Comparative Genomics of Chromosome Replication Among Budding Yeasts

芽殖酵母染色体复制的比较基因组学

• 批准号: 1243710
• 负责人: Bonita Brewer
• 金额: $ 84.71万
• 依托单位: University of Washington
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-06-15 至 2018-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1243710&HistoricalAwards=false
• 关键词: Comparative; Genomics; Chromosome; Replication; Among

Faithful chromosome replication is a central mission of every dividing cell. Although the machinery for DNA replication is among the most conserved across the tree of life, the regions of chromosomes at which replication initiates 'origins of replication' vary widely across species both in their structure and in their locations. Chromosome replication has been best studied in the model organism baker's yeast. Replication origins in yeast are defined by short stretches of DNA sequence, with ten to fifty origins scattered across each chromosome. In contrast, human chromosomes have many hundreds to thousands of origins per chromosome unspecified by DNA sequences. Despite these striking differences in origin structures, little is known about how origins of replication evolve, and how they may relate to chromosomal rearrangements that take place during evolution. Baker's yeast and its other budding yeast relatives offer an unparalleled advantage in addressing these gaps in our knowledge: many strains and species have been sequenced and are amenable to experiments first performed in baker's yeast. This research will capitalize on the suite of chromosome-wide assays to discover yeast replication origins, delineate their essential sequences, and measure the regulation at each site in its native chromosomal context. Moreover, the opportunity to compare multiple yeast species that had undergone a whole genome duplication (WGD) with other species that hadn't experienced the event can provide unique insights into the forces shaping replication and chromosome organization in the face of a massive genome upheaval. The work will focus on how origins evolved over a 500 million year timescale. The aims are grounded in the context of testing the following broad hypotheses: First, post-­WGD species will show greater diversity of origin sequences and locations than pre-­WGD species due to relaxation of selection during genome loss following the WGD event. Second, in contrast, closely related species will share common origin sequences but not chromosomal locations. Finally, changes that occur to the protein machinery that recognizes origins are responsible for driving the diversification of the DNA sequences of origins. Given the increasingly appreciated role of origins in maintenance of chromosome integrity, the results will add an important missing element to understand the evolution of chromosome structure.Broader Impacts:This work will have broad impacts in undergraduate and public science education, inclusion of underrepresented groups, and scientific understanding. A new partnership with Shoreline Community College has been proposed specifically for this project and will, in particular, result in access to research and student-­driven, inquiry-­based learning for a wider cross-­section of students than would otherwise be possible. In particular, the intern experience will build confidence and prepare students for jobs as technicians in university or biotech research labs, and may spark their interest in pursuing further education. All three principal investigators have strong records of educating undