Macrophages and their precursors monocytes play a key role in inflammation and chronic inflammatory disorders. Monocyte-to-macrophage differentiation and activation programs are accompanied by significant epigenetic remodeling where DNA methylation associates with cell identity. Here we show that DNA methylation changes characteristic for monocyte-to-macrophage differentiation occur at transcription factor binding sites, and, in contrast to what was previously described, are generally highly localized and encompass both losses and gains of DNA methylation. We compared genome-wide DNA methylation across 440,292 CpG sites between human monocytes, naïve macrophages and macrophages further activated toward a pro-inflammatory state (using LPS/IFNγ), an anti-inflammatory state (IL-4) or foam cells (oxLDL and acLDL). Moreover, we integrated these data with public whole-genome sequencing data on monocytes and macrophages to demarcate differentially methylated regions. Our analysis showed that differential DNA methylation was most pronounced during monocyte-to-macrophage differentiation, was typically restricted to single CpGs or very short regions, and co-localized with lineage-specific enhancers irrespective of whether it concerns gain or loss of methylation. Furthermore, differentially methylated CpGs were located at sites characterized by increased binding of transcription factors known to be involved in monocyte-to-macrophage differentiation including C/EBP and ETS for gain and AP-1 for loss of methylation. Our study highlights the involvement of subtle, yet highly localized remodeling of DNA methylation at regulatory regions in cell differentiation.

中文翻译：

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人单核细胞向巨噬细胞的分化涉及转录因子结合位点的高度甲基化的局部甲基化。

巨噬细胞及其前体单核细胞在炎症和慢性炎性疾病中起关键作用。单核细胞到巨噬细胞的分化和激活程序伴随着明显的表观遗传重塑，其中DNA甲基化与细胞身份有关。在这里，我们显示了单核细胞向巨噬细胞分化的特征性DNA甲基化变化发生在转录因子结合位点，并且与先前描述的相反，它们通常高度局限，既包含DNA甲基化的损失，也包含DNA甲基化的获得。我们比较了人类单核细胞，幼稚巨噬细胞和进一步活化为促炎状态（使用LPS /IFNγ），抗炎状态（IL-4）或泡沫细胞（oxLDL和acLDL）。而且，我们将这些数据与单核细胞和巨噬细胞上的公共全基因组测序数据进行了整合，以划定差异甲基化区域。我们的分析表明，差异DNA甲基化在单核细胞向巨噬细胞分化过程中最为明显，通常仅限于单个CpGs或非常短的区域，并且与谱系特异性增强子共定位，无论它是否涉及甲基化的获得或丧失。此外，差异甲基化的CpG位于特征在于转录因子结合增加的位点，这些转录因子已知与单核细胞向巨噬细胞分化有关，包括C / EBP和ETS用于增加甲基化，AP-1用于甲基化损失。我们的研究突出了细胞分化调控区域中DNA甲基化的微妙而高度局部化的重塑。