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Research Paper

Age-related epigenome-wide DNA methylation and hydroxymethylation in longitudinal mouse blood

ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon & ORCID Icon
Pages 779-792 | Received 11 Apr 2018, Accepted 25 Jul 2018, Published online: 23 Aug 2018

References

  • Medvedeva YA, Khamis AM, Kulakovskiy IV, et al. Effects of cytosine methylation on transcription factor binding sites. BMC Genomics. 2014;15:119.
  • Slotkin RK, Martienssen R. Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet. 2007;8:272–285.
  • Reik W, Dean W, Walter J. Epigenetic reprogramming in mammalian development. Science. 2001;293:1089–1093.
  • Smallwood SA, Kelsey G. De novo DNA methylation: a germ cell perspective. Trends Genet. 2012;28:33–42.
  • Messerschmidt DM, Knowles BB, Solter D. DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos. Genes Dev. 2014;28:812–828.
  • Jung M, Pfeifer GP. Aging and DNA methylation. BMC Biol. 2015;13:7.
  • Kochmanski J, Montrose L, Goodrich JM, et al. Environmental deflection: the impact of toxicant exposures on the aging epigenome. Toxicol Sci. 2017;156:325–335.
  • Jones MJ, Goodman SJ, Kobor MS. DNA methylation and healthy human aging. Aging Cell. 2015;14:924–932.
  • Shen L, Song CX, He C, et al. Mechanism and function of oxidative reversal of DNA and RNA methylation. Annu Rev Biochem. 2014;83:585–614.
  • Wu H, D’Alessio AC, Ito S, et al. Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes Dev. 2011;25:679–684.
  • Hahn MA, Szabó PE, Pfeifer GP. 5-Hydroxymethylcytosine: a stable or transient DNA modification? Genomics. 2014;104:314–323.
  • Mellén M, Ayata P, Dewell S, et al. MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system. Cell. 2012;151:1417–1430.
  • Spruijt CG, Gnerlich F, Smits AH, et al. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell. 2013;152:1146–1159.
  • Globisch D, Münzel M, Müller M, et al. Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS One. 2010;5:e15367.
  • Nestor CE, Ottaviano R, Reddington J, et al. Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes. Genome Res. 2012;22:467–477.
  • Wen L, Li X, Yan L, et al. Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain. Genome Biol. 2014;15:R49.
  • Hernandez Mora JR, Sanchez-Delgado M, Petazzi P, et al. Profiling of oxBS-450K 5-hydroxymethylcytosine in human placenta and brain reveals enrichment at imprinted loci. Epigenetics. 2018;13:182–191.
  • Kochmanski J, Marchlewicz EH, Savidge M, et al. Longitudinal effects of developmental bisphenol A and variable diet exposures on epigenetic drift in mice. Reprod Toxicol. 2017;68:154–163.
  • Kochmanski J, Marchlewicz EH, Cavalcante RG, et al. Longitudinal effects of developmental bisphenol A exposure on epigenome-wide DNA hydroxymethylation at imprinted loci in mouse blood. Env Heal Perspect 2018. In revision.
  • López V, Fernández AF, Fraga MF. The role of 5-hydroxymethylcytosine in development, aging and age-related diseases. Ageing Res Rev. 2017;37:28–38.
  • Xiong J, Jiang H-P, Peng C-Y, et al. DNA hydroxymethylation age of human blood determined by capillary hydrophilic-interaction liquid chromatography/mass spectrometry. Clin Epigenet. 2015;7:72.
  • Truong TP, Sakata-Yanagimoto M, Yamada M, et al. Age-dependent decrease of DNA hydroxymethylation in human T cells. J Clin Exp Hematop. 2015;55:1–6.
  • Heyn H, Li N, Ferreira HJ, et al. Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci USA. 2012;109:10522–10527.
  • Horvath S. DNA methylation age of human tissues and cell types. Genome Biol. 2013;14:R115.
  • Stroud H, Feng S, Kinney SM, et al. 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biol. 2011;12:R54.
  • Harris L, Genovesi LA, Gronostajski RM, et al. Nuclear factor one transcription factors: divergent functions in developmental versus adult stem cell populations. Dev Dyn. 2015;244:227–238.
  • Chaudhry AZ, Lyons GE, Gronostajski RM. Expression patterns of the four nuclear factor I genes during mouse embryogenesis indicate a potential role in development. Dev Dyn. 1997;208:313–325.
  • Gronostajski RM. Roles of the NFI/CTF gene family in transcription and development. Gene. 2000;249:31–45.
  • Edelmann S, Fahrner R, Malinka T, et al. Nuclear Factor I-C acts as a regulator of hepatocyte proliferation at the onset of liver regeneration. Liver Int. 2015;35:1185–1194.
  • Lee D-S, Choung H-W, Kim H-J, et al. Regulates osteoblast differentiation via control of osterix expression. Stem Cells. 2014;32:2467–2479.
