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通常发现在着丝粒，端粒附近，和Y染色体上，卫星DNA 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。 尽管作为基因组的一个普遍存在的部分，并对细胞功能有重要影响，缺乏 研究串联重复序列的遗传学、基因组学和分子学工具阻碍了 了解卫星DNA的进化和功能。例如，卫星DNA特别具有挑战性， 排序、组装和操纵。测序和基因组编辑技术的最新进展 规避其中的一些问题。该提案整合了基因组学、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。PI开发了 新的基因组方法和资源，以前所未有的分辨率研究卫星DNA进化。的 PI将使用比较基因组学方法研究卫星DNA序列，丰度和 组织在进化时间，并确定驱动这些变化的进化力量。这 该提案还旨在开发卫星DNA进化的全面人口遗传模型， 考虑到不同类型的自然选择的基础上的功能方面的卫星DNA的研究， 这个建议，并利用经验数据卫星DNA组织产生的PI。之甚少 目前已知的卫星DNA功能：精确的基因操纵卫星DNA与位点特异性 由于缺乏独特的靶位点，基因编辑方法在过去是不可能的。主要研究者有 利用他们的卫星基因座组合来鉴定靶位点，并成功地操纵了卫星DNA基因座 使用基于CRISPR/Cas9的基因组编辑技术他们精确地删除了基因组， 他们将用果蝇中卫星DNA的复制来检验关于 调节，健身效果，自私的遗传行为的卫星DNA。该提案还将利用 PI创建了新的分子遗传资源来操纵卫星DNA表达， 它们在染色体分离和染色质组织中的功能。这些实验将具有广泛的 这不仅对基因组进化和物种形成有意义，而且对理解卫星调控也有意义。 DNA与癌症和衰老

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 effects on cellular functions, 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, assemble, and manipulate. Recent developments in sequencing and genome editing 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 approaches and resources to study satellite DNA evolution with unprecedented resolution. The PI will use a comparative genomics approach to study changes in satellite DNA sequence, abundance and organization over evolutionary time and to determine the evolutionary forces driving these changes. This proposal also aims to develop comprehensive population genetic models of satellite DNA evolution that take into consideration different types of natural selection based on functional aspects of satellite DNAs studied in this proposal and leverage empirical data about satellite DNA organization generated by the PI. Little is currently known of satellite DNA function: the precise genetic manipulation of satellite DNAs with site-specific gene editing approaches had not been possible in the past due to a lack of unique target sites. The PI has used their assemblies of satellite loci to identify target sites and has successfully manipulated satellite DNA loci using CRISPR/Cas9-based genome editing techniques. They have made precise genomic deletions and duplications of satellite DNA in Drosophila melanogaster that they will use to test specific hypotheses about the regulation, fitness effects, and selfish genetic behavior of satellite DNA. This proposal will also leverage the new molecular genetic resources the PI created to manipulate satellite DNA expression to ask questions about their functions in chromosome segregation and chromatin organization. These experiments will have broad implications not only for genome evolution and speciation, but also for understanding the regulation of satellite DNA in cancer and aging.