in adult mice with alterations in fibroblast growth factor 21, Aging Cell, 13, 817, 10.1111/acel.12238 · DOI
  23. Leng, 2013, EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments, Bioinformatics, 29, 1035, 10.1093/bioinformatics/btt087 · DOI
  24. Li, 2011, RSEM: accurate transcript quantification from RNA-seq data with or without a reference genome, BMC Bioinformatics, 12, 323, 10.1186/1471-2105-12-323 · DOI · Paper page
  25. Li, 2009, The Sequence Alignment/Map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352 · DOI · Paper page
  26. Li, 2015, Serine and SAM responsive complex SESAME regulates histone modification crosstalk by sensing cellular metabolism, Mol. Cell, 60, 408, 10.1016/j.molcel.2015.09.024 · DOI
  27. Li, 2011, RSEM: accurate transcript quantification from RNA-seq data with or without a reference genome, BMC Bioinformatics, 12, 10.1186/1471-2105-12-323 · DOI · Paper page
  28. Li, 2018, Regulation of chromatin and gene expression by metabolic enzymes and metabolites, Nat. Rev. Mol. Cell Biol., 19, 563, 10.1038/s41580-018-0029-7 · DOI
  29. Liu, 2013, Discovery of an in vivo chemical probe of the lysine methyltransferases G9a and GLP, J. Med. Chem., 56, 8931, 10.1021/jm401480r · DOI
  30. Loyola, 2006, PTMs on H3 variants before chromatin assembly potentiate their final epigenetic state, Mol. Cell, 24, 309, 10.1016/j.molcel.2006.08.019 · DOI
  31. Loyola, 2009, The HP1alpha-CAF1-SetDB1-containing complex provides H3K9me1 for Suv39-mediated K9me3 in pericentric heterochromatin, EMBO Rep., 10, 769, 10.1038/embor.2009.90 · DOI
  32. MacLean, 2010, Skyline: an open source document editor for creating and analyzing targeted proteomics experiments, Bioinformatics, 26, 966, 10.1093/bioinformatics/btq054 · DOI · Paper page
  33. Mauger, 2015, Alternative splicing regulates the expression of G9A and SUV39H2 methyltransferases, and dramatically changes SUV39H2 functions, Nucleic Acids Res., 43, 1869, 10.1093/nar/gkv013 · DOI
  34. Melamud, 2010, Metabolomic analysis and visualization engine for LC-MS data, Anal. Chem., 82, 9818, 10.1021/ac1021166 · DOI
  35. Mentch, 2015, Histone methylation dynamics and gene regulation occur through the sensing of one-carbon metabolism, Cell Metab., 22, 861, 10.1016/j.cmet.2015.08.024 · DOI
  36. Miller, 2005, Methionine-deficient diet extends mouse lifespan, slows immune and lens aging, alters glucose, T4, IGF-I and insulin levels, and increases hepatocyte MIF levels and stress resistance, Aging Cell, 4, 119, 10.1111/j.1474-9726.2005.00152.x · DOI · Paper page
  37. Mootha, 2003, PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes, Nat. Genet., 34, 267, 10.1038/ng1180 · DOI · Paper page
  38. Mostoslavsky, 2006, Genomic instability and aging-like phenotype in the absence of mammalian SIRT6, Cell, 124, 315, 10.1016/j.cell.2005.11.044 · DOI · Paper page
  39. Ni, 2012, Two SET domain containing genes link epigenetic changes and aging in Caenorhabditis elegans, Aging Cell, 11, 315, 10.1111/j.1474-9726.2011.00785.x · DOI
  40. Northcott, 2009, Multiple recurrent genetic events converge on control of histone lysine methylation in medulloblastoma, Nat. Genet., 41, 465, 10.1038/ng.336 · DOI
  41. Orentreich, 1993, Low methionine ingestion by rats extends life span, J. Nutr., 123, 269, 10.1093/jn/123.2.269 · DOI
  42. Peters, 2001, Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability, Cell, 107, 323, 10.1016/S0092-8674(01)00542-6 · DOI · Paper page
  43. Pinheiro, 2012, Prdm3 and Prdm16 are H3K9me1 methyltransferases required for mammalian heterochromatin integrity, Cell, 150, 948, 10.1016/j.cell.2012.06.048 · DOI
