Deciphering the gene regulatory network controlling vertebrate endodermal fates

破译控制脊椎动物内胚层命运的基因调控网络

• 批准号: 8561007
• 负责人: Ken W.Y. Cho
• 金额: $ 62.8万
• 依托单位: UNIVERSITY OF CALIFORNIA-IRVINE
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-07-05 至 2018-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8561007
• 关键词: Adult; Binding; Bioinformatics; Biological Models; Biology; Cell Lineage; ChIP-seq; Collaborations; Communities; Complex; Computer Simulation; Coupled; DNA; DNA Binding; Data; Data Set; Development; Developmental Process; Ectoderm; Embryo; Embryonic Development; Endoderm; Endoderm Cell; Engineering; Feeds; Gene Expression Regulation; Genes; Genetic Transcription; Genome; Genomics; Germ Layers; Goals; Graph; Human; Intestines; Knowledge; Liver; Logic; Lung; Measurement; Measures; Mediating; Mesoderm; Methods; Modeling; Molecular; Molecular Profiling; Mus; NIH Program Announcements; Organ; Organogenesis; Outcome; Output; Pancreas; Pathway interactions; Pattern; Play; Production; RNA; Rana; Regulator Genes; Research; Research Personnel; Staging; Stem cells; Surveys; System; Testing; Thyroid Gland; Time; Tissues; Translating; Tube; United States National Institutes of Health; Xenopus; base; cell type; computerized tools; epigenomics; gastrulation; genome-wide; human data; human disease; human stem cells; insight; network models; programs; public health relevance; skills; stem cell biology; tool; transcription factor; transcriptome sequencing; vertebrate genome

DESCRIPTION (provided by applicant): Many human diseases are associated with organs originating from the embryonic gut tube, including the intestine, pancreas, liver, lungs, and thyroid. So far, only a handful of transcription factors (TFs) are known to play key roles in endoderm development, and how these TFs functionally interact in a gene regulatory network (GRN) is poorly understood and the extent to which they modulate endoderm patterning and early organogenesis is unknown. Large-scale genomic analyses are needed to generate a GRN with predictive power and to gain a systems-level understanding of the regulatory logic controlling endoderm development. We propose to utilize the experimental advantages of the Xenopus embryo coupled with several high- throughput sequencing methods to survey the global landscape of cis-regulatory modules (CRMs) active in the early Xenopus embryo and use these datasets to build and to analyze an endoderm GRN that is robust enough to be predictive when perturbed. Our modeling will provide testable hypotheses for performing double knockdowns to test the predictive quality of our GRN and to reveal the importance of multifactorial control over endodermal genes. Double knockdowns are difficult to perform in developing mammalian embryos, but are straightforward in Xenopus. This results in further elaboration of the GRN and yields deeper insights into gene regulation, which is not possible by performing additional single gene knockdown studies. We will compare our resulting GRNs in Xenopus to human data and identify critical network interactions that can be manipulated to engineer endodermal tissues from human stem cells. Our specific aims are: Aim 1: Generate genome-wide datasets of the inputs and outputs of transcriptional networks in order to build an endodermal GRN. Aim 2: Computationally integrate ChIP-seq, DNA-seq, and RNA-seq across a developmental time course to build an embryonic interactome graph. Aim 3: Model an endodermal GRN, make predictions that identify critical nodes, and test the model. This project will generate a predictive GRN model with an unprecedented systems level view of endoderm development in the vertebrate embryo. This will have a significant impact on our understanding of germ layer formation and how GRNs coordinate embryogenesis. Our GRN models will have an impact beyond the Xenopus community because researchers studying mammalian development and stem cell biology will derive testable hypotheses to drive their research programs. Similarly, the tools developed in this proposal will be applicable to building GRNs for other vertebrate and mammalian systems.

描述（由申请人提供）：许多人类疾病与源自胚胎肠道管的器官有关，包括肠道，胰腺，肝脏，肺和甲状腺。到目前为止，已知只有少数转录因子（TF）在内胚层发育中起关键作用，并且这些TF在基因调节网络（GRN）中的功能如何相互作用，并且对它们调节内胚层构图和早期器官的程度尚不清楚。需要进行大规模的基因组分析来产生具有预测能力的GRN，并对控制内胚层发育的调节逻辑的了解。我们建议利用爪蟾胚胎的实验优势，再加上几种高吞吐量测序方法，以调查顺式调节模块（CRMS）的全球景观（CRMS）活跃在早期Xenopus Embryo中，并使用这些数据集中使用这些数据集，以便在构建和分析具有强大的内胚层时，以预测能够进行珀斯的耐药性。我们的建模将提供可测试的假设，用于进行双重敲低以测试GRN的预测质量，并揭示多因素控制对内胚层基因的重要性。在开发哺乳动物胚胎时，双重敲低难以执行，但在Xenopus中很简单。这导致进一步阐述GRN，并对基因调节产生更深入的见解，这是通过进行其他单个基因敲低研究而不可能的。我们将比较Xenopus中所得的GRNS与人类数据，并确定可以针对人类干细胞中的内胚层组织操纵的关键网络相互作用。我们的具体目的是：目标1：生成转录网络输入和输出的全基因组数据集，以构建内胚层GRN。 AIM 2：在开发时间过程中将芯片序列，DNA-seq和RNA-Seq整合在一起，以构建胚胎相互作用图。 AIM 3：模拟内胚层GRN，做出识别关键节点的预测并测试模型。该项目将生成一个预测性GRN模型，具有脊椎动物胚胎中内胚层开发的前所未有的系统级别的视图。这将对我们对生殖层形成的理解以及GRN如何坐标胚胎发生产生重大影响。我们的GRN模型将在Xenopus社区之外产生影响，因为研究哺乳动物开发和干细胞生物学的研究人员将提出可检验的假设以推动其研究计划。同样，本提案中开发的工具将适用于为其他脊椎动物和哺乳动物系统构建GRN。