Genome-wide promoter methylation patterns are altered by a food component, genistein, during embryonic stem cell differentiation

发育过程中的环境挑战会影响胎儿的表观基因组，但易受表观遗传失调影响的时期(S)尚不清楚。通过使用大豆植物雌激素Genistein，已知在胚胎发生期间改变Avy等位基因的表观遗传状态，我们探索了表观遗传调节的敏感期。植入后，当从头DNA甲基化积极进行时，可以使用小鼠胚胎干细胞分化系统进行体外分析。在有或没有金雀异黄素的情况下分化小鼠ES细胞，并通过基于基因芯片的启动子甲基化分析和甲基化敏感内切酶(HpaII/McrBC)依赖的浓缩程序来比较第10天的DNA甲基化模式。金雀异黄素治疗后，观察到部分启动子的甲基化水平发生了适度的变化。对Ucp1和Sytl1启动子的详细研究进一步表明，金雀异黄素不影响发生在第0天到第4天之间的从头甲基化，但干扰了随后的调控过程，并导致这两个启动子的甲基化水平降低。金雀异黄素在从头甲基化后扰乱分化的ES细胞的甲基化模式。我们的观察表明，对于一个基因子集，早期胚胎中从头DNA甲基化后的调节可能对金雀异黄素敏感。

Environmental challenges during development affect the fetal epigenome, but the period(s) vulnerable to epigenetic dysregulation are not clear. By employing a soy phytoestrogen, genistein, that is known to alter the epigenetic states of the Avy allele during embryogenesis, we have explored the sensitive period for epigenetic regulation. The post-implantation period, when de novo DNA methylation actively proceeds, is amenable to in vitro analysis using a mouse embryonic stem(ES) cell differentiation system. Mouse ES cells were differentiated in the presence or absence of genistein, and DNA methylation patterns on day 10 were compared by microarray-based promoter methylation analysis coupled with a methylation-sensitive endonuclease(HpaII/McrBC)-dependent enrichment procedure. Moderate changes in methylation levels were observed in a subset of promoters following genistein treatment. Detailed investigation of the Ucp1 and Sytl1 promoters further revealed that genistein does not affect de novo methylation occurring between day 0 and day 4, but interferes with subsequent regulatory processes and leads to a decrease in methylation level for both promoters. Genistein perturbed the methylation pattern of differentiated ES cells after de novo methylation. Our observations suggest that, for a subset of genes, regulation after de novo DNA methylation in the early embryo may be sensitive to genistein.