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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：
10630108
负责人：
Jiang Qian
金额：
$ 42.65万
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/10630108
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 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 Work XCL1 gene aged axon regeneration 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 retinal ganglion cell regeneration 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.

总结长距离轴突再生是神经再生的重要方面之一，也是神经再生成功的先决条件视神经损伤后的功能恢复。虽然在加强内源性轴突再生能力通过各种途径，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。我们认为扩大足够数量的伤员不同亚型的RGC轴突进入脑内是功能恢复的主要任务在视觉伤害之后。因此，需要一种新的策略来1）提高RGC存活率，2）识别能够增强从不同亚型的RGC再生的另外的基因靶标，和3）促进广泛的长距离视神经再生，受抑制环境的影响较小。期间随着RGC成熟，其染色质结构随时间变化，导致转录组学改变导致支持轴突再生的内在能力丧失。相反，目前已鉴定的基因这种增强视神经再生的作用可能会改变转录组学的发育变化，以某种方式。因此，重要的是要揭示染色质和转录组学景观的RGCs有利轴突再生，并确定关键的转录因子和/或染色质调节剂，这种再生RGCs的染色质状态。在目的1中，通过进行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，我们将使用先进的综合生物信息学分析，以揭示RGC有利的染色质和转录组学景观轴突再生，并确定关键的转录因子和/或染色质调节剂的基础，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，以及它们的潜在作用。机制等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，可能导致广泛的长距离视神经损伤。神经再生基于这些结果，在目标3中，我们将探索是否将新发现的 UTX和myosin IIA/B基因敲除可诱导视神经长距离再生进入大脑。拟议中的研究不仅将产生转录组学变化的详细图像， RGC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点和优化重建视觉回路的方法。