  44. Quinlan, 2010, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, 26, 841, 10.1093/bioinformatics/btq033 · DOI · Paper page
  45. Rhyu, 2014, Expression of human endogenous retrovirus env genes in the blood of breast cancer patients, Int. J. Mol. Sci., 15, 9173, 10.3390/ijms15069173 · DOI
  46. Sanderson, 2019, Methionine metabolism in health and cancer: a nexus of diet and precision medicine, Nat. Rev. Cancer, 19, 625, 10.1038/s41568-019-0187-8 · DOI
  47. Scaffidi, 2006, Lamin A-dependent nuclear defects in human aging, Science, 312, 1059, 10.1126/science.1127168 · DOI · Paper page
  48. Shiraki, 2014, Methionine metabolism regulates maintenance and differentiation of human pluripotent stem cells, Cell Metab., 19, 780, 10.1016/j.cmet.2014.03.017 · DOI
  49. Shyh-Chang, 2013, Influence of threonine metabolism on S-adenosylmethionine and histone methylation, Science, 339, 222, 10.1126/science.1226603 · DOI · Paper page
  50. Simon, 2019, LINE1 derepression in aged wild-type and SIRT6-deficient mice drives inflammation, Cell Metab., 29, 871, 10.1016/j.cmet.2019.02.014 · DOI · Paper page
  51. Strekalova, 2019, S-adenosylmethionine biosynthesis is a targetable metabolic vulnerability of cancer stem cells, Breast Cancer Res. Treat., 175, 39, 10.1007/s10549-019-05146-7 · DOI
  52. Tang, 2017, Methionine metabolism is essential for SIRT1-regulated mouse embryonic stem cell maintenance and embryonic development, EMBO J., 36, 3175, 10.15252/embj.201796708 · DOI
  53. Watson, 2014, SUV39H1/H3K9me3 attenuates sulforaphane-induced apoptotic signaling in PC3 prostate cancer cells, Oncogenesis, 3, e131, 10.1038/oncsis.2014.47 · DOI
  54. Wood, 2010, Chromatin remodeling in the aging genome of Drosophila, Aging Cell, 9, 971, 10.1111/j.1474-9726.2010.00624.x · DOI · Paper page
  55. Wu, 1983, Chiral instability at sulfur of S-adenosylmethionine, Biochemistry, 22, 2828, 10.1021/bi00281a009 · DOI
  56. Ye, 2017, A metabolic function for phospholipid and histone methylation, Mol. Cell, 66, 180, 10.1016/j.molcel.2017.02.026 · DOI
  57. Yu, 2018, Short-term methionine deprivation improves metabolic health via sexually dimorphic, mTORC1-independent mechanisms, FASEB J., 32, 3471, 10.1096/fj.201701211R · DOI
  58. Zee, 2010, In vivo residue-specific histone methylation dynamics, J. Biol. Chem., 285, 3341, 10.1074/jbc.M109.063784 · DOI
  59. Zhang, 2008, Model-based analysis of ChIP-seq (MACS), Genome Biol., 9, R137, 10.1186/gb-2008-9-9-r137 · DOI · Paper page

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Metadata

Authors
Haws, S. A., Yu, D., Ye, C., Wille, C. K., Nguyen, L. C., Krautkramer, K. A., Tomasiewicz, J. L., Yang, S. E., Miller, B. R., Liu, W. H., Igarashi, K., Sridharan, R., Tu, B. P., Cryns, V. L., Lamming, D. W., & Denu, J. M.
Venue
Molecular Cell
Publisher
Elsevier BV
Published
2020-04
Volume
78
Issue
2
Pages
210-223.e8
ISSN
1097-2765
Cited by
94
References
15
Language
en
Funders
  • National Institutes of Health (R37 GM059785, T32 DK007665, AG041765, AG051974, AG056771, K99 GM129415, AG050135, R01 GM094314, F32 GM128399, AG062328, GM113033)
  • School of Medicine and Public Health, University of Wisconsin-Madison
  • College of Engineering, University of Wisconsin-Madison
  • V Foundation for Cancer Research
  • American Foundation for Aging Research
  • Japan Society for the Promotion of Science (18H05374)
  • U.S. Department of Veterans Affairs (I01-BX004031)
  • American Heart Association (17PRE33410983)
  • Glenn Foundation for Medical Research
  • American Federation for Aging Research

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