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| Status |
Public on Mar 01, 2012 |
| Title |
Human cerebral cortex DNA methylation by MeDIP-Chip |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by genome tiling array
|
| Summary |
The highly improved cognitive function is the most significant change in human evolutionary history. Recently, several large-scale studies reported the evolutionary roles of DNA methylation; however, the role of DNA methylation on brain evolution is largely unknown. To test if DNA methylation has contributed to the evolution of human brain, with the use of MeDIP-Chip and SEQUENOM MassARRAY, we conducted a genome-wide analysis to identify differentially methylated regions (DMRs) in the brain between humans and rhesus macaques. We first identified a total of 150 candidate DMRs by the MeDIP-Chip method, among which 4DMRs were confirmed by the MassARRAY analysis. All 4 DMRs are within or close to the CpG islands, and a MIR3 repeat element was identified in one DMR, but no repeat sequence was observed in the other 3 DMRs. For the 4 DMR genes, their proteins tend to be conserved and two genes have neural related functions. Bisulfite sequencing and phylogenetic comparison among human, chimpanzee, rhesus macaque and rat suggested several regions of lineage specific DNA methylation, including a human specific hypomethylated region in the promoter of K6IRS2 gene. Our study provides a new angle of studying human brain evolution and understanding the evolutionary role of DNA methylation in the central nervous system. The results suggest that the patterns of DNA methylation in the brain are in general similar between humans and non-human primates, and only a few DMRs were identified.
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| |
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| Overall design |
Compare the DNA methylation levels between human and rhesus macaque
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| |
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| Contributor(s) |
Wang J, Cao X, Zhang Y, Su B |
| Citation(s) |
22899776 |
| |
| Submission date |
Feb 23, 2011 |
| Last update date |
Aug 30, 2012 |
| Contact name |
Jinkai Wang |
| Organization name |
University of California, Los Angeles
|
| Street address |
650 Charles E. Young Drive South, CHS 33-228
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-7278 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL9448 |
NimbleGen Human HG18 RefSeq Promoter 385K tiling array |
|
| Samples (3) |
| GSM678519 |
NimbleGen: Human cerebral cortex H1 |
| GSM678520 |
NimbleGen: Human cerebral cortex H2 |
| GSM678521 |
NimbleGen: Human cerebral cortex H3 |
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| This SubSeries is part of SuperSeries: |
| GSE27461 |
Genome-wide DNA methylation analyses in the brain reveal four differentially methylated regions between humans and non-human primates |
|
| Relations |
| BioProject |
PRJNA141755 |
