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

项目摘要 转座因子（Transposable elements，TE）是可在宿主DNA内繁殖的移动的遗传因子， 对基因组的组织和功能产生重大影响。TE在生命之树中无处不在， 占动物基因组的很大一部分-约占D.黑腹动物，以及45-50%的人类和 小鼠的基因组由在进化过程中积累的TE片段组成，活性TE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TE的不寻常特征和高 拷贝数使它们的注释很差，并且是最神秘和研究不足的遗传元件。 TE通常被认为是有害的，因为它们的移动性会导致DNA损伤，并可能影响宿主基因组 通过直接破坏功能元件或引入用于转录的异位结合位点， 和表观遗传调节因子。为了防止它们的有害活性，通过各种沉默靶向TE。 机制等其中，皮尔纳途径实施TE的转录和转录后抑制 在动物生殖系，这是至关重要的生育能力和保持遗传信息的完整性， 代另一方面，TE是进化创新的重要来源， 大量关于TE衍生的调控区和功能性产物的文献， 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的特点是 至少在小鼠中，特异性TE的及时激活对于正常的 发展进程然而，TE产物的多样性及其在体细胞中的功能作用， 这两种系统中的细胞的特征仍然很差，主要是由于长期存在的技术困难， 对高拷贝数存在的元件进行基因组分析。 TE调节的分子机制和TE活性的功能意义是核心领域 对我的实验室感兴趣。我提出了一个研究计划，解决两个主要方面的关键问题 TE生物学：1）生殖系中piRNA介导的TE沉默的机制和调控，2） 在发育过程中体细胞TE表达的特征和功能，使用经典模型果蝇 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皮尔纳的调控和功能， 基于我以前的发现，蛋白质SUMO化在皮尔纳中起着重要作用， 生物发生和TE沉默。同时，我计划利用最先进的长读码和单细胞测序 技术，以克服对TE衍生转录组的基因组分析的历史局限性， 长期的目标是阐明的分子基础和功能后果的体细胞TE活动， 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.