Cell-type– and developmental stage–specific regulation of gene expression in the retina

视网膜中基因表达的细胞类型和发育阶段的特异性调控

基本信息

批准号：
10333227
负责人：
Michael A Dyer
金额：
$ 43.53万
依托单位：
ST. JUDE CHILDREN'S RESEARCH HOSPITAL
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：
2020-02-01 至 2024-01-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10333227
关键词：
3-Dimensional Affect Basic Science Binding Binding Sites Biology Biomedical Research Bipolar Neuron Birth Order Cell Death Cell Differentiation process Cell physiology Cells Cellular Structures ChIP-seq Child Chimeric Proteins Chromatin Chromatin Loop Communities Complex Computer Analysis DNA Data Databases Defect Development Disease Elements Enhancers Epigenetic Process Euchromatin Evaluation Foundations Future Gene Expression Gene Expression Profile Gene Expression Regulation Genes Genetic Genetic Enhancer Element Genome Goals Government Heterochromatin Histones Human Individual Knowledge Light Link Maps Mass Spectrum Analysis Medicine Microphthalmos Microscopy Modification Molecular Muller&apos s cell Mus Mutate Neuroglia Organoids Pecans Persons Process Publishing Regulation Regulatory Element Research Research Personnel Research Project Grants Retina Retinal Diseases Retinoblastoma Role Saint Jude Children&apos s Research Hospital Series Slice Structure Study models Testing Transcription Coactivator Transcription Repressor Upstream Enhancer VP 16 Vision cell fate specification cell type cloud based combinatorial data portal data sharing experimental study human embryonic stem cell in utero in vivo insight multidimensional data preservation promoter retinal imaging retinal progenitor cell retinogenesis stem cell proliferation transcription factor tumor

项目摘要

PROJECT SUMMARY During retinal development, more than 8,000 genes change in their expression as multipotent retinal progenitor cells produce each of the 7 classes of cell types in an evolutionarily conserved birth order. Although it has been well established that changes in the covalent modifications to the DNA and histones and higher-order DNA looping accompany changes in gene expression, little is known about how those processes are coordinated during retinal development. Over the past 5 years, we developed a detailed map of the structure and accessibility of the human and mouse retinal genome during development. Specifically, we performed a multifaceted integrated analysis that included profiling of the covalent modifications to the DNA and histones, promoter structure, chromatin accessibility, looping interactions, and euchromatin/heterochromatin localization. All these published and unpublished data are shared freely with the biomedical research community through our integrated retinal nucleome database (iRNDb) (https://pecan.stjude.cloud/retinalnucleome). One of the most significant discoveries to come from the iRNDb was the identification of a series of core regulatory circuit super-enhancers (CRC-SEs) adjacent to genes having important roles in retinal development, including Vsx2, Crx, Six3, Otx2, Fgf15, and Ascl1. The CRC-SE upstream of the Vsx2 gene was particularly exciting because it had activity consistent with bipolar cell development. We deleted the Vsx2-CRC-SE in mice and showed that bipolar neurons are absent yet all other cell types develop normally. Importantly, retinal progenitor cell proliferation was normal, indicating that we had separated the bipolar cell regulatory elements from that of retinal progenitor cells. In this proposal, we will elucidate the structure and organization of the Vsx2 CRC-SE, identify other transcription factors that may cooperate with Vsx2 to regulate bipolar cell type–specific expression and test the consequences of loss of bipolar cells on other cell types in the retina. The results of these studies will be important for filling a fundamental gap in our knowledge about the role of CRC-SEs in retinal development and will set the stage for characterization of CRC-SEs in other genes required for retinogenesis. All published and unpublished data are shared through the iRNDb to accelerate discovery on retinal development and disease.

项目概要在视网膜发育过程中，超过 8,000 个基因的表达发生变化，成为多能基因视网膜祖细胞在进化上保守的出生过程中产生 7 类细胞类型中的每一种尽管已经明确 DNA 的共价修饰发生了变化，组蛋白和高阶 DNA 环伴随着基因表达的变化，但人们对此知之甚少在过去的 5 年里，我们研究了视网膜发育过程中如何协调这些过程。人类和小鼠视网膜基因组的结构和可及性的详细图谱具体来说，我们进行了多方面的综合分析，其中包括对开发的分析。 DNA 和组蛋白的共价修饰、启动子结构、染色质可及性、循环相互作用，以及常染色质/异染色质定位。所有这些已发表和未发表的数据。通过我们的整合视网膜核组与生物医学研究界免费共享数据库（iRNDb）（https://pecan.stjude.cloud/retinalnucleome）最重要的发现之一。来自 iRNDb 的是一系列核心调节电路超级增强剂的鉴定 (CRC-SE) 邻近在视网膜发育中起重要作用的基因，包括 Vsx2、Crx、Six3、 Vsx2 基因上游的 CRC-SE 特别令人兴奋，因为它具有 Otx2、Fgf15 和 Ascl1。我们在小鼠中删除了 Vsx2-CRC-SE，并具有与双极细胞发育一致的活性。结果表明，双极神经元不存在，但所有其他细胞类型均正常发育。祖细胞增殖正常，表明我们已经分离出双极细胞调节在本提案中，我们将阐明视网膜祖细胞的结构和成分。 Vsx2 CRC-SE 的组织，识别可能与 Vsx2 合作的其他转录因子调节双极细胞类型特异性表达并测试双极细胞丢失的后果这些研究的结果对于填补视网膜中的其他细胞类型非常重要。根据我们对 CRC-SE 在视网膜发育中的作用的了解，将为视网膜发生所需的其他基因中 CRC-SE 的表征所有已发表和未发表的内容。数据通过 iRNDb 共享，以加速视网膜发育和疾病的发现。