Characterizing enhancers regulating transcription factor expression for cell-type specification across neurodevelopment

表征神经发育过程中细胞类型规范调节转录因子表达的增强子

• 批准号: 10552560
• 负责人: Victoria Honnell
• 金额: $ 4.38万
• 依托单位: ST. JUDE CHILDREN'S RESEARCH HOSPITAL GRADUATE SCHOOL OF BIOMEDICAL SCIENCES, LLC
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-01 至 2023-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10552560
• 关键词: Affect; Architecture; Binding Sites; Bipolar Neuron; Blindness; Brain; CRISPR/Cas technology; Central Nervous System Diseases; Cerebellum; ChIP-seq; Chromatin; Complex; Computer Analysis; Development; Disease; Embryo; Enhancers; Epigenetic Process; Exhibits; Fellowship; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Genes; Genomic DNA; Genomic Segment; Genomics; Human; Human Development; Individual; Knock-out; Knockout Mice; Knowledge; Label; Learning; Measures; Microphthalmos; Modeling; Muller' s cell; Mus; Mutation; Neuraxis; Neurodegenerative Disorders; Neurodevelopmental Disorder; Neuroglia; Organoids; Pattern; Persons; Phase; Phenotype; Protocols documentation; Regulator Genes; Research; Research Project Grants; Retina; Role; Spinal Cord; Technology; Tissues; Training; Upstream Enhancer; Work; blind; cell type; human embryonic stem cell; human embryonic stem cell line; human model; innovation; insight; interest; knockout gene; neurodevelopment; neurogenesis; retinal bipolar neuron; retinal progenitor cell; retinogenesis; skills; stem cell proliferation; transcription factor; transcriptome sequencing

Project Summary/Abstract Super-enhancers (SEs) are expansive regions of genomic DNA comprised of multiple putative enhancers that contribute to dynamic gene expression patterns during development. This is particularly important in neurogenesis because many essential transcription factors have complex developmental stage– and cell–type specific expression patterns across the central nervous system. In the developing retina, Vsx2 is expressed in all retinal progenitor cells and is maintained in differentiated bipolar neurons and Müller glia. Mutations in the Vsx2 gene cause microphthalmia in humans and mice because it is required for retinal progenitor cell proliferation. Due to this severe early developmental phenotype, it has been difficult to elucidate the role of Vsx2 in bipolar neuron and Müller glia differentiation. Victoria Honnell has found that a single SE controls this complex and dynamic pattern of expression in mice. The deletion of one region disrupts retinal progenitor cell proliferation in early retinal development. The deletion of another region has no effect on retinal progenitor cell proliferation but instead leads to a complete loss of bipolar neurons. This prototypical SE may serve as a model for dissecting the complex gene expression patterns for neurogenic transcription factors during development. Moreover, it provides a unique opportunity to alter expression of individual transcription factors in distinct cell types at specific stages of development. This provides a deeper understanding of function that cannot be achieved with traditional gene knockout mouse approaches. In the F99-phase of this proposed research, Victoria will examine the modularity of the Vsx2 SE in human retinal organoid models. This will inform the field’s understanding of how distinct enhancer regions affect retinal cell-type specification in a model of human development. In the K00-phase of this proposed research, Victoria will examine the modularity of other SEs controlling gene expression in the brain. She will characterize the looping interactions and epigenetic landscape of these SE regions to understand how they influence gene expression at multiple stages across brain development, and how aberrations in these mechanisms contribute to neurodevelopmental disorders and neurodegenerative disease. This proposed work will yield an innovative approach to uncouple the early and late stage effects of genes with complex expression patterns and provide an understanding of how the epigenetic landscape of enhancers affect the expression of neurogenic transcription factors. Ultimately, this will inform the field’s understanding of enhanceropathies that contribute to disorders and diseases of the central nervous system.

项目总结/摘要 超增强子（Super-enhancers，SE）是基因组DNA中由多个增强子组成的扩展区域 在发育过程中形成动态基因表达模式。这一点特别重要 因为许多必需的转录因子具有复杂的发育阶段和细胞类型， 在中枢神经系统中的特定表达模式。在发育中的视网膜中，Vsx 2表达于 所有的视网膜祖细胞，并维持在分化的双极神经元和Müller胶质细胞。突变 VSX 2基因导致人类和小鼠的小眼球，因为它是视网膜祖细胞所必需的 增殖由于这种严重的早期发育表型，很难阐明Vsx 2在细胞内的作用。 在双极神经元和Müller胶质细胞分化中。 维多利亚·霍内尔发现，一个单一的SE控制着这种复杂而动态的表达模式， 小鼠一个区域的缺失破坏了早期视网膜发育中视网膜祖细胞的增殖。的 另一个区域的缺失对视网膜祖细胞增殖没有影响，而是导致完全的 双极神经元的丧失。这种典型的SE可以作为一个模型来解剖复杂的基因表达 神经源性转录因子的模式。此外，它提供了一个独特的机会， 在特定发育阶段改变不同细胞类型中单个转录因子的表达。这 提供了对传统基因敲除小鼠无法实现的功能的更深入理解 接近。 在这项拟议研究的F99阶段，维多利亚将检查人类Vsx 2 SE的模块化 视网膜类器官模型。这将告知该领域的理解，不同的增强子区域如何影响视网膜神经元的功能。 人类发育模型中的细胞类型规格。在这项拟议研究的K 00阶段，维多利亚 将检查其他SE控制大脑中基因表达的模块性。她将描述 这些SE区域的循环相互作用和表观遗传景观，以了解它们如何影响基因 在大脑发育的多个阶段表达，以及这些机制中的畸变如何促成 神经发育障碍和神经退行性疾病。 这项拟议的工作将产生一个创新的方法来解开基因的早期和晚期效应 与复杂的表达模式，并提供了一个了解如何表观遗传景观的增强子 影响神经源性转录因子的表达。最终，这将使该领域了解 增强子病变，其导致中枢神经系统的病症和疾病。

项目成果

Identification of Evolutionarily Conserved VSX2 Enhancers in Retinal Development.

视网膜发育中进化保守的 VSX2 增强子的鉴定。

• DOI: 10.1101/2023.10.17.562742
• 发表时间: 2023
• 期刊: bioRxiv : the preprint server for biology
• 作者: Honnell,Victoria;Sweeney,Shannon;Norrie,Jackie;Ramirez,Cody;Xu,Beisi;Teubner,Brett;Lee,AhYoung;Bell,Claire;Dyer,MichaelA
• 通讯作者: Dyer,MichaelA