Abstract
BackgroundThe recent discovery that methylated cytosines are converted to 5-hydroxymethylated cytosines (5hmC) by the family of ten-eleven translocation enzymes has sparked significant interest on the genomic location, the abundance in different tissues, the putative functions, and the stability of this epigenetic mark. 5hmC plays a key role in the brain, where it is particularly abundant and dynamic during development.ResultsHere, we comprehensively characterize 5hmC in the prefrontal cortices of 24 subjects. We show that, although there is inter-individual variability in 5hmC content among unrelated individuals, approximately 8 % of all CpGs on autosomal chromosomes contain 5hmC, while sex chromosomes contain far less. Our data also provide evidence suggesting that 5hmC has transcriptional regulatory properties, as the density of 5hmC was highest in enhancer regions and within exons. Furthermore, we link increased 5hmC density to histone modification binding sites, to the gene bodies of actively transcribed genes, and to exon-intron boundaries. Finally, we provide several genomic regions of interest that contain gender-specific 5hmC.ConclusionsCollectively, these results present an important reference for the growing number of studies that are interested in the investigation of the role of 5hmC in brain and mental disorders.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1875-8) contains supplementary material, which is available to authorized users.
Highlights
The recent discovery that methylated cytosines are converted to 5-hydroxymethylated cytosines (5hmC) by the family of ten-eleven translocation enzymes has sparked significant interest on the genomic location, the abundance in different tissues, the putative functions, and the stability of this epigenetic mark. 5hmC plays a key role in the brain, where it is abundant and dynamic during development
Research has shown that 5mC can be oxidized to 5hydroxymethylcytosine (5hmC) by the ten-eleven translocation (TET) family of proteins [1,2,3]. 5hmC has been shown to be most abundant in brain tissue [4,5,6] and to influence transcriptional regulatory activity [7,8,9,10]
Our sequencing results consistently showed that 40–45 % of all reads contained cytosine and guanine bases, respectively, at the 11th and 12th positions after the adaptor sequence (Fig. 1a)
Summary
The recent discovery that methylated cytosines are converted to 5-hydroxymethylated cytosines (5hmC) by the family of ten-eleven translocation enzymes has sparked significant interest on the genomic location, the abundance in different tissues, the putative functions, and the stability of this epigenetic mark. 5hmC plays a key role in the brain, where it is abundant and dynamic during development. The recent discovery that methylated cytosines are converted to 5-hydroxymethylated cytosines (5hmC) by the family of ten-eleven translocation enzymes has sparked significant interest on the genomic location, the abundance in different tissues, the putative functions, and the stability of this epigenetic mark. 5hmC plays a key role in the brain, where it is abundant and dynamic during development. 5hmC has been shown to be most abundant in brain tissue [4,5,6] and to influence transcriptional regulatory activity [7,8,9,10]. Its role is not yet completely understood, 5hmC has been increasingly investigated in neuropsychiatric phenotypes, likely due to its involvement in neuronal development and enrichment in brain tissue [11, 12]. The descriptive data presented here provide a map of 5hmC at single base resolution, which is of interest to future studies of 5hmC in the cortex of the human brain
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