Transposon control as a checkpoint during regeneration

转座子控制作为再生过程中的检查点

• 批准号: 10607420
• 负责人: Krista Marie Angileri
• 金额: $ 7.18万
• 依托单位: CORNELL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-12-01 至 2026-11-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10607420
• 关键词: Ablation; Affect; Animals; Biological Assay; Cells; Chemicals; Chromatin; Complex; Cone; DNA Damage; DNA Transposable Elements; Data; Data Set; Defect; Development; Elements; Environment; Eukaryota; Eye; Family; Foundations; Gene Expression Profile; Genetic; Genome; Genomics; Gonadal structure; Homeostasis; Human; Inflammation; Inflammatory; Inflammatory Response; Injury; Mediating; Mobile Genetic Elements; Modeling; Molecular; Mus; Natural regeneration; Neurons; Nucleic Acids; Organism; Outcome; Pathway interactions; Pattern; Photoreceptors; Planarians; Process; Proliferating; Proteins; Recovery; Recovery of Function; Regenerative Medicine; Regenerative capacity; Regulation; Reporting; Repression; Resolution; Retina; Role; Salamander; Sea Cucumbers; Specificity; Structure; Study models; System; Testing; Time; Tissue-Specific Gene Expression; Tissues; Up-Regulation; Urochordata; Variant; Work; Zebrafish; cell type; comparative; experimental study; eye regeneration; functional restoration; genetic analysis; genome integrity; improved; in vivo; inhibitor; injured; insight; model organism; multimodality; multiple omics; mutant; novel; pharmacologic; regenerative; regenerative therapy; response to injury; retinal neuron; retinal regeneration; single-cell RNA sequencing; stem cell self renewal; stem cells; timeline; tissue injury; tissue regeneration; tissue repair; transcriptome sequencing; transcriptomics; transposon/insertion element

PROJECT SUMMARY / ABSTRACT Tissue regeneration is the process through which damaged tissue is restored to its original structure and function. There is wide variation across species in their regenerative ability. For example, zebrafish can regenerate all retinal neurons after injury while humans and mice cannot. Understanding the genetic basis and molecular underpinnings of complex tissue regeneration in model species holds the promise to enhance human regenerative medicine. Here I am using zebrafish to test the novel hypothesis that the control of transposable elements (TEs) is a necessary checkpoint for complex tissue regeneration. TEs are mobile DNA elements capable of self-replication that are ubiquitous and abundant in eukaryotes. Uncontrolled TE activity leads to accumulation of TE-encoded nucleic acids and proteins that interfere with cell homeostasis and can result in DNA damage, disrupting genome integrity. TE upregulation has been reported during tissue regeneration in salamanders, sea cucumbers, and worms. I hypothesize that TE activation is a hallmark of tissue injury that must be suppressed for successful regeneration, and an inability to suppress TEs will stall regeneration. Supporting this hypothesis, my preliminary analyses of bulk RNA-seq data reveal TE upregulation during early stages of eye regeneration that are later restored to control levels prior to tissue repair. I predict that zebrafish and other organisms with a strong regenerative capacity deploy specific control systems to suppress TE activity during regeneration. Here I will directly test the role of the Piwi pathway in suppressing TE activity during zebrafish eye regeneration. The Piwi pathway is known to repress TEs in animal gonads, including zebrafish, but there is growing evidence that the pathway is active in somatic tissues and required for regeneration in planarians. Furthermore, I have detected piwil1 expression in the zebrafish eye, raising the testable hypothesis that it functions during eye regeneration. I will utilize a model of zebrafish retinal regeneration and a 2-pronged approach combining multimodal genomics and manipulative experimentation. First, I will further establish that TE upregulation is a hallmark of tissue injury by profiling TE expression changes across five regenerating tissues using publicly available single- cell transcriptomic data. Second, I will generate a multi-omic single-cell dataset to assess TE expression changes during cone regeneration from the onset of injury through to functional recovery. These data will provide the most comprehensive and precise view of TE expression dynamics during regeneration for any species. Lastly, I will directly test whether TE repression is required for regeneration by modulating TE activity using Piwi pathway mutants and chemical inhibitors of TE activity. Together the outcomes of this project will be the first to directly assess the role of TE activity and regulation during complex tissue regeneration. Moreover, these studies will lay the foundation for new testable hypotheses surrounding differences between regeneratively competent versus incompetent organisms and lead to the development of novel regenerative therapies.

项目概要/摘要 组织再生是受损组织恢复其原始结构并恢复其原有结构的过程。 功能。不同物种的再生能力存在很大差异。例如，斑马鱼可以 损伤后所有视网膜神经元都能再生，而人类和小鼠则不能。了解遗传基础和 模型物种复杂组织再生的分子基础有望增强人类 再生医学。在这里，我使用斑马鱼来测试转座子控制的新假设 元素（TE）是复杂组织再生的必要检查点。 TE 是能够自我复制的移动 DNA 元件，在真核生物中普遍存在且含量丰富。 不受控制的 TE 活性会导致 TE 编码的核酸和蛋白质积累，从而干扰细胞 体内平衡并可能导致 DNA 损伤，破坏基因组完整性。据报道 TE 上调 蝾螈、海参和蠕虫的组织再生过程中。我假设 TE 激活是 必须抑制组织损伤才能成功再生的标志，并且无法抑制 TE 将阻碍再生。支持这一假设的是，我对批量 RNA-seq 数据的初步分析揭示了 TE 在眼睛再生的早期阶段上调，随后在组织修复之前恢复到控制水平。 我预测斑马鱼和其他具有强大再生能力的生物会部署特定的控制系统 抑制再生过程中的 TE 活性。这里我直接测试Piwi通路在抑制中的作用 斑马鱼眼睛再生过程中的 TE 活性。已知 Piwi 通路可抑制动物性腺中的 TE， 包括斑马鱼，但越来越多的证据表明该途径在体细胞组织中活跃，并且是 涡虫的再生。此外，我在斑马鱼的眼睛中检测到了 piwil1 的表达，从而提高了 可检验的假设，即它在眼睛再生过程中发挥作用。 我将利用斑马鱼视网膜再生模型和结合多模式的双管齐下的方法 基因组学和操作实验。首先，我将进一步确定 TE 上调是 通过使用公开可用的单点分析 5 个再生组织的 TE 表达变化来分析组织损伤 细胞转录组数据。其次，我将生成一个多组学单细胞数据集来评估 TE 表达变化 从损伤开始到功能恢复的视锥细胞再生过程中。这些数据将提供最 全面、精确地了解任何物种再生过程中的 TE 表达动态。最后，我会 通过使用 Piwi 途径调节 TE 活性，直接测试再生是否需要 TE 抑制 TE 活性的突变体和化学抑制剂。该项目的成果将是第一个直接 评估 TE 活性和调节在复杂组织再生过程中的作用。此外，这些研究将 为围绕再生能力之间差异的新的可检验假设奠定基础 对抗无能的生物体并导致新型再生疗法的发展。