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

• 批准号: 9886721
• 负责人: Michael A Dyer
• 金额: $ 44.88万
• 依托单位: ST. JUDE CHILDREN'S RESEARCH HOSPITAL
• 依托单位国家: 美国
• 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/9886721
• 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' 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' 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

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.

项目摘要 在视网膜发育过程中，超过8,000个基因的表达变化 视网膜祖细胞在进化的生日中产生7种细胞类型中的每一种 秩序。尽管已经有很好的确定，即对DNA的共价修改变化 希斯汀和高阶DNA循环涉及基因表达的变化，关于 在视网膜开发过程中，这些过程如何协调。在过去的5年中，我们开发了 人类和小鼠常规基因组的结构和可访问性的详细地图 特别是，我们进行了多方面的综合分析，其中包括对 对DNA和组蛋白，启动子结构，染色质可及性，循环的共价修改 相互作用，以及白染料/异染色质定位。所有这些已发布和未发布的数据 通过我们的综合永久核心与生物医学研究界自由共享 数据库（irndb）（https://pecan.stjude.cloud/retinalnucleome）。最重要的发现之一 来自IRNDB的是一系列核心监管电路超级增强剂的识别 （CRC-SES）与在剩余发育中具有重要作用的基因相邻，包括VSX2，CRX，SIX3， OTX2，FGF15和ASCL1。 VSX2基因的CRC-SE上游特别令人兴奋，因为它 具有与双极细胞发育一致的活性。我们在小鼠中删除了VSX2-CRC-SE， 表明双极神经元不存在，但所有其他细胞类型正常发展。重要的是，残留 祖细胞的增殖正常，表明我们已经分离了双极细胞调节 来自视网膜祖细胞细胞的元素。在此提案中，我们将阐明结构和 VSX2 CRC-SE的组织，确定可能与VSX2协调的其他转录因子 调节双极细胞类型 - 特异性表达并测试双极细胞在 视网膜中的其他细胞类型。这些研究的结果对于填补基本差距很重要 在我们了解CRC-SE在剩余发展中的作用的知识，并将为 CRC-SES在视网膜发生所需的其他基因中的表征。全部出版和未出版 数据通过IRNDB共享，以加速有关残余发育和疾病的发现。