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Series GSE63330 Query DataSets for GSE63330
Status Public on Aug 05, 2015
Title DNA methylation in mammalian placentas
Organisms Macaca mulatta; Homo sapiens; Canis lupus familiaris; Equus caballus; Bos taurus; Mus musculus; Monodelphis domestica; Saimiri boliviensis
Experiment type Methylation profiling by high throughput sequencing
Summary 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.
Overall design MethylC-seq on placentas of 7 mammals, trophoblasts of rhesus, brains of 3 mammals, oocytes of cow, and human cordblood
Contributor(s) Schroeder DI, LaSalle JM
Citation(s) 26241857
Submission date Nov 17, 2014
Last update date May 15, 2019
Contact name Janine LaSalle
Organization name UC Davis
Street address Medical Microbiology and Immunology
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
Platforms (8)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL14954 Illumina HiSeq 2000 (Macaca mulatta)
Samples (20)
GSM1545827 rhesus_placenta
GSM1545828 squirrel_monkey_ placenta
GSM1545829 mouse_placenta
BioProject PRJNA267523
SRA SRP049936

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Supplementary file Size Download File type/resource
GSE63330_RAW.tar 1.9 Gb (http)(custom) TAR (of TAR)
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Raw data are available in SRA
Processed data provided as supplementary file

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