Deciphering the regulatory code that specifies different cell fates in development using single cell genomics

摘要 脊椎动物胚胎包含数百种功能不同的细胞类型，然而我们缺乏完整的 了解规定每种细胞类型的监管代码以及该代码中的中断如何影响 血统之间的关系。在这里，我们提出了两个目标来剖析染色质的可接近区域， 调节基序和可能的转录因子调节多种细胞类型的特性 在胚胎发育过程中。首先，(目标1)，我们将利用单细胞atac-seq和scRNA-seq来揭示 染色质可及性的动态和早期定义离散细胞类型的转录图谱 发展。我们将定义染色质可访问区域中优先考虑的调控基序 从事不同类型的细胞。第二(目标2)，我们将使用多种学习方法来定义联合 调控基因模块，并应用scRNA-seq和scatac-seq的调控网络推理框架 数据，并通过突变关键先锋因素来测试监管交互作用，并调查它们是如何合作的 与其他转录因子一起调节染色质的可及性和发育过程中的细胞分化。这个项目将 生成广泛、高质量的数据集以及新的计算方法，以实现量化和 胚胎发育的预测模型，目标是破译基因调控网络 发育过程中的细胞身份。鉴于早期发育在脊椎动物物种中是保守的，我们的 这些发现有可能为人类的发展提供信息，并为研究糖尿病的病因奠定基础。 人类发育障碍，并在体外设计新的细胞类型和谱系以进行再生 医药。

Summary The vertebrate embryo contains hundreds of functionally diverse cell types, however we lack a complete understanding of the regulatory code that specifies each cell type and how disruptions in this code affect relationships between lineages. Here, we propose two aims to dissect the accessible regions of the chromatin, the regulatory motifs and the putative transcription factors that mediate the specification of multiple cell types during embryogenesis. First, (Aim 1), we will utilize single cell ATAC-seq and scRNA-seq to uncover the dynamics of chromatin accessibility and the transcriptional profiles that define discrete cell types during early development. We will define the regulatory motifs in accessible regions of the chromatin that are preferentially engaged in different cell types. Second (Aim 2), we will use manifold learning approaches to define co- regulated gene modules and apply a regulatory network inference framework for scRNA-seq and scATAC-seq data, and test the regulatory interactions by mutating key pioneer factors and investigate how they cooperate with other TFs to regulate chromatin accessibility and cell differentiation during development. This project will generate extensive, high-quality datasets as well as novel computational methods to enable quantitative and predictive models of embryonic development with the goal to decipher the gene regulatory network specifying cellular identity during development. Given that early development is conserved across vertebrate species, our findings have the potential to inform human development, and lay the foundation to investigate the etiologies of human developmental disorders and to engineer novel cell types and lineages in vitro for regenerative medicine.