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

使用单细胞基因组学破译指定发育过程中不同细胞命运的监管代码

基本信息

批准号：
10160929
负责人：
Antonio J Giraldez
金额：
$ 56.04万
依托单位：
YALE UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-05-07 至 2025-02-28
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10160929
关键词：
ATAC-seq Address Affect Architecture Binding Cell Differentiation process Cell Lineage Cells Chromatin Code Collaborations Complex Computing Methodologies DNA Data Data Set Development Disease Embryo Embryonic Development Engineering Epigenetic Process Etiology Evolution Fertilization Foundations Gene Expression Gene Expression Profile Genes Genetic Genetic Transcription Genome Genomics Goals Human Human Development In Vitro Individual Lead Learning Logic Maps Mathematics Mediating Molecular Mutate Outcome Regenerative Medicine Regulator Genes Repression Shapes Signal Transduction Specific qualifier value System Tail Testing Time To specify Totipotent Vertebrates Work base cell fate specification cell type chromatin remodeling combinatorial computer framework developmental disease in vivo loss of function mutant novel predictive modeling programs recruit segregation single cell sequencing single-cell RNA sequencing transcription factor vertebrate embryos

项目摘要

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.

概括脊椎动物胚胎包含数百种功能多样的细胞类型，但是我们缺乏完整的了解指定每种单元格的监管代码以及此代码中的破坏程度血统之间的关系。在这里，我们提出了两个目标，以剖析染色质的可访问区域，调节多种细胞类型规范的调节基序和推定的转录因子在胚胎发生过程中。首先，（AIM 1），我们将利用单细胞ATAC-SEQ和SCRNA-SEQ揭示染色质可及性的动力学和在早期定义离散单元类型的转录轮廓的动力学发展。我们将在染色质的可访问区域中定义调节基序优先参与不同的细胞类型。第二（AIM 2），我们将使用多种学习方法来定义共同调节基因模块，并为SCRNA-SEQ和SCATAC-SEQ应用调节网络推理框架数据，并通过突变关键的先驱因素来测试调节性相互作用并研究它们如何合作与其他TF一起调节发育过程中染色质的可及性和细胞分化。这个项目将生成广泛的高质量数据集以及新颖的计算方法，以实现定量和胚胎开发的预测模型，目的是破译基因调节网络指定发育过程中的细胞身份。鉴于早期发展是跨脊椎动物物种的保守的，我们调查结果有可能为人类发展提供信息，并为研究的病因奠定了基础人类发育障碍，并在体外设计新颖的细胞类型和谱系药品。