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

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. Overall design: 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

5-羟甲基胞嘧啶（5-Hydroxymethylcytosine, hmC）在哺乳动物大脑中富集度颇高，但其具体功能迄今尚未阐明。本研究报道了人类大脑中全基因组范围、单碱基分辨率的hmC与甲基化胞嘧啶（methylated cytosine, mC）图谱。研究证实，从胎儿期至成年阶段，hmC水平显著升高；在成年大脑中，13.4%的CpG位点发生高度羟甲基化，且此类位点在基因区域与远端调控元件中显著富集。值得注意的是，研究在外显子-内含子边界的5'剪接位点处发现了hmC富集峰，这提示hmC与RNA剪接过程之间存在潜在的机制关联。本研究还报道了一项意外发现：与转录相关的hmC偏向基因体的正义链，而mC则偏向基因体的反义链。此外，hmC与带有组蛋白H3赖氨酸27三甲基化（H3K27me3）标记的抑制性基因组区域呈负相关，且在预备增强子（poised enhancer）中的富集程度高于活性增强子。本研究结果为解析人类大脑中hmC的多种潜在功能提供了重要线索。实验整体设计：取自同一成年个体额叶的神经元特异性核蛋白（Neuronal Nuclei, NeuN）阳性神经元的细胞类型特异性羟甲基化组样本，其TAB测序（TAB-Seq）数据已提交至GSE46710。