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Epigenetics Volume 15, 2020 - Issue 3
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Research Paper

Age-related DNA hydroxymethylation is enriched for gene expression and immune system processes in human peripheral blood

Nicholas D. JohnsonDepartment of Human Genetics, Emory University, Atlanta, GA, USA;Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA, USACorrespondence[email protected]
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Luoxiu HuangDepartment of Human Genetics, Emory University, Atlanta, GA, USAView further author information
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Ronghua LiDepartment of Human Genetics, Emory University, Atlanta, GA, USAView further author information
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Yun LiDepartment of Genetics, University of North Carolina, Chapel Hill, NC, USA;Department of Biostatistics, Department of Computer Science, University of North Carolina, Chapel Hill, NC, USAORCID Iconhttps://orcid.org/0000-0002-9275-4189View further author information
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Yuchen YangDepartment of Genetics, University of North Carolina, Chapel Hill, NC, USAView further author information
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Hye Rim KimDepartment of Human Genetics, Emory University, Atlanta, GA, USA;Cancer Biology Graduate Program, Emory University, Atlanta, GA, USAORCID Iconhttps://orcid.org/0000-0002-6879-2644View further author information
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Crystal GrantDepartment of Human Genetics, Emory University, Atlanta, GA, USA;Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA, USAORCID Iconhttps://orcid.org/0000-0002-5623-7002View further author information
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Hao WuDepartment of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USAView further author information
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Eric A. WhitselDepartment of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA;Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USAORCID Iconhttps://orcid.org/0000-0003-4843-3641View further author information
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Douglas P. KielHebrew SeniorLife, Department of Medicine Beth Israel Deaconess Medical Center and Harvard Medical School, Hinda and Arthur Marcus Institute for Aging Research, Boston, MA, USAORCID Iconhttps://orcid.org/0000-0001-8474-0310View further author information
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Andrea A. BaccarelliDepartment of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USAView further author information
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Peng JinDepartment of Human Genetics, Emory University, Atlanta, GA, USAORCID Iconhttps://orcid.org/0000-0001-6137-6659View further author information
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Joanne M. MurabitoNational Heart Lung and Blood Institute’s and Boston University’s Framingham Heart Study, Framingham, MA, USA;Section of General Internal Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USAView further author information
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Karen N. ConneelyDepartment of Human Genetics, Emory University, Atlanta, GA, USA;Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA, USAView further author information
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Pages 294-306 | Received 17 May 2019, Accepted 06 Sep 2019, Published online: 26 Sep 2019

Figures & data

Figure 1. Overlapping reads per kbp across genomic features. To calculate read density, reads that overlapped a genomic feature were counted and averaged across individuals.

Figure 1. Overlapping reads per kbp across genomic features. To calculate read density, reads that overlapped a genomic feature were counted and averaged across individuals.

Table 1. Total number (and percentages) of DhMRs showing decreased DNAhm with age, denoted (-) DhMRs, and DhMRs showing increased DNAhm, denoted (+) DhMRs, and for reference, all 2,000 bp bins overlapping at least one promoter, enhancer, or gene body.

Figure 2. Manhattan plot of DhMR analysis. The y-axis represents the signed negative log10-p-value and the x-axis represents the chromosome number and position, with chromosome X appearing to the very right.

Figure 2. Manhattan plot of DhMR analysis. The y-axis represents the signed negative log10-p-value and the x-axis represents the chromosome number and position, with chromosome X appearing to the very right.

Figure 3. Volcano plot of DhMRs in 2000 bp bins. Bins in light blue are those with FDR<0.05.

Figure 3. Volcano plot of DhMRs in 2000 bp bins. Bins in light blue are those with FDR<0.05.

Figure 4. Heatmap of log10-normalized read counts of the 6,650 DhMRs. The numbers along the x-axis indicate ages.

Figure 4. Heatmap of log10-normalized read counts of the 6,650 DhMRs. The numbers along the x-axis indicate ages.

Table 2. Significantly enriched GO terms by direction of differential DNAhm and genomic feature showing differential DNAhm.

Supplemental material

Supplemental Material

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Related Research Data

Age-related DNA hydroxymethylation is enriched for gene expression and immune system processes in human peripheral blood.
Source: Taylor & Francis
Age-related DNA hydroxymethylation is enriched for gene expression and immune system processes in human peripheral blood
Source: Taylor & Francis
Age-related DNA hydroxymethylation is enriched for gene expression and immune system processes in human peripheral blood
Source: Taylor & Francis

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