Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel.
PLoS Genet. 2021 Apr 12;17(4):e1009498. doi: 10.1371/journal.pgen.1009498. eCollection 2021 Apr.
In mammals, cellular identity is defined through strict regulation of chromatin modifications and DNA methylation that control gene expression. Methylation of cytosines at CpG sites in the genome is mainly associated with suppression; however, the reason for enhancer-specific methylation is not fully understood. We used sequential ChIP-bisulfite-sequencing for H3K4me1 and H3K27ac histone marks. By collecting data from the same genomic region, we identified enhancers differentially methylated between these two marks. We observed a global gain of CpG methylation primarily in H3K4me1-marked nucleosomes during mouse embryonic stem cell differentiation. This gain occurred largely in enhancer regions that regulate genes critical for differentiation. The higher levels of DNA methylation in H3K4me1- versus H3K27ac-marked enhancers, despite it being the same genomic region, indicates cellular heterogeneity of enhancer states. Analysis of single-cell RNA-seq profiles demonstrated that this heterogeneity correlates with gene expression during differentiation. Furthermore, heterogeneity of enhancer methylation correlates with transcription start site methylation. Our results provide insights into enhancer-based functional variation in complex biological systems.
在哺乳动物中，细胞身份通过严格调控染色质修饰和 DNA 甲基化来控制基因表达来定义。基因组中 CpG 位点上的胞嘧啶甲基化主要与抑制相关；然而，增强子特异性甲基化的原因尚不完全清楚。我们使用了用于 H3K4me1 和 H3K27ac 组蛋白标记的顺序 ChIP-bisulfite-sequencing。通过从同一基因组区域收集数据，我们确定了这两个标记之间差异甲基化的增强子。我们观察到在小鼠胚胎干细胞分化过程中，H3K4me1 标记核小体中主要发生了 CpG 甲基化的全局获得。这种获得主要发生在调节分化关键基因的增强子区域。尽管在同一基因组区域，但 H3K4me1 标记的增强子中的 DNA 甲基化水平高于 H3K27ac 标记的增强子，这表明增强子状态具有细胞异质性。单细胞 RNA-seq 谱分析表明，这种异质性与分化过程中的基因表达相关。此外，增强子甲基化的异质性与转录起始位点甲基化相关。我们的研究结果为复杂生物系统中基于增强子的功能变异提供了新的见解。
