Kraiczy J, Nayak K, Ross A, Raine T, Mak T N, Gasparetto M, Cario E, Rakyan V, Heuschkel R, Zilbauer M
University Department of Paediatrics, University of Cambridge, Cambridge, UK.
Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK.
Mucosal Immunol. 2016 May;9(3):647-58. doi: 10.1038/mi.2015.88. Epub 2015 Sep 16.
DNA methylation is one of the major epigenetic mechanisms implicated in regulating cellular development and cell-type-specific gene expression. Here we performed simultaneous genome-wide DNA methylation and gene expression analysis on purified intestinal epithelial cells derived from human fetal gut, healthy pediatric biopsies, and children newly diagnosed with inflammatory bowel disease (IBD). Results were validated using pyrosequencing, real-time PCR, and immunostaining. The functional impact of DNA methylation changes on gene expression was assessed by employing in-vitro assays in intestinal cell lines. DNA methylation analyses allowed identification of 214 genes for which expression is regulated via DNA methylation, i.e. regulatory differentially methylated regions (rDMRs). Pathway and functional analysis of rDMRs suggested a critical role for DNA methylation in regulating gene expression and functional development of the human intestinal epithelium. Moreover, analysis performed on intestinal epithelium of children newly diagnosed with IBD revealed alterations in DNA methylation within genomic loci, which were found to overlap significantly with those undergoing methylation changes during intestinal development. Our study provides novel insights into the physiological role of DNA methylation in regulating functional maturation of the human intestinal epithelium. Moreover, we provide data linking developmentally acquired alterations in the DNA methylation profile to changes seen in pediatric IBD.
DNA甲基化是参与调节细胞发育和细胞类型特异性基因表达的主要表观遗传机制之一。在此，我们对源自人类胎儿肠道的纯化肠上皮细胞、健康儿科活检样本以及新诊断为炎症性肠病（IBD）的儿童进行了全基因组DNA甲基化和基因表达同步分析。结果通过焦磷酸测序、实时PCR和免疫染色进行了验证。通过在肠细胞系中进行体外试验评估了DNA甲基化变化对基因表达的功能影响。DNA甲基化分析确定了214个通过DNA甲基化调节表达的基因，即调节性差异甲基化区域（rDMRs）。rDMRs的通路和功能分析表明，DNA甲基化在调节人类肠上皮的基因表达和功能发育中起关键作用。此外，对新诊断为IBD的儿童肠上皮进行的分析揭示了基因组位点内DNA甲基化的改变，这些改变被发现与肠道发育过程中发生甲基化变化的位点显著重叠。我们的研究为DNA甲基化在调节人类肠上皮功能成熟中的生理作用提供了新的见解。此外，我们提供了数据，将DNA甲基化谱中发育过程中获得的改变与儿科IBD中观察到的变化联系起来。
