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

总结 脊椎动物胚胎含有数百种功能多样的细胞类型，但我们缺乏一个完整的 了解指定每种细胞类型的调控代码以及该代码的中断如何影响 血统之间的关系在这里，我们提出了两个目标，解剖染色质的可访问区域， 介导多种细胞类型特化的调节基序和推定的转录因子 在胚胎发育过程中。首先，（目的1），我们将利用单细胞ATAC-seq和scRNA-seq来揭示细胞内的DNA序列。 染色质可及性的动态和在早期细胞分化过程中定义离散细胞类型的转录谱 发展我们将定义在染色质的可接近区域中的调控基序， 参与不同的细胞类型。第二（目标2），我们将使用多种学习方法来定义协同学习。 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，并通过改变关键的先驱因子来测试监管相互作用，并调查它们如何合作 与其他TF一起调节发育过程中的染色质可及性和细胞分化。该项目将 生成广泛的，高质量的数据集以及新颖的计算方法，以实现定量和 胚胎发育的预测模型，目标是破译基因调控网络， 在发育过程中的细胞特性考虑到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发展提供信息，并为调查 人发育障碍和体外工程化新细胞类型和谱系用于再生 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.