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Title: Array-based assay detects genome-wide 5-methylcytosine and 5-hydroxymethlycytosine in non-human primates and mice      
keywords:
Epigenomics
ID:
PRJNA213232
description:
Murine and non-human primates (e.g. rhesus monkeys) represent excellent model systems to study human health and disease. However, use of these model systems for genomic studies is limited, particularly with array-based tools, as most have only been developed to survey the human genome. Here we present the optimization of a widely used human DNA methylation array, designed to detect 5-methylcytosine (5-mC), and show that non-human data generated using the optimized array reproducibly distinguishes tissue types within and between chimpanzee, rhesus, and mouse, with correlations near the human DNA level (R2 > 0.99). Genome-wide methylation analysis, using this approach, reveals 6,102 differentially methylated loci between rhesus placental and fetal tissues with pathways analysis significantly overrepresented for developmental processes. Restricting the analysis to oncogenes and tumor suppressors genes finds 125 differentially methylated loci, suggesting that rhesus placental tissue carries a cancer epigenetic signature. Moreover, we adapted the assay to detect 5-hydroxymethylcytosine (5-hmC) and find highly reproducible 5-hmC levels within human, rhesus, and mouse brain tissue that is species-specific with a hierarchical abundance among the three species (human > rhesus >> mouse). Together, these data show that this array-based methylation assay is generalizable to all mammals for the detection of both 5-mC and 5-hmC, greatly improving the utility of mammalian model systems to study the role of epigenetics in human health, disease, and evolution. Overall design: Here we present the optimization of a widely used human DNA methylation array, designed to detect 5-methylcytosine (5-mC), and show that non-human data generated using the optimized array reproducibly distinguishes tissue types within and between chimpanzee, rhesus, and mouse, with correlations near the human DNA level (R2 > 0.99).
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landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA213232
authentication:
none
authorization:
none
ID:
pmid:24524199
abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject
  • P30NS055077/NS/NINDS NIH HHS/United States

  • MH081884/MH/NIMH NIH HHS/United States

  • MH046729/MH/NIMH NIH HHS/United States

  • MH089606/MH/NIMH NIH HHS/United States

  • MH084051/MH/NIMH NIH HHS/United States

  • P51 OD011106/OD/NIH HHS/United States

  • P50 AG025688/AG/NIA NIH HHS/United States

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