Identifying gene regulatory networks controlling photoreceptor specification by transcriptomic and epigenomic analysis of retinal development in cone-dominant retina

通过锥体优势视网膜视网膜发育的转录组和表观基因组分析来识别控制光感受器规格的基因调控网络

• 批准号: 10116765
• 负责人: Seth Blackshaw
• 金额: $ 24.56万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-01-01 至 2022-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10116765
• 关键词: ATAC-seq; Address; Adolescent; Age; American; BCL9 gene; Blindness; Breeding; Candidate Disease Gene; Cell Therapy; Cells; Chromatin; Code; Cone; Data; Data Set; Defect; Development; Disease; Electroporation; Embryo; Future; Gene Activation; Gene Expression; Gene Expression Regulation; Generations; Genes; Genome; Human; Mammals; Midwestern United States; Molecular; Muller' s cell; Mus; Mutation; Peripheral; Photoreceptors; Proteins; Protocols documentation; Regulation; Regulator Genes; Resolution; Retina; Retinal Cone; Rod; Rodent; Specific qualifier value; Spermophilus; Staging; Testing; Therapeutic; Transplantation; Vertebrate Photoreceptors; Wild Type Mouse; base; cell type; design; epigenomics; fovea centralis; gene function; improved; in vivo; induced pluripotent stem cell; insight; loss of function; mRNA Expression; neurogenesis; overexpression; postnatal; protein function; regenerative therapy; retinal progenitor cell; retinal rods; single-cell RNA sequencing; stem cells; tool; transcription factor; transcriptomics

Project Summary While degeneration of cone photoreceptors is the ultimate cause of blindness in photoreceptor dystrophies, mouse and human retinas are rod photoreceptor-dominant, a fact that has hindered progress in understanding how cones are specified. New insight into this problem can potentially come from studying the molecular mechanisms of photoreceptor development in mammalian species with naturally cone-dominant retinas. One such species is the 13-lined ground squirrel (13-LGS) Ictidomys tridecemlineatus, which is endemic to the American Midwest. The genome of 13-LGS is fully sequenced, and their developmental staging is well- characterized and readily comparable to mouse. We propose to comprehensively profile gene expression and chromatin accessibility during retinal neurogenesis in 13-LGS using single-cell RNA- and ATAC-Seq. We will then use computational approaches to identify gene regulatory networks predicted to control cone photoreceptor development in 13-LGS, and compare these with results obtained from mouse and human retinas to identify species-specific differences in gene expression and regulation that underlie differences in the rod:cone ratio. We will also test whether the 13-LGS orthologue of the Nrl gene, a master regulator of photoreceptor specification, shows reduced ability to promote rod, and repress cone, development relative to its mouse counterpart. We expect these studies will identify multiple previously unidentified genes that are strong candidate positive and negative regulators of cone development, and can be functionally tested in future studies. Ultimately, this may help improve protocols for directed differentiation of cone photoreceptors from stem and progenitor cells for use in therapeutic transplantation.

项目概要 虽然视锥细胞退化是光感受器营养不良导致失明的最终原因， 小鼠和人类视网膜以杆状光感受器为主，这一事实阻碍了理解的进步 如何指定锥体。对这个问题的新见解可能来自于分子研究 具有天然视锥细胞优势的视网膜的哺乳动物物种的光感受器发育机制。一 这种物种是 13 线地松鼠 (13-LGS) Ictidomys tridecemlineatus，它是特有的 美国中西部。 13-LGS 的基因组已完全测序，其发育阶段良好- 具有特征并且易于与小鼠进行比较。我们建议全面分析基因表达和 使用单细胞 RNA 和 ATAC-Seq 检测 13-LGS 视网膜神经发生过程中染色质的可及性。我们将 然后使用计算方法来识别预测控制视锥细胞的基因调控网络 13-LGS 中光感受器的发育，并将这些结果与从小鼠和人类获得的结果进行比较 视网膜识别基因表达和调控的物种特异性差异，这些差异是物种差异的基础 杆：锥比。我们还将测试 Nrl 基因的 13-LGS 直系同源物是否是 光感受器规格，显示出促进视杆细胞和抑制视锥细胞发育的能力降低 它的鼠标对应物。我们期望这些研究将鉴定出多个先前未鉴定的基因 锥体发育的强有力的候选正负调节因子，并且可以在未来进行功能测试 研究。最终，这可能有助于改进锥体光感受器与视锥细胞定向分化的方案 用于治疗性移植的干细胞和祖细胞。