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，但是我们缺乏完整的细胞类型 了解指定每种细胞类型的监管代码以及该代码的破坏如何影响 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及区域， 调节多种细胞类型的调节基序和假定的转录因子 在胚胎发生过程中。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定义早期离散细胞类型的转录谱 发展。我们将优先定义染色质可及区域中的调控基序 参与不同的细胞类型。其次（目标 2），我们将使用多种学习方法来定义共同 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，并通过改变关键先锋因素来测试监管相互作用并调查它们如何合作 与其他转录因子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，旨在破译指定的基因调控网络 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 研究结果有可能为人类发展提供信息，并为调查病因奠定基础 人类发育障碍并在体外设计新的细胞类型和谱系以实现再生 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.