  • Roh SY, Park J-C. The role of nuclear factor I-C in tooth and bone development. J Korean Assoc Oral Maxillofac Surg. 2017;43:63.
  • Sérandour AA, Avner S, Oger F, et al. Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers. Nucleic Acids Res. 2012;40:8255–8265.
  • Ehrlich M, Ehrlich KC. DNA cytosine methylation and hydroxymethylation at the borders. Epigenomics. 2014;6:563–566.
  • Greco CM, Kunderfranco P, Rubino M, et al. DNA hydroxymethylation controls cardiomyocyte gene expression in development and hypertrophy. Nat Commun. 2016;7:12418.
  • Cancro MP, Hao Y, Scholz JL, et al. B cells and ag-ing: molecules and mechanisms. Trends Immunol. 2009;30:313–318.
  • Moro-García MA, Alonso-Arias R, López-Larrea C. When aging reaches CD4+ T-cells: phenotypic and functional changes. Front Immunol. 2013;4:1–12.
  • Jaffe AE, Irizarry RA. Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol. 2014;15:R31.
  • Lokk K, Modhukur V, Rajashekar B, et al. DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns. Genome Biol. 2014;15:3248.
  • Maegawa S, Hinkal G, Kim HS, et al. Widespread and tissue specific age-related DNA methylation changes in mice. Genome Res. 2010;20:332–340.
  • Garrett-Bakelman FE, Sheridan CK, Kacmarczyk TJ, et al. Enhanced reduced representation bisulfite sequencing for assessment of DNA methylation at base pair resolution. J Vis Exp. 2015;96:e52246.
  • Zampieri M, Ciccarone F, Calabrese R, et al. Reconfiguration of DNA methylation in aging. Mech Ageing Dev. 2015;151:60–70.
  • Ziller MJ, Hansen KD, Meissner A, et al. Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing. Nat Methods. 2015;12:230–232.
  • Booth MJ, Ost TWB, Beraldi D, et al. Oxidative bisulfite sequencing of 5-methylcytosine and 5- hydroxymethylcytosine. Nat Protoc. 2013;8:1841–1851.
  • Waterland RA, Jirtle RL. Transposable elements: targets for early nutritional effects on epigenetic gene regulation. Mol Cell Biol. 2003;23:5293–5300.
  • Weinhouse C, Anderson OS, Bergin IL, et al. Dose-dependent incidence of hepatic tumors in adult mice following perinatal exposure to bisphenol A. Env Heal Perspect. 2014;122:485–491.
  • National Research Council (US). Committee for the update of the guide for the care and use of laboratory animals. In: Guide for the care and use of laboratory animals. Washington, D.C.: National Academies Press (U.S.); 2011.
  • Tan L, Xiong L, Xu W, et al. Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method. Nucleic Acids Res. 2013;41:e84.
  • Akalin A, Kormaksson M, Li S, et al. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol. 2012;13:R87.
  • Cavalcante RG, Patil S, Park Y, et al. Integrating DNA methylation and hydroxymethylation data with the mint pipeline. Cancer Res. 2017;77:e27–e30.
  • Wu H, Wang C, Wu Z. A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data. Biostatistics. 2013;14:232–243.
  • Feng H, Conneely KN, Wu HA. Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data. Nucleic Acids Res. 2014;42:1–11.
  • Wu H, Xu T, Feng H, et al. Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates. Nucleic Acids Res. 2015;43:1–9.
  • Park Y, Wu H. Differential methylation analysis for BS-seq data under general experimental design. Bioinformatics. 2016;32:1446–1453.
  • Lun ATL, Smyth GK. csaw: a bioconductor package for differential binding analysis of ChIP-seq data using sliding windows. Nucleic Acids Res. 2016;44:e45–e45.
  • Benjamini Y, Hochberg Y. Multiple hypotheses testing with weights. Scand J Stat. 1997;24:407–418.
  • Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc SeR B. 1995;57:289–300.
  • Cavalcante RG, Sartor MA. annotatr: genomic regions in context. Bioinformatics. 2017;33:2381–2383.
  • Assenov Y, Müller F, Lutsik P, et al. Comprehensive analysis of DNA methylation data with RnBeads. Nat Methods. 2014;11:1138–1140.
  • Hahne F, Ivanek R. Visualizing genomic data us-ing gviz and bioconductor. I Methods Mol Biol. 2016;1418:335–351.
  • Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods. 2001;25:402–408.
  • Dolinoy DC, Weinhouse C, Jones TR, et al. Variable histone modifications at the A(vy) metastable epiallele. Epigenetics. 2010;5:637–644.
  • La Salle S, Mertineit C, Taketo T, et al. Windows for sex-specific methylation marked by DNA methyltransferase expression profiles in mouse germ cells. Dev Biol. 2004;268:403–415.
  • Welch RP, Lee C, Imbriano PM, et al. ChIP-enrich: gene set enrichment testing for ChIP-seq data. Nucleic Acids Res. 2014;42:e105–e105.

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