Investigating the Molecular Basis of Transposon Regulation and Function in Animal Development

项目摘要 转座元件(TES)是一种可移动的遗传元件，可以在宿主DNA内繁殖，并具有 对基因组的组织和功能产生重大影响。在生命之树上，TES无处不在， 占据动物基因组的很大一部分--大约20%的黑腹金龟子，以及45%-50%的人类和 小鼠基因组由在进化过程中积累的TE片段组成，而活跃的TE片段是一种 遗传和表观遗传变异的主要来源。尽管它们普遍存在，但TES的不同寻常的特征和高 拷贝数量使得它们的注释很差，而且是最神秘和最未被研究的遗传因素之一。 TES通常被认为是有害的，因为它们的迁移性会导致DNA损伤，并可能影响宿主基因组 和转录组，通过直接干扰功能元件或引入异位结合位点来转录 和表观遗传调节器。为了防止他们的有害活动，TES被各种沉默作为目标 机械装置。其中，pirna途径对tes的转录和转录后抑制起作用。 在动物种系中，这对于繁殖力和保持遗传信息的完整性至关重要 几代人。另一方面，TES是进化创新的重要来源，并且有一个不断增长的 关于TE衍生的调节区和纳入宿主的功能产品的文献正文 监管网络。有趣的是，脊椎动物和无脊椎动物的早期胚胎发生都具有特征 通过TE活性的激增，至少在小鼠中，特定TES的及时激活对于正常是必不可少的 发育进程。然而，TES产物的多样性及其在体细胞中的功能作用 这两个系统中的电池特性仍然很差，主要是由于在 对以高拷贝数存在的元素的基因组分析。 TE调节的分子机制和TE活性的功能含义是中心领域 对我的实验室很有兴趣。我提出了一个研究计划，从两个主要方面解决关键问题 TE生物学：1)在生殖系中，piRNA介导的TE沉默的机制和调节；2) 利用经典果蝇模型研究发育过程中体细胞TE表达的特点和功能 作为一个范例。首先，我提出了一个有针对性的策略来剖析几个关键的pirna的调控和功能。 途径组件，基于我之前的发现，即蛋白质SUMO化在piRNA中起着至关重要的作用 生物发生和TE沉默。同时，我计划利用最先进的长读和单细胞测序 克服TE衍生转录组基因组分析的历史局限性的技术， 阐明躯体TE活动的分子基础和功能后果的长期目标 发育中的有机体。

Project Summary Transposable elements (TEs) are mobile genetic elements that can propagate within the host DNA and have a significant impact on the genome organization and function. TEs are ubiquitous across the tree of life and occupy substantial fractions of animal genomes - about 20% of the D. melanogaster, and 45-50% of human and mouse genomes consist of TE fragments that have accumulated throughout evolution, and active TEs are a major source of genetic and epigenetic variation. Despite their prevalence, TEs’ unusual characteristics and high copy numbers left them poorly annotated, and among the most enigmatic and understudied genetic elements. TEs are typically seen as harmful, as their mobility causes DNA damage and can impact the host genome and transcriptome by directly disrupting functional elements or introducing ectopic binding sites for transcriptional and epigenetic regulators. To prevent their deleterious activities, TEs are targeted by various silencing mechanisms. Among these, the piRNA pathway enforces transcriptional and post-transcription repression of TEs in animal germlines, which is crucial for fertility and preserving the integrity of genetic information across generations. On the other hand, TEs are an important source of evolutionary innovation and there is a growing body of literature on TE-derived regulatory regions and functional products that became incorporated into host regulatory networks. Interestingly, early embryogenesis of both vertebrates and invertebrates is characterized by a spike of TE activity, and at least in mice, timely activation of specific TEs is essential for normal developmental progression. However, the diversity of products from TEs and their functional roles in somatic cells in both systems remain poorly characterized, largely owing to long-standing technical difficulties in the genomic analysis of elements that exist in high copy numbers. The molecular mechanisms of TE regulation and the functional implications of TE activity are central areas of interest for my laboratory. I present a research program that addresses key questions within two major aspects of TE biology: 1) the mechanism and regulation of piRNA-mediated TE silencing in the germline and 2) the characteristics and functions of somatic TE expression during development, using the classic model Drosophila as a paradigm. First, I propose a focused strategy to dissect the regulation and function of several key piRNA pathway components, building on my previous findings that protein SUMOylation plays essential roles in piRNA biogenesis and TE silencing. In parallel, I plan to leverage state-of-the-art long-read and single-cell sequencing technologies to overcome historical limitations to the genomic analysis of the TE-derived transcriptome, with the long-term goal of elucidating the molecular basis and functional consequences of somatic TE activity in the developing organism.