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: 9256494
• 负责人: Ken W.Y. Cho
• 金额: $ 56.04万
• 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/9256494
• 关键词: Adult; Binding; Bioinformatics; Biological Models; Biology; Cell Lineage; ChIP-seq; Collaborations; Communities; Complex; Computer Simulation; Coupled; DNA Binding; DNA sequencing; DNase I hypersensitive sites sequencing; 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; High-Throughput Nucleotide Sequencing; Human; Intestines; Knowledge; Liver; Logic; Lung; Measurement; Measures; Mediating; Mesoderm; Methods; Modeling; Molecular; Molecular Profiling; Mus; NIH Program Announcements; Organ; Organogenesis; Output; Pancreas; Pathway interactions; Pattern; Play; Production; RNA; Rana; Regulator Genes; Research; Research Personnel; Stem cells; Surveys; System; Testing; Thyroid Gland; Time; Translating; Tube; United States National Institutes of Health; Xenopus; cell type; computerized tools; epigenomics; feeding; gastrulation; genome-wide; human data; human disease; human stem cells; human tissue; insight; knock-down; model building; network models; outcome prediction; programs; public health relevance; skills; stem cell biology; tool; transcription factor; transcriptome sequencing; vertebrate embryos; 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管的器官有关，包括肠、胰腺、肝脏、肺和甲状腺。到目前为止，只有少数的转录因子（TF）是已知的内胚层发育中发挥关键作用，这些TF如何在基因调控网络（GRN）功能相互作用知之甚少，他们调节内胚层模式和早期器官发生的程度是未知的。需要大规模的基因组分析来产生具有预测能力的GRN，并获得对控制内胚层发育的调控逻辑的系统级理解。我们建议利用非洲爪蟾胚胎的实验优势，结合几种高通量测序方法来调查早期非洲爪蟾胚胎中活性的顺式调节模块（CRM）的全局景观，并使用这些数据集来构建和分析内胚层GRN，其足够稳健以在扰动时具有预测性。我们的建模将提供可测试的假设进行双敲除，以测试我们的GRN的预测质量，并揭示多因素控制内胚层基因的重要性。双敲除在哺乳动物胚胎发育中很难进行，但在非洲爪蟾中很简单。这导致GRN的进一步阐述，并对基因调控产生更深入的了解，这是不可能通过进行额外的单基因敲除研究来实现的。我们将比较我们在非洲爪蟾中得到的GRNs与人类数据，并确定关键的网络相互作用，可以操纵这些网络相互作用来从人类干细胞中工程化内胚层组织。我们的具体目标是：目标1：生成转录网络的输入和输出的全基因组数据集，以建立内胚层GRN。目标2：在发育时间过程中计算整合ChIP-seq、DNA-seq和RNA-seq，以构建胚胎相互作用组图。目标3：对内胚层GRN进行建模，做出识别关键节点的预测，并测试模型。该项目将产生一个预测GRN模型，具有脊椎动物胚胎内胚层发育的前所未有的系统水平视图。这将对我们理解胚层形成以及GRNs如何协调胚胎发生产生重大影响。我们的GRN模型将产生超出非洲爪蟾社区的影响，因为研究哺乳动物发育和干细胞生物学的研究人员将得出可验证的假设来推动他们的研究计划。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GRNs。

项目成果

Biallelic genome modification in F(0) Xenopus tropicalis embryos using the CRISPR/Cas system.

• DOI: 10.1002/dvg.22719
• 发表时间: 2013-12
• 期刊: GENESIS
• 影响因子: 1.5
• 作者: Blitz, Ira L.;Biesinger, Jacob;Xie, Xiaohui;Cho, Ken W. Y.
• 通讯作者: Cho, Ken W. Y.

Early Xenopus gene regulatory programs, chromatin states, and the role of maternal transcription factors.

• DOI: 10.1016/bs.ctdb.2020.02.009
• 发表时间: 2020
• 期刊: Current topics in developmental biology
• 作者: Kitt D. Paraiso;J. Cho;Junseok Yong;Ken W. Y. Cho

Prospects for Declarative Mathematical Modeling of Complex Biological Systems.

复杂生物系统声明式数学建模的前景。

• DOI: 10.1007/s11538-019-00628-7
• 发表时间: 2019
• 期刊: Bulletin of mathematical biology
• 影响因子: 3.5
• 作者: Mjolsness,Eric

Occupancy of tissue-specific cis-regulatory modules by Otx2 and TLE/Groucho for embryonic head specification.

• DOI: 10.1038/ncomms5322
• 发表时间: 2014-07-09
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Yasuoka Y;Suzuki Y;Takahashi S;Someya H;Sudou N;Haramoto Y;Cho KW;Asashima M;Sugano S;Taira M
• 通讯作者: Taira M

DNase-seq to Study Chromatin Accessibility in Early Xenopus tropicalis Embryos.

• DOI: 10.1101/pdb.prot098335
• 发表时间: 2019-04-01
• 期刊: Cold Spring Harbor protocols
• 作者: Cho, Jin Sun;Blitz, Ira L;Cho, Ken W Y
• 通讯作者: Cho, Ken W Y