Remodeling of chromatin and transcriptomic landscape to enhance optic nerve regeneration

重塑染色质和转录组景观以增强视神经再生

基本信息

批准号：
10413199
负责人：
Jiang Qian
金额：
$ 41.35万
依托单位：
JOHNS HOPKINS UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-08-01 至 2024-05-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10413199
关键词：
ATAC-seq Affect Axon Bioinformatics Brain CRISPR/Cas technology Candidate Disease Gene Cell Maturation Cell Survival Cells ChIP-seq Chromatin Chromatin Structure Collaborations Cytoskeleton Data Development Environment Epigenetic Process Gene Expression Gene Targeting Genes Genetic Transcription Goals Growth Factor In Vitro Injury Knock-out Lead Molecular Molecular Target Multiomic Data Mus Natural regeneration Neurons Nonmuscle Myosin Type IIA Optic Chiasm Optic Nerve Optic Nerve Injuries Pathway interactions Protocols documentation RNA Recovery of Function Regenerative capacity Regulation Retinal Ganglion Cells Role Site Spinal cord injury Survival Rate Three-Dimensional Imaging Tissues Vision Visual Visual system structure Work XCL1 gene aged axon regeneration base chromatin remodeling experimental study genomic locus histone demethylase imaging study in vivo injured innovation multiple omics nerve injury non-muscle myosin novel optic nerve regeneration regeneration function regenerative screening tool transcription factor transcriptome sequencing transcriptomics

项目摘要

Summary Long distance axon regeneration is one of the most important aspects and a prerequisite for successful functional recovery after optic nerve injuries. Although great progress has been made to enhance the intrinsic axon regeneration ability via various approaches, long distance optic nerve regeneration reaching the original targets in the brain remains a major challenge. We think that extending sufficient number of injured RGC axons from different RGC subtypes into the brain should be the major tasks for functional recovery after visual injuries. Therefore, a new strategy is needed to 1) enhance RGC survival rate, 2) identify additional gene targets capable of enhance regeneration from a diverse subtypes of RGCs, and 3) promote extensive long-distance optic nerve regeneration that is less affected by the inhibitory environment. During RGC maturation, their chromatin structures change temporally, leading to changed transcriptomics underlying the loss of intrinsic ability to support axon regeneration. Conversely, the current identified genes that act to enhance optic nerve regeneration presumably alter the developmental changes in transcriptomics in some way. Thus, it is important to reveal the chromatin and transcriptomics landscape of RGCs favorable for axon regeneration, and identify key transcription factors and/or chromatin modulators underlying such chromatin state of regenerating RGCs. In Aim 1, by performing RNA-seq, ATAC-seq and ChIP-seq of purified RGCs at different maturation stages, and different regenerative states, we will use advanced integrative bioinformatics analyses to reveal the chromatin and transcriptomics landscape of RGCs favorable for axon regeneration, and identify key transcription factors and/or chromatin modulators underlying such chromatin state of regenerating RGCs. In Aim 2, we will perform functional screening experiments to determine their roles in regulation of RGC survival and/or optic nerve regeneration, and their underlying mechanisms. Our recent work showed that deleting non-muscle myosin IIA/B or histone demethylase UTX, when combined with enhanced intrinsic axon regeneration ability, could lead to extensive long-distance optic nerve regeneration. Based on these results, in Aim 3, we will explore if combining the newly identified transcription factors with UTX and myosin IIA/B knockout could induce long distance optic nerve regeneration into the brain. The proposed studies will not only generate a detailed picture of changes in transcriptomics, chromatin accessibility and epigenetic landscape of RGCs during maturation and regeneration, but also identify novel molecular targets and optimized approaches to re-establish visual circuity.

概括长距离轴突再生是最重要的方面之一，也是成功的先决条件视神经损伤后的功能恢复。尽管在加强内在的轴突再生能力通过多种途径，远距离视神经再生达到大脑中的原始目标仍然是一个重大挑战。我们认为扩大受伤人数不同RGC亚型的RGC轴突进入大脑应该是功能恢复的主要任务视觉损伤后。因此，需要一种新的策略来 1) 提高 RGC 存活率，2) 识别能够增强 RGC 不同亚型再生的其他基因靶标，以及 3) 促进广泛的远距离视神经再生，受抑制环境的影响较小。期间 RGC 成熟，其染色质结构暂时发生变化，导致转录组学发生变化导致支持轴突再生的内在能力丧失。相反，目前已发现的基因增强视神经再生的作用可能会改变转录组学的发育变化某种方式。因此，揭示 RGC 的染色质和转录组学景观非常重要用于轴突再生，并确定关键的转录因子和/或染色质调节剂再生 RGC 的染色质状态。在目标 1 中，通过执行 RNA-seq、ATAC-seq 和 ChIP-seq 纯化的RGC在不同的成熟阶段和不同的再生状态下，我们将使用先进的综合生物信息学分析揭示 RGC 的染色质和转录组学景观用于轴突再生，并确定其背后的关键转录因子和/或染色质调节剂再生 RGC 的染色质状态。在目标 2 中，我们将进行功能筛选实验确定它们在调节 RGC 存活和/或视神经再生中的作用及其潜在的作用机制。我们最近的工作表明，删除非肌肉肌球蛋白 IIA/B 或组蛋白去甲基化酶 UTX，当与增强的内在轴突再生能力相结合时，可能会导致广泛的长距离光学神经再生。基于这些结果，在目标 3 中，我们将探索是否将新确定的敲除 UTX 和肌球蛋白 IIA/B 的转录因子可诱导远距离视神经再生进入大脑。拟议的研究不仅将生成转录组学变化的详细图片， RGC 在成熟和再生过程中的染色质可及性和表观遗传景观，而且确定新的分子靶标和重建视觉回路的优化方法。