Dynamic DNA methylation turnover at the exit of pluripotency epigenetically primes gene regulatory elements for hematopoietic lineage specification
Dynamic DNA methylation turnover at the exit of pluripotency epigenetically primes gene regulatory elements for hematopoietic lineage specification
复制标题
DOI：
10.1101/2023.01.11.523441
复制
发表时间：
2023-01
期刊：
影响因子：
--
通讯作者：
Aled J. Parry;C. Krueger;T. Lohoff;S. Wingett;S. Schoenfelder;W. Reik
中科院分区：
文献类型：
--
作者：
Aled J. Parry;C. Krueger;T. Lohoff;S. Wingett;S. Schoenfelder;W. Reik
表观遗传机制支配着发育细胞的命运决定，但DNA甲基化如何与染色质结构和三维DNA折叠协调来制定细胞类型特异性基因表达程序仍然知之甚少。在这里，我们使用5-甲基胞嘧啶或其氧化衍生物（5-羟基-，5-甲酰基-和5-羧基-胞嘧啶）缺乏小鼠胚胎干细胞和外胚层样细胞来剖析基因调控机制，控制细胞谱系规范在出口的多能性。DNA甲基转移酶（Dnmt）或10 - 11-易位（泰特）活性的基因消融产生了很大程度上不同的失调基因组，揭示了DNA胞嘧啶甲基化循环的各个分支扰动后的不同转录缺陷。出乎意料的是，我们发现破坏DNA甲基化或氧化会干扰关键的增强子特征，包括染色质可及性，增强子特征性组蛋白修饰以及染色质与推定靶基因的长程相互作用。除了影响多能干细胞中选择基因的转录外，我们还观察到增强子启动受损，包括三维相互作用的丧失，与发育后期所需的关键谱系指定基因相关的调控元件，正如我们对关键造血基因Klf 1和Lyl 1所证明的那样。因此，我们观察到敲除细胞在胚状体分化过程中血液基因的转录激活受损。我们的研究结果确定了一个新的作用，在退出多能性的DNA甲基化的动态营业额，以建立和维持染色质的状态，表观遗传学总理增强子在发育细胞多样化的后期激活。亮点我们在野生型、泰特三重敲除（TKO）和Dnmt TKO系中对小鼠胚胎干细胞（ESC）向外胚层样细胞（EpiLC）的转变进行了详细的表观遗传学表征，并开发了一种新的聚类方法来询问数据。泰特TKO在多能性退出时降低增强子元件之间的H3 K4 me 1和H3 K27 ac水平，而Dnmt TKO仅影响H3 K4 me 1水平，表明氧化衍生物在H3 K4 me 1沉积中的新作用。泰特TKO和Dnmt TKO影响EpiLC中的增强子引发，这与分化后不能上调造血基因有关。在Dnmt和泰特TKO中，引发的增强子与其靶基因之间的长距离染色体相互作用减弱。
Epigenetic mechanisms govern developmental cell fate decisions, but how DNA methylation coordinates with chromatin structure and three-dimensional DNA folding to enact cell-type specific gene expression programmes remains poorly understood. Here, we use mouse embryonic stem and epiblast-like cells deficient for 5-methyl cytosine or its oxidative derivatives (5-hydroxy-, 5-formyl- and 5-carboxy-cytosine) to dissect the gene regulatory mechanisms that control cell lineage specification at the exit of pluripotency. Genetic ablation of either DNA methyltransferase (Dnmt) or Ten-eleven-translocation (Tet) activity yielded largely distinct sets of dysregulated genes, revealing divergent transcriptional defects upon perturbation of individual branches of the DNA cytosine methylation cycle. Unexpectedly, we found that disrupting DNA methylation or oxidation interferes with key enhancer features, including chromatin accessibility, enhancer-characteristic histone modifications, and long-range chromatin interactions with putative target genes. In addition to affecting transcription of select genes in pluripotent stem cells, we observe impaired enhancer priming, including a loss of three-dimensional interactions, at regulatory elements associated with key lineage-specifying genes that are required later in development, as we demonstrate for the key hematopoietic genes Klf1 and Lyl1. Consistently, we observe impaired transcriptional activation of blood genes during embryoid body differentiation of knockout cells. Our findings identify a novel role for the dynamic turnover of DNA methylation at the exit of pluripotency to establish and maintain chromatin states that epigenetically prime enhancers for later activation during developmental cell diversification. Highlights We perform a detailed epigenetic characterisation of the mouse embryonic stem cell (ESC) to epiblast-like cell (EpiLC) transition in wild type, Tet triple-knockout (TKO) and Dnmt TKO lines and develop a novel clustering approach to interrogate the data. Tet TKO reduces H3K4me1 and H3K27ac levels across enhancer elements upon pluripotency exit whilst Dnmt TKO affects only H3K4me1 levels, suggesting a novel role for oxidative derivatives in H3K4me1 deposition. Tet TKO and Dnmt TKO affect enhancer priming in EpiLCs which is associated with failure to upregulate hematopoietic genes upon differentiation. Long-range chromosomal interactions between primed enhancers and their target genes are weakened in both Dnmt and Tet TKO.