Cytosine hydroxymethylation (5hmC) in mammalian DNA is the product of oxidation of methylated cytosines (5mC) by Ten-Eleven-Translocation (TET) enzymes. While it has been shown that the TETs influence 5mC metabolism, pluripotency and differentiation during early embryonic development, the functional relationship between gene expression and 5hmC in adult (somatic) stem cell differentiation is still unknown. Here we report that 5hmC levels undergo highly dynamic changes during adult stem cell differentiation from intestinal progenitors to differentiated intestinal epithelium. We profiled 5hmC and gene activity in purified mouse intestinal progenitors and differentiated progeny to identify 43425 differentially hydroxymethylated regions and 5325 differentially expressed genes. These differentially marked regions showed both losses and gains of 5hmC after differentiation, despite lower global levels of 5hmC in progenitor cells. In progenitors, 5hmC did not correlate with gene transcript levels, however, upon differentiation the global increase in 5hmC content showed an overall positive correlation with gene expression level as well as prominent associations with histone modifications that typify active genes and enhancer elements. Our data support a gene regulatory role for 5hmC that is predominant over its role in controlling DNA methylation states.

中文翻译：

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小鼠肠道分化中的 5-羟甲基胞嘧啶和基因活性。

哺乳动物 DNA 中的胞嘧啶羟甲基化 (5hmC) 是 10-11 易位 (TET) 酶氧化甲基化胞嘧啶 (5mC) 的产物。虽然已经表明 TET 在早期胚胎发育过程中影响 5mC 代谢、多能性和分化，但成人（体细胞）干细胞分化中基因表达与 5hmC 之间的功能关系仍然未知。在此，我们报告在成体干细胞从肠祖细胞分化为分化的肠上皮的过程中，5hmC 水平经历高度动态的变化。我们对纯化的小鼠肠道祖细胞和分化后代中的 5hmC 和基因活性进行了分析，以确定 43425 个差异羟甲基化区域和 5325 个差异表达基因。尽管祖细胞中 5hmC 的总体水平较低，但这些差异标记区域在分化后显示出 5hmC 的损失和增加。在祖细胞中，5hmC 与基因转录水平无关，然而，分化后 5hmC 含量的整体增加显示出与基因表达水平总体正相关，以及与代表活性基因和增强子元件的组蛋白修饰显着相关。我们的数据支持 5hmC 的基因调控作用，其在控制 DNA 甲基化状态方面的作用更为突出。