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.

项目总结/摘要 组织再生是受损组织恢复到其原始结构的过程， 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， 模型物种中复杂组织再生的分子基础有望提高人类 再生医学在这里，我用斑马鱼来测试新的假设，即控制转座基因 元件（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的DNA元件，在真核生物中普遍存在且丰富。 不受控制的TE活性导致TE编码的核酸和蛋白质的积累，这些核酸和蛋白质干扰细胞增殖。 体内平衡，并可能导致DNA损伤，破坏基因组的完整性。已经报道了TE上调 在蝾螈海参和蠕虫的组织再生过程中。我假设TE激活是一种 组织损伤的标志，必须抑制成功再生，不能抑制TE 将停止再生。我对大量RNA-seq数据的初步分析支持了这一假设， 在眼睛再生的早期阶段上调，其随后在组织修复之前恢复到对照水平。 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 以抑制再生期间的TE活性。在这里，我将直接测试Piwi通路在抑制 斑马鱼眼睛再生过程中TE的活性。已知Piwi通路抑制动物性腺中的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是活跃的， 真涡虫的再生此外，我还检测到piwil 1在斑马鱼眼睛中的表达，提高了斑马鱼的视力。 它在眼睛再生过程中起作用的假说是可以验证的。 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， 基因组学和操纵实验。首先，我将进一步确定TE上调是 组织损伤，通过使用公开可用的单克隆抗体分析五种再生组织中TE表达的变化， 细胞转录组学数据。其次，我将生成一个多组学单细胞数据集，以评估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 全面而精确地观察任何物种再生过程中TE的表达动态。最后，我将 通过使用Piwi途径调节TE活性来直接测试再生是否需要TE阻遏 突变体和TE活性的化学抑制剂。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 与无能的生物体，并导致新的再生疗法的发展。