title: Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain.
abstract: 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 genome-wide and single-base resolution maps of hmC and mC in the human brain by combined application of Tet-assisted bisulfite sequencing and bisulfite sequencing. We demonstrate that hmCs increase markedly from the fetal to the adult stage, and in the adult brain, 13% of all CpGs are highly hydroxymethylated with strong enrichment at genic regions and distal regulatory elements. Notably, hmC peaks are identified at the 5'splicing sites at the exon-intron boundary, suggesting a mechanistic link between hmC and splicing. We report a surprising transcription-correlated hmC bias toward the sense strand and an mC bias toward the antisense strand of gene bodies. Furthermore, hmC is negatively correlated with H3K27me3-marked and H3K9me3-marked repressive genomic regions, and is more enriched at poised enhancers than active enhancers.
  
  
  CONCLUSIONS
  We provide single-base resolution hmC and mC maps in the human brain and our data imply novel roles of hmC in regulating splicing and gene expression. Hydroxymethylation is the main modification status for a large portion of CpGs situated at poised enhancers and actively transcribed regions, suggesting its roles in epigenetic tuning at these regions.
authors.forename: Lu
authors.initials: L
authors.lastname: Wen
authors.forename: Xianlong
authors.initials: X
authors.lastname: Li
authors.forename: Liying
authors.initials: L
authors.lastname: Yan
authors.forename: Yuexi
authors.initials: Y
authors.lastname: Tan
authors.forename: Rong
authors.initials: R
authors.lastname: Li
authors.forename: Yangyu
authors.initials: Y
authors.lastname: Zhao
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.forename: Jingcheng
authors.initials: J
authors.lastname: Xie
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.forename: Chunxiao
authors.initials: C
authors.lastname: Song
authors.forename: Miao
authors.initials: M
authors.lastname: Yu
authors.forename: Xiaomeng
authors.initials: X
authors.lastname: Liu
authors.forename: Ping
authors.initials: P
authors.lastname: Zhu
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Li
authors.forename: Yu
authors.initials: Y
authors.lastname: Hou
authors.forename: Hongshan
authors.initials: H
authors.lastname: Guo
authors.forename: Xinglong
authors.initials: X
authors.lastname: Wu
authors.forename: Chuan
authors.initials: C
authors.lastname: He
authors.forename: Ruiqiang
authors.initials: R
authors.lastname: Li
authors.forename: Fuchou
authors.initials: F
authors.lastname: Tang
authors.forename: Jie
authors.initials: J
authors.lastname: Qiao
mesh_terms: D044503:5-Methylcytosine / Q000378:metabolism* / Q000031:analogs & derivatives; D000328:Adult; D001921:Brain / Q000196:embryology / Q000254:growth & development / Q000378:metabolism*; D018899:CpG Islands; D003596:Cytosine / Q000031:analogs & derivatives* / Q000378:metabolism; D019175:DNA Methylation; D016373:DNA, Antisense / Q000378:metabolism; D005091:Exons; D005260:Female; D018507:Gene Expression Regulation, Developmental; D015894:Genome, Human; D006657:Histones / Q000235:genetics; D006801:Humans; D007438:Introns; D008297:Male; D014158:Transcription, Genetic
chemical_list: D016373:DNA, Antisense; D006657:Histones; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine