Landscape of DNA methylation on the X chromosome reflects CpG density, functional chromatin state and X-chromosome inactivation.. Homo sapiens

X-chromosome inactivation (XCI) achieves dosage compensation between males and females through the silencing of the majority of genes on one X chromosome, with approximately 15% of genes reported to show inactive X (Xi) expression. We examined the interplay between ChromHMM states, CpG density, expression and DNAm from over 1800 female samples with the Illumina 450K array. The interaction between CpG density and histone marks differed between the active X (Xa) and the Xi, with X-linked promoters reflecting transcriptional status, while the Xi showed lower DNAm than the Xa at all non-promoter regions. Promoter DNAm was used to determine a novel XCI status for more than 100 transcription start sites and a comparison across 27 tissues revealed the majority of genes were consistently subject to XCI. Inter-female and twin data supported a model of predominately cis-acting influences on escape, or variable escape, from XCI. Increased promoter DNAm at escape genes correlated with decreased relative Xi expression up to ~15% female DNAm but above this threshold DNAm was not correlated with the stability of silencing. Xi DNAm was ~12% lower than Xa DNAm within the gene bodies of subject genes and between genes while there was equivalent DNAm at escape genes. In addition to offering insight into sex-specific difference in disease, female X chromosomes provide the opportunity to compare euchromatin and heterochromatin of allelic regions within the same nuclear environment and demonstrate the correlation of DNAm with transcription and the influences of CpG density and chromatin marks. Overall design: This cohort consist of genomic DNA extracted from 927 indiviudals representing 5 tissues, bisulphite converted and hybridized to the Illumina Infinium HumanMethylation450 Beadchip for genome wide DNA methylation profiling from only the X chromosome.

X染色体失活（X-chromosome inactivation, XCI）通过沉默一条X染色体上的绝大多数基因实现雌雄个体间的剂量补偿，据报道约有15%的基因可在失活X染色体（inactive X, Xi）上表达。本研究针对1800余份女性样本的Illumina 450K芯片数据，分析了ChromHMM状态、CpG密度、基因表达与DNA甲基化（DNA methylation, DNAm）之间的相互作用。CpG密度与组蛋白修饰的相互作用在活性X染色体（active X, Xa）与失活X染色体之间存在显著差异：X连锁启动子的DNA甲基化水平可反映其转录状态，而在所有非启动子区域，失活X染色体的DNA甲基化水平均低于活性X染色体。研究人员通过启动子区域的DNA甲基化水平，为超过100个转录起始位点（transcription start site, TSS）确定了全新的XCI状态；对27种组织的比较分析显示，绝大多数基因均稳定受XCI调控。个体间及双生子数据支持了“XCI逃逸或可变逃逸主要受顺式作用元件影响”的模型。逃逸XCI的基因的启动子DNA甲基化水平升高，与相对失活X染色体表达量降低相关，该相关性在女性样本DNA甲基化水平约15%时达到峰值；当甲基化水平超过该阈值后，DNA甲基化与基因沉默的稳定性不再具有相关性。在受XCI调控的基因的基因本体区及基因间区，失活X染色体的DNA甲基化水平较活性X染色体低约12%，而逃逸XCI的基因的两条X染色体甲基化水平无显著差异。除了为疾病的性别差异研究提供新视角外，女性X染色体为在同一核环境下比较等位基因区域的常染色质与异染色质状态提供了契机，同时也阐明了DNA甲基化与转录的相关性，以及CpG密度和染色质修饰的调控作用。实验设计：本队列的基因组DNA提取自927名个体的5种组织样本，经亚硫酸氢盐转化后与Illumina Infinium HumanMethylation450 Beadchip进行杂交，仅针对X染色体开展全基因组DNA甲基化谱分析。