建立调控区互作图谱的捕获方法以研究早期胚胎中功能性增强子的选择模式

The promoter-specific activation by enhancers is the key for precise expression of genes. However, the number of enhancers on vertebrate genome is far greater than that of genes, indicates that different enhancers may regulate the same target gene dependent on developmental stage or cell type. Independent of epigenetic features or open chromatin states, the formation of chromatin loops alone can provide more reliable evidence to define the authentic enhancers playing significant regulatory functions and their target promoters. The methods currently used to reveal the three-dimensional structure of chromatin usually require a large amount of starting material and are not applicable for studying the chromatin architecture in early embryos. In my previous studies, I used high resolution interactome to identify the conservation of the formation mechanism of topologically associating domains (TADs) among different species, and have accumulated abundant experience in technical improvement. In this project, we aim to identify the genuine functional enhancers in samples with low cell numbers by establishing a new method in which the interactions among chromatin regulatory regions are enriched. Further, we will reveal the selection pattern of enhancers and its impact on gene expression in early stage embryos of zebrafish using this new method. In addition, we will investigate the major factors affecting the selection of enhancers during early embryonic development by utilizing transcription factor data combined with epigenomics datasets.

增强子元件对启动子的特异性激活是基因精确表达的基础，而基因组上增强子的数目远多于基因数目，暗示着增强子的选择具有发育阶段或细胞类型的特异性。不同于染色质的表观特征或开放状态，与启动子所形成的染色质环结构可以更准确地定义真正发挥调控功能的增强子元件及其目的基因。目前用于揭示染色质三维结构的方法通常需要较多的起始样本，难以应用于早期胚胎研究。前期工作中，申请人利用高分辨互作图谱揭示了不同物种间基本结构单元形成机制的保守性，并积累了大量技术改进的经验。因此，本项目拟建立一种通过富集染色质调控区的相互作用，进而实现在少量细胞中鉴定功能性增强子元件的方法。利用该方法，申请人将以斑马鱼为模型，获取胚胎发育不同时间点的功能性增强子元件图谱，以明确早期发育进程中增强子元件的选择模式及其与基因表达的关系。此外，本项目将结合转录因子及表观遗传修饰等数据，进一步探索影响早期胚胎中增强子元件选择的主要因素。

基因组上鉴定出的增强子的数目远多于基因数目，暗示着增强子的选择具有发育阶段或细胞类型的特异性，即细胞局部环境对基因表达调控有重要的影响。相比于染色质的表观遗传学特征或开放状态，通过与启动子所形成的染色质环结构可以更准确地定义真正发挥调控功能的增强子元件并明确增强子的靶基因。目前用于揭示染色质三维结构的方法通常需要较多的起始样本，难以应用于早期胚胎研究。因此，本项目利用可识别染色质开放区的NicK Enzyme (NicE) 对基因组上的调控区进行非生物素的标记后再进行相应的构象捕获操作，该方法被命名为NicE Hi-C。由于本项目采用的标记方法可同时标识并断裂基因组，减少了相应操作步骤的损失，有效地降低了样本起始量，使得该方法适用于斑马鱼早期胚胎中增强子选择模式的研究。此外，申请人的工作阐述了细胞外微环境显著影响基因组功能相关的三维结构，揭示了目前常用的体外培养的细胞并不能反映组织内真实的结构信息，为疾病相关的工作在细胞培养环境的选择上提供了重要参考，相关成果发表了研究论文2篇。