Comparison of DNA methylation in human tissues
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Diane Schroeder
PROVIDER: E-GEOD-39777 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
The human placenta methylome.
Schroeder Diane I DI Blair John D JD Lott Paul P Yu Hung On Ken HO Hong Danna D Crary Florence F Ashwood Paul P Walker Cheryl C Korf Ian I Robinson Wendy P WP LaSalle Janine M JM
Proceedings of the National Academy of Sciences of the United States of America 20130325 15
Tissue-specific DNA methylation is found at promoters, enhancers, and CpG islands but also over larger genomic regions. In most human tissues, the vast majority of the genome is highly methylated (>70%). Recently, sequencing of bisulfite-treated DNA (MethylC-seq) has revealed large partially methylated domains (PMDs) in some human cell lines. PMDs cover up to 40% of the genome and are associated with gene repression and inactive chromatin marks. However, to date, only cultured cells and cancers ...[more]
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Project description:As genome-scale DNA methylation sequencing technologies have improved it has become apparent that tissue-specific methylation can occur not only at promoters, enhancers, and CpG islands but also over larger genomic regions. In most human tissues, the vast majority of the genome is highly methylated (>70%). However, genomic sequencing of bisulfite-treated DNA (MethylC-seq) has revealed large partially methylated domains (PMDs) in some human cell lines. However, to date only cultured cells and some cancers have shown evidence for PMDs, suggesting that PMDs may not be observed in normal human tissues. Here we performed MethylC-seq in a set of human tissues and found that full-term human placenta shows clear evidence of PMDs. Examination of four human tissue samples by MethylC-seq, with one tissue (placenta) having a technical replicate (taken from same placenta) and two additional biological replicates (from different placentas)
2013-03-28 | E-GEOD-39775 | biostudies-arrayexpress
Project description:Over the last 20-80 million years the mammalian placenta has taken on a variety of morphologies through both divergent and convergent evolution. Recently we have shown that the human placenta genome has a unique epigenetic pattern of large partially methylated domains (PMDs) and highly methylation domains (HMDs) with gene body DNA methylation positively correlating with level of gene expression. In order to determine the evolutionary conservation of DNA methylation patterns and transcriptional regulatory programs in the placenta, we performed a genome-wide methylome (MethylC-seq) analysis of human, rhesus macaque, squirrel monkey, mouse, dog, horse, and cow placentas as well as opossum extraembryonic membrane. We found that, similar to human placenta, mammalian placentas and opossum extraembryonic membrane have globally lower levels of methylation compared to somatic tissues. However, not all species have clear PMD/HMDs in their placentas. Instead what is conserved is higher methylation over the bodies of genes involved in mitosis, vesicle-mediated transport, protein phosphorylation, and chromatin modification compared with the rest of the genome. As in human placenta, high gene body methylation is associated with higher gene expression across species. Analysis of DNA methylation in mouse and cow oocytes shows the same pattern of gene body methylation over many of the same genes as in the placenta, suggesting that this conserved pattern of active gene body methylation of the placenta may be established very early in development. MethylC-seq on placentas of 7 mammals, trophoblasts of rhesus, brains of 3 mammals, oocytes of cow, and human cordblood
2015-08-05 | E-GEOD-63330 | biostudies-arrayexpress
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2014-07-01 | E-GEOD-43094 | biostudies-arrayexpress
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2014-05-28 | E-GEOD-43473 | biostudies-arrayexpress