The evolutionary and functional genomics of satellite DNA

项目摘要 真核生物基因组中含有一系列串联重复的非编码序列，而我们目前对此知之甚少 关于卫星DNA卫星DNA通常存在于着丝粒、端粒和Y染色体附近， 可以包含超过50%的真核基因组。已知它们的顺序变化很快， 基因组定位，这可能导致密切相关的物种之间的遗传不相容性。的 卫星DNA的错误调节可对基因组稳定性和癌症形成产生严重后果。 尽管是基因组中无处不在的一部分，并具有重要的功能性后果，但我们所知甚少。 关于卫星DNA缺乏遗传学、基因组学和分子学工具来研究串联重复序列 阻碍了对卫星DNA进化和功能的理解。例如，卫星DNA 尤其难以测序和组装。下一代测序的最新进展 技术解决了这些问题中的一些。该方案整合了基因组学、分子学和细胞学 方法研究果蝇基因组中卫星DNA的进化和功能基因组学。主要研究者有 开发了新的基因组和细胞学方法来研究进化动力学，基因组结构和 以前所未有的分辨率表达卫星DNA。主要研究者将使用这些方法研究 卫星DNA序列，丰度和组织在进化的时间，并确定进化 对这些变化负责的力量。该提案旨在开发卫星DNA的综合模型 进化，考虑到不同类型的自然选择的基础上的功能方面， 卫星DNA目前对卫星DNA的功能知之甚少：精确的基因操纵卫星DNA。 由于缺乏独特的靶位点，过去不可能采用位点特异性方法的DNA。的 在这项提议中开发的新的基因组学方法提供了一个机会， 卫星DNA可以作为基因组编辑技术的目标。该提案将建立精确的 黑腹果蝇中卫星DNA的基因组缺失以测试关于调控的特定假设， 适合度效应和自私的遗传行为的卫星DNA。这项建议还将使用新的分子遗传学 技术来操纵卫星DNA在生殖系中的表达， 在染色体分离和染色质组织中起作用。这些实验将具有广泛的 这不仅对基因组进化，而且对理解癌症中卫星DNA的调控具有重要意义。 和衰老。

Project summary Eukaryotic genomes contain arrays of tandemly repeated non-coding sequences that we currently know little about—satellite DNAs. Typically found near centromeres, telomeres and on Y chromosomes, satellite DNAs can comprise over 50% of some eukaryotic genomes. They are known to change rapidly in sequence and genomic location, which can cause genetic incompatibilities between closely related species. The misregulation of satellite DNA can have serious consequences for genomic stability and cancer formation. Despite being a ubiquitous part of genomes and having important functional consequences, we know little about satellite DNA. The lack of genetic, genomic and molecular tools to study tandemly repeated sequences has stymied progress towards understanding satellite DNA evolution and function. For example, satellite DNAs are particularly challenging to sequence and assemble. Recent developments in next-generation sequencing technologies circumvent some of these problems. This proposal integrates genomic, molecular and cytological methods to study the evolutionary and functional genomics of satellite DNA in Drosophila genomes. The PI has developed new genomic and cytological methods to study the evolutionary dynamics, genomic structure and expression of satellite DNA with unprecedented resolution. The PI will use these methods to study changes in satellite DNA sequence, abundance and organization over evolutionary time and to determine the evolutionary forces responsible for these changes. This proposal aims to develop comprehensive models of satellite DNA evolution that take into consideration different types of natural selection based on the functional aspects of satellite DNAs. Little is currently known of satellite DNA function: the precise genetic manipulation of satellite DNAs with site-specific approaches had not been possible in the past due to a lack of unique target sites. The new genomic methods developed in this proposal provide an opportunity to discover unique sites flanking satellite DNAs that may serve as targets for genome editing techniques. The proposal will create precise genomic deletions of satellite DNA in Drosophila melanogaster to test specific hypotheses about the regulation, fitness effects and selfish genetic behavior of satellite DNA. This proposal will also use new molecular genetic techniques to manipulate the expression of satellite DNAs in the germline to ask questions about their functions in chromosome segregation and chromatin organization. These experiments will have broad implications not only for genome evolution, but also for understanding the regulation of satellite DNA in cancer and aging.