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.

项目总结 在视网膜发育期间，超过8000个基因的表达发生了变化，成为多能性的 在进化保守的出生中，视网膜祖细胞产生7种细胞类型中的每一种 秩序。尽管已经很好地证实了DNA和DNA的共价修饰的变化 组蛋白和高阶DNA环伴随着基因表达的变化，人们对此知之甚少 在视网膜发育过程中这些过程是如何协调的。在过去的5年里，我们开发了 人类和小鼠视网膜基因组的结构和可及性的详细图 发展。具体地说，我们执行了一项多方面的综合分析，包括对 DNA和组蛋白的共价修饰、启动子结构、染色质可及性、环化 相互作用，常染色质/异染色质定位。所有这些已发布和未发布的数据 通过我们集成的视网膜核组与生物医学研究社区免费共享 数据库(IRNDb)(https://pecan.stjude.cloud/retinalnucleome).最重大的发现之一 来自iRNDB的是一系列核心调控回路超级增强剂的鉴定 (CRC-Ses)与在视网膜发育中起重要作用的基因相邻，包括Vsx2，CRx，Six3， OTX2、FGF15和Ascl1。Vsx2基因上游的CRC-SE特别令人兴奋，因为它 具有与双极细胞发育相一致的活性。我们在小鼠体内删除了Vsx2-CRC-SE 显示双极神经元不存在，但所有其他类型的细胞发育正常。重要的是，视网膜 祖细胞增殖正常，表明我们已经分离了双极细胞的调控 来自视网膜祖细胞的成分。在这项提案中，我们将阐明结构和 Vsx2 CRC-SE的组织，确定其他可能与Vsx2协同作用的转录因子 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 视网膜中的其他细胞类型。这些研究的结果对于填补一个根本性的空白将是重要的 在我们对CRC-SE在视网膜发育中的作用的了解中，将为 视网膜发生所需的其他基因中CRC-Ses的特征。所有已发布和未发布 通过iRNDb共享数据，以加速发现视网膜发育和疾病。