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| Status |
Public on Sep 30, 2012 |
| Title |
Genome-wide DNA hydroxymethylation changes are associated with neurodevelopmental genes in the developing human brain |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
5-hydroxymethylcytosine (5-hmC) is a newly discovered modified form of cytosine that has been suspected to be an important epigenetic modification in neurodevelopment. While DNA methylation dynamics have already been implicated during neurodevelopment, little is known about hydroxymethylation in this process. Here we report DNA hydroxymethylation dynamics during cerebellum development in the human brain. Overall, we find a positive correlation between 5-hmC levels and cerebellum development. Genome-wide profiling reveals that 5-hmC is highly enriched on specific gene regions, including exons and especially the untranslated regions (UTRs), but it is depleted on introns and intergenic regions. Furthermore, we have identified fetus-specific and adult-specific differentially hydroxymethylated regions (DhMRs), most of which overlap with genes and CpG island shores. Surprisingly, during development DhMRs are highly enriched in genes encoding mRNAs that can be regulated by fragile X mental retardation protein (FMRP), some of which are disrupted in autism, as well as in many known autism genes. Our results suggest that 5-hmC-mediated epigenetic regulation may broadly impact the development of the human brain, and its dysregulation could contribute to the molecular pathogenesis of neurodevelopmental disorders.
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| Overall design |
We generated comprehensive genome-wide profiles of 5hmC in human cerebellum.
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| Contributor(s) |
Wang T |
| Citation(s) |
23042784 |
| Submission date |
Aug 31, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Tao Wang |
| E-mail(s) |
twang9@emory.edu
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| Phone |
4047270405
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| Organization name |
Emory University
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| Department |
Human Genetics
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| Lab |
Warren Lab
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| Street address |
615 Michael Street
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (1) |
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| Relations |
| BioProject |
PRJNA174249 |
| SRA |
SRP015342 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE40539_RAW.tar |
570.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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