Genomics

Dataset Information

239

Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain


ABSTRACT: 5-Hydroxymethylcytosine (hmC) is particularly abundant in mammalian brains with yetto be revealed functions. Here, we present genome-wide and single-base-resolutionmaps of hmC and mC in the human brain. We demonstrated that hmCs increasemarkedly from the fetal to the adult stage, and in the adult brain, 13.4% of all CpGs arehighly hydroxymethylated with strong enrichment at genic regions and distal regulatoryelements. Notably, hmC peaks were identified at the 5' splicing sites at the exon-intronboundary, suggesting a mechanistic link between hmC and splicing. We also report asurprising transcription-correlated hmC bias toward the sense strand and an mC biastoward the antisense strand of gene bodies. Furthermore, hmC is negatively correlatedwith H3K27me3-marked repressive genomic regions, and is more enriched in poisedenhancers than active enhancers. Our results provide insights into understanding themultiple potential functions of hmC in the human brain. A cell type specific hydroxymethylome sample of NeuN+ neurons in frontal lobe from the same adult individual, whose TAB-Seq data was deposited in GSE46710

ORGANISM(S): Homo sapiens  

SUBMITTER: Liying Yan   Xianlong Li  Jie Qiao  Lu Wen  Fuchou Tang  Yuexi Tan 

PROVIDER: E-GEOD-55249 | ArrayExpress | 2014-02-22

SECONDARY ACCESSION(S): SRP038730GSE55249PRJNA238997

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications


BACKGROUND: 5-methylcytosine (mC) can be oxidized by the tet methylcytosine dioxygenase (Tet) family of enzymes to 5-hydroxymethylcytosine (hmC), which is an intermediate of mC demethylation and may also be a stable epigenetic modification that influences chromatin structure. hmC is particularly abundant in mammalian brains but its function is currently unknown. A high-resolution hydroxymethylome map is required to fully understand the function of hmC in the human brain. RESULTS: We present geno  ...[more]

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