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Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE49909 | GEO | 2013/08/16

SECONDARY ACCESSION(S): PRJNA215303

REPOSITORIES: GEO

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Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape.

Project description:BACKGROUND: DNA methylation is an epigenetic modification that changes with age in human tissues, although the mechanisms and specificity of this process are still poorly understood. We compared CpG methylation changes with age across 283 human blood, brain, kidney, and skeletal muscle samples using methylation arrays to identify tissue-specific age effects. RESULTS: We found age-associated CpGs (ageCGs) that are both tissue-specific and common across tissues. Tissue-specific age CGs are frequently located outside CpG islands with decreased methylation, and common ageCGs show the opposite trend. AgeCGs are significantly associated with poorly expressed genes, but those with decreasing methylation are linked with higher tissue-specific expression levels compared with increasing methylation. Therefore, tissue-specific gene expression may protect against common age-dependent methylation. Distinguished from other tissues, skeletal muscle age CGs are more associated with expression, enriched near genes related to myofiber contraction, and closer to muscle-specific CTCF binding sites. Kidney-specific ageCGs are more increasingly methylated compared to other tissues as measured by affiliation with kidney-specific expressed genes. Underlying chromatin features also mark common and tissue-specific age effects reflective of poised and active chromatin states, respectively. In contrast with decreasingly methylated ageCGs, increasingly methylated ageCGs are also generally further from CTCF binding sites and enriched within lamina associated domains. CONCLUSIONS: Our data identified common and tissue-specific DNA methylation changes with age that are reflective of CpG landscape and suggests both common and unique alterations within human tissues. Our findings also indicate that a simple epigenetic drift model is insufficient to explain all age-related changes in DNA methylation.

| S-EPMC4053985 | biostudies-literature

Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-08-16 | E-GEOD-49909 | biostudies-arrayexpress

Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape [brain]

Project description:Genome wide DNA methylation profiling of 4 human tissues of various ages: 78 samples from Brodmann area 19 of the cerebral cortex.The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Sentrix barcode included for batch normalization 1ug of genomic DNA was bisulfite converted using EZ-96 DNA Methylation Kit from ZymoResearch, and hybridized to beadchips according to Illumina Infinium 27k Human DNA methylation standard procedures

2013-08-16 | E-GEOD-49905 | biostudies-arrayexpress

Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape [blood]

Project description:Genome wide DNA methylation profiling of 4 human tissues of various ages: 71 human buffy coat samples. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Sentrix barcode provided for batch correction Buffy coats obtained from Conversant Bio and genomic DNAs isolated by Agencourt Genfind v2; 1ug of genomic DNA was bisulfite converted using EZ-96 DNA Methylation Kit from ZymoResearch; samples hybridized to beadchips according to Illumina Infinium 27k Human DNA methylation standard procedures

2013-08-16 | E-GEOD-49904 | biostudies-arrayexpress

Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape [kidney]

Project description:Genome wide DNA methylation profiling of 4 human tissues of various ages: 83 samples of normal adjacent resected kidney tissue .The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Sentrix barcode provided for batch normalization 1ug of genomic DNA was bisulfite converted using EZ-96 DNA Methylation Kit from ZymoResearch, and hybridized to beadcheaps according to Illumina Infinium 27k Human DNA methylation standard procedures

2013-08-16 | E-GEOD-49907 | biostudies-arrayexpress

Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape [muscle]

Project description:Genome wide DNA methylation profiling of 4 human tissues of various ages: 51 vastus lateralis samples.The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Sentrix barcode provided for batch normalization 500ng of genomic DNA was bisulfite converted using EZ-96 DNA Methylation Kit from ZymoResearch, and hybridized to beadcheaps according to Illumina Infinium 27k Human DNA methylation standard procedures.

2013-08-16 | E-GEOD-49908 | biostudies-arrayexpress

Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape [muscle]

2013-08-16 | GSE49908 | GEO

Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape [brain]

2013-08-16 | GSE49905 | GEO

Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape [blood]

2013-08-16 | GSE49904 | GEO

Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape [kidney]

2013-08-16 | GSE49907 | GEO