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.

项目摘要/摘要 组织再生是受损组织恢复到其原始结构和 功能。不同物种的再生能力有很大的差异。例如，斑马鱼可以 所有视网膜神经元在损伤后都会再生，而人类和小鼠则不能。了解遗传基础和 模式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这个新的假设，即控制转座 元素(TES)是复杂组织再生的必要关卡。 TES是一种能够自我复制的可移动DNA元件，在真核生物中普遍存在并丰富。 不受控制的TE活动会导致TE编码的核酸和蛋白质堆积，从而干扰细胞 并可能导致DNA损伤，破坏基因组的完整性。据报道，Te基因上调 在火蜥蜴、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，必须抑制才能成功再生，并且无法抑制TES 会阻碍再生。支持这一假设的是，我对大量rna-seq数据的初步分析显示， 在眼睛再生的早期阶段上调，后来恢复到组织修复前的对照水平。 我预测斑马鱼和其他具有很强再生能力的生物会部署特定的控制系统 以抑制再生过程中的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的TE活性。众所周知，Piwi途径可以抑制动物性腺中的TES， 包括斑马鱼，但越来越多的证据表明，该途径在躯体组织中活跃，并需要 行星动物的再生。此外，我在斑马鱼的眼睛中检测到了piwil1的表达，提高了 可检验的假说是，它在眼睛再生过程中起作用。 我将利用斑马鱼视网膜再生的模型和结合多模式的双管齐下的方法 基因组学和操纵性实验。首先，我将进一步确定，上调是 组织损伤通过使用公开可用的单个- 细胞转录数据。其次，我将生成一个多组单细胞数据集来评估TE表达的变化 在从损伤开始到功能恢复的视锥再生过程中。这些数据将提供最多 全面而精确地观察任何物种在再生过程中的TE表达动态。最后，我会 通过使用Piwi通路调节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。总而言之，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中的作用。此外，这些研究将 为围绕再生能力差异的新的可检验假说奠定基础 对抗无能生物，并导致新的再生疗法的开发。