BACKGROUND Epigenetic mechanisms provide an interface between environmental factors and the genome and are influential in various diseases. These mechanisms, including DNA methylation, influence the regulation of development, differentiation, and establishment of cellular identity. Here, we performed high-throughput methylome profiling to determine whether differential patterns of DNA methylation correlate with Down syndrome (DS). MATERIALS AND METHODS We extracted DNA from the chorionic villi cells of five normal and five DS fetuses at the early developmental stage (12-13 weeks of gestation). Methyl-capture sequencing (MC-Seq) was used to investigate the methylation levels of CpG sites distributed across the whole genome to identify differentially methylated CpG sites (DMCs) and regions (DMRs) in DS. New functional annotations of DMR genes using bioinformatics tools were predicted. RESULTS DNA hypermethylation was observed in DS fetal chorionic villi cells. Significant differences were evident for 4,439 DMCs, including hypermethylation (n = 4,261) and hypomethylation (n = 178). Among them, 140 hypermethylated DMRs and only 1 hypomethylated DMR were located on 121 genes and 1 gene, respectively. One hundred twenty-two genes, including 141 DMRs, were associated with heart morphogenesis and development of the ear, thyroid gland, and nervous systems. The genes were significantly associated with DS and various diseases, including hepatopulmonary syndrome, conductive hearing loss, holoprosencephaly, heart diseases, glaucoma, and musculoskeletal abnormalities. CONCLUSIONS This is the first study to compare the whole-epigenome DNA methylation pattern of the chorionic villi cells from normal and DS fetuses at the early developmental-stage using MC-seq. Overall, our results indicate that the chorionic villi cells of DS fetuses are hypermethylated in all autosomes and suggested that altered DNA methylation may be a recurrent and functionally relevant downstream response to DS in human cells. This study provides basic information for future research focused on the pathophysiology of the DS and its potential effects, as well as the role DNA methylation plays in the early developmental stage of DS fetuses.

中文翻译：

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利用甲基捕获测序技术对唐氏综合症胎儿绒毛膜绒毛膜DNA甲基化进行表观基因组范围的碱基分辨率分析。

背景技术表观遗传机制提供了环境因素与基因组之间的接口，并在各种疾病中具有影响力。这些机制，包括DNA甲基化，影响发育，分化和细胞身份建立的调控。在这里，我们进行了高通量甲基化分析，以确定DNA甲基化的差异模式是否与唐氏综合症（DS）相关。材料与方法在发育的早期阶段（妊娠12-13周），我们从5名正常胎儿和5名DS胎儿的绒毛膜绒毛细胞中提取了DNA。甲基捕获测序（MC-Seq）用于研究分布在整个基因组中的CpG位点的甲基化水平，以鉴定DS中差异甲基化的CpG位点（DMC）和区域（DMR）。预测了使用生物信息学工具的DMR基因的新功能注释。结果在DS胎儿绒毛膜绒毛细胞中观察到DNA超甲基化。对于4,439个DMC，存在显着差异，包括高甲基化（n = 4,261）和低甲基化（n = 178）。其中，140个高甲基化DMR和1个低甲基化DMR分别位于121个基因和1个基因上。包括141个DMR在内的122个基因与心脏的形态发生以及耳朵，甲状腺和神经系统的发育有关。这些基因与DS和各种疾病显着相关，包括肝肺综合征，传导性听力减退，全前脑，心脏病，青光眼和肌肉骨骼异常。结论这是第一项使用MC-seq在发育早期比较正常和DS胎儿绒毛膜细胞全表观基因组DNA甲基化模式的研究。总体而言，我们的结果表明，DS胎儿的绒毛膜细胞在所有常染色体中都被高度甲基化，并表明改变的DNA甲基化可能是人类细胞中DS的复发性和功能相关的下游反应。这项研究为将来的研究提供了基础信息，这些研究的重点是DS的病理生理及其潜在作用，以及DNA甲基化在DS胎儿早期发育中的作用。我们的结果表明，DS胎儿的绒毛膜细胞在所有常染色体中均被高度甲基化，这表明改变的DNA甲基化可能是人类细胞中对DS的复发性和功能相关的下游反应。这项研究为将来的研究提供了基础信息，这些研究的重点是DS的病理生理及其潜在作用，以及DNA甲基化在DS胎儿早期发育中的作用。我们的结果表明，DS胎儿的绒毛膜细胞在所有常染色体中均被高度甲基化，这表明改变的DNA甲基化可能是人类细胞中对DS的复发性和功能相关的下游反应。这项研究为将来的研究提供了基础信息，这些研究的重点是DS的病理生理及其潜在作用，以及DNA甲基化在DS胎儿早期发育中的作用。