The evolutionary and functional genomics of satellite DNA

卫星DNA的进化和功能基因组学

• 批准号: 10328694
• 负责人: Amanda Marie Larracuente
• 金额: $ 42.11万
• 依托单位: UNIVERSITY OF ROCHESTER
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-08-01 至 2026-12-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10328694
• 关键词: Affect; Aging; Behavioral Genetics; CRISPR/Cas technology; Cell physiology; Centromere; Chromatin; Chromosome Segregation; Cytology; DNA Sequence; Data; Development; Drosophila genome; Drosophila melanogaster; Evolution; Genes; Genetic; Genetic Models; Genome; Genome Stability; Genomic Instability; Genomic approach; Genomics; Location; Malignant Neoplasms; Methods; Molecular; Molecular Genetics; Natural Selections; Population Genetics; Regulation; Resolution; Resources; Satellite DNA; Site; Tandem Repeat Sequences; Techniques; Technology; Testing; Time; Untranslated RNA; Y Chromosome; base; comparative genomics; driving force; experimental study; fitness; functional genomics; genetic manipulation; genetic resource; genome editing; telomere; tool

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.

项目摘要 真核基因组包含一系列串联重复的非编码序列，我们目前知道这些序列很少 关于 - 卫星DNA。通常在Centromeres，端粒和Y染色体附近发现，卫星DNA 可以完成一些超过50％的真核基因组。众所周知，它们会按顺序迅速变化，并且 基因组位置，这可能会在密切相关的物种之间引起遗传不相容。 卫星DNA的不正调会对基因组稳定性和癌症形成产生严重的影响。 尽管是基因组无处不在的部分，并且对细胞功能具有重要影响，但缺乏 研究串联重复序列的遗传，基因组和分子工具阻碍了进步 了解卫星DNA的演化和功能。例如，卫星DNA特别具有挑战性 序列，组装和操纵。测序和基因组编辑技术的最新发展 规避其中一些问题。该建议将基因组，分子和细胞学方法整合到 研究果蝇基因组中卫星DNA的进化和功能基因组学。 PI已经发展 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。这 PI将使用比较基因组学方法来研究卫星DNA序列，丰度和 在进化时间内组织，并确定推动这些变化的进化力量。这 提案还旨在开发卫星DNA进化的全面人群遗传模型 根据卫星DNAS研究的功能方面的不同类型的自然选择。 该建议并利用PI产生的有关卫星DNA组织的经验数据。几乎没有 目前已知卫星DNA功能：具有特定位点特异性的卫星DNA的精确遗传操纵 由于缺乏独特的目标位点，过去无法使用基因编辑方法。 Pi具有 使用其卫星基因座组装来识别目标位点，并成功操纵了卫星DNA位点 使用基于CRISPR/CAS9的基因组编辑技术。他们已经进行了精确的基因组缺失，并且 果蝇中卫星DNA的重复，它们将用于测试有关该假设的特定假设 卫星DNA的调节，适应性效应和自私的遗传行为。该建议还将利用 PI创建的新分子遗传资源来操纵卫星DNA表达以询问有关 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 不仅对基因组进化和规格的含义，而且对理解卫星的调节 癌症和衰老的DNA。