Gene Regulatory Networks of Synaptic Specificity

突触特异性的基因调控网络

• 批准号: 10351552
• 负责人: Mehmet Neset Ozel
• 金额: $ 12.69万
• 依托单位: NEW YORK UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-01-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10351552
• 关键词: ATAC-seq; Address; Adult; Affect; Algorithms; Award; Biological Models; Blindness; Blood Coagulation Factor VII; Brain; Brain Injuries; Brain region; Calcium; Candidate Disease Gene; Cell Surface Proteins; Cells; Chromatin; Code; Collaborations; Complex; Computational Technique; Computer Models; Data; Data Set; Defect; Detection; Development; Developmental Gene; Drosophila genus; Electrophysiology (science); Engineering; Environment; Equilibrium; Gene Expression Regulation; Genes; Genetic; Genetic Transcription; Genetic study; Genomics; Goals; Human; Image; Individual; Knowledge; Lead; Learning; Link; Logic; Mediating; Mentors; Mentorship; Methods; Modeling; Modification; Molecular; Morphology; Motion; Nerve Degeneration; Nervous system structure; Neurodevelopmental Disorder; Neurons; Neurophysiology - biologic function; New York; Optic Lobe; Output; Phase; Physiological; Physiology; Process; Property; RNA; Regenerative Medicine; Regulator Genes; Research; Resources; Retina; Specificity; Synapses; System; Techniques; Testing; Time; Training; Transplantation; Universities; Visual; Visual system structure; Work; XCL1 gene; base; cell replacement therapy; cell type; effective therapy; experimental study; fly; gene regulatory network; improved; in vivo; in vivo calcium imaging; induced pluripotent stem cell; interest; machine learning framework; nerve stem cell; network models; neural circuit; neuron development; neuroregulation; novel strategies; postsynaptic; programs; relating to nervous system; response; single-cell RNA sequencing; stem cells; synaptogenesis; tool; transcription factor; transcriptome; transdifferentiation

Project Summary/Abstract Neuronal type identity is central to the development and function of neural circuits, as it instructs both the connectivity of neurons as well as their synaptic and electrophysiological properties. Neuronal fates are thought to be controlled by combinations of transcription factors (TF) known as terminal selectors, but very little is known about the gene regulatory mechanisms that link differential TF expression to specific neuronal features. The Drosophila visual system, a well-characterized brain region that has an organization analogous to the vertebrate retina and cortex, provides the ideal balance of complexity and accessibility to investigate these mechanisms. The first aim of this project will be to decipher the terminal selector TF codes that establish and maintain the unique identity of approximately 200 neuronal types that make the Drosophila optic lobes. Using a single-cell RNA sequencing (scRNA-seq) dataset I generated from developing optic lobes, I identified the combinations of TFs that are stably maintained in each neuronal type throughout their differentiation. Under the mentorship of Claude Desplan (K99 phase), I will test the hypothesis that these TFs function as terminal selectors by modifying the TF codes of specific optic lobe neurons in vivo, with the goal of predictably transdifferentiating them into other cell types. This will demonstrate the sufficiency of terminal selectors to confer neuronal identity and benefit the field of regenerative medicine. The conserved mechanisms in mammalian systems could be exploited to induce differentiation of pluripotent cells into specific neurons that could be transplanted to treat blindness or neurodegeneration. The second aim of this project will link the terminal selector TFs to their downstream targets. In collaboration with Richard Bonneau, I will learn to use the “Inferelator” algorithm to generate computational models of gene regulatory networks by combining my existing scRNA-seq data with new chromatin accessibility (scATAC-seq) data I will acquire. During the K99 phase, I will test the effects of perturbating key predicted downstream effectors on the morphology and connectivity of a select group of neurons to establish proof-of- concept. I will then generalize this approach in the R00 phase by inferring gene regulatory networks for all optic lobe neurons at multiple developmental stages. The third aim will be performed in my independent lab (R00) to utilize the network models for engineering precise modifications in visual circuits. I will seek to selectively uncouple the circuit that computes wide-field motion from the one that detects small moving objects. I will use synaptic tracing methods as well as intravital calcium imaging to demonstrate the functional consequences of developmental perturbations. Altogether, this project will establish direct mechanistic links between the encoding of neuronal identity and the molecules that mediate intercellular interactions during synaptic partner selection, which are commonly affected in neurodevelopmental disorders. The mentorship I will receive from Dr. Desplan and Dr. Bonneau, combined with the impressive resources of New York University provide the ideal environment for preparing me to build a successful independent research program that link gene regulation to brain wiring.

项目摘要/摘要 神经元类型的身份对于神经回路的发展和功能是核心 神经元作为其突触和电生理特性的连通性。 由称为终端选择器的转录因子（TF）的组合控制，但鲜为人知 关于将差异TF与特定神经元特征联系起来的基因调节机制 果蝇视觉系统，一个特征良好的大脑区域，具有类似于脊椎动物的组织 视网膜和皮层提供了研究这些机制的复杂性和可及性的理想平衡。 该项目的第一个目的是破译终端选择器TF代码，以建立和维护 大约200个神经元类型的独特身份，这些神经元类型使果蝇裂片。 我从开发光叶产生的RNA测序（SCRNA-SEQ）数据集，我确定了组合 在每种神经元类型中稳定保持其分化的TF。 Claude Desplan（K99阶段），我将通过修改TFS作为终端选择器的效果来测试以下假设 体内特定光叶神经元的TF代码，目的是将它们分解为其他 细胞类型。 再生医学领域 多能细胞分化为特定神经元可能的 神经变性。 与理查德·邦诺（Richard Bonneau）合作，我将学习使用“地狱者”算法来生成计算 通过将我现有的SCRNA-SEQ数据与新的染色质可访问性相结合，基因调节网络的模型 （scatac-seq）我将在K99阶段获取数据。 一组神经元的形态和连通性的下游效应子，以建立证明证明 概念，我将通过推断所有光学的基因调节网络在R00阶段进行仿制 在我的独立实验室（R00）将执行多个发育阶段的LOBE神经元。 利用网络模型在视觉电路中进行工程精确的修改。 从检测小型移动对象的电路中取消计算宽场运动的电路 突触跟踪方法以及浸润性钙成像以证明功能的关闭 发展扰动。 神经元认同和在突触伴侣选择过程中介导细胞间相互作用的分子的 通常受到神经发育障碍的影响。 Bonneau博士，加上纽约大学的令人印象深刻的资源是理想的环境 为了使我准备建立成功的独立研究计划，该计划将基因调节与大脑接线联系起来。