Transcriptomics

Dataset Information

4

Genomic mapping of 5-hydroxymethylcytosine in the human brain


ABSTRACT: Methylation at the 5-position of cytosine is a well-studied epigenetic pathway. In addition to 5-methylcytosine (5mC), substantial amounts of 5-hydroxymethylcytosine (5hmC) also referred to as the 6th DNA base, have been detected in certain tissues, most notably the brain. However, the genomic distribution of this cytosine modification is unknown. Here, we have developed an immunoprecipitation technique (5hmC-IP) to examine the occurrence of 5hmC in human DNA from brain frontal lobe tissue. The distribution of 5hmC was compared to that of 5mC. We show that 5hmC is more selectively targeted to genes than is 5mC. 5hmC is found at promoters and is particularly enriched in intragenic regions (gene bodies) but is largely absent from non-gene regions. 5hmC peaks at transcription start sites did not correlate with gene expression levels or H3K4me3 peaks. However, presence of 5hmC in gene bodies was more positively correlated with gene expression levels than was presence of 5mC. Promoters of testis-specific genes showed strong 5mC peaks in brain DNA but were almost completely devoid of 5hmC. Our data provide a first overview of the genomic distribution of 5hmC in human brain and will set the stage for further functional characterization of this novel DNA modification. Comparison between 5hmC and 5mC profiles

ORGANISM(S): Homo sapiens  

SUBMITTER: Xiwei Wu   Xuejun Li  Seung-Gi Jin  Gerd Pfeifer 

PROVIDER: E-GEOD-27051 | ArrayExpress | 2011-03-01

SECONDARY ACCESSION(S): GSE27051PRJNA137633

REPOSITORIES: GEO, ArrayExpress

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Publications

Genomic mapping of 5-hydroxymethylcytosine in the human brain.

Jin Seung-Gi SG   Wu Xiwei X   Li Arthur X AX   Pfeifer Gerd P GP  

Nucleic acids research 20110304 12


Methylation at the 5-position of cytosine is a well-studied epigenetic pathway. In addition to 5-methylcytosine (5mC), substantial amounts of 5-hydroxymethylcytosine (5hmC) also referred to as the sixth DNA base have been detected in certain tissues, most notably the brain. However, the genomic distribution of this cytosine modification is unknown. Here, we have used an immunoprecipitation technique (5hmC-IP) to examine the occurrence of 5hmC in DNA from human brain frontal lobe tissue. The dist  ...[more]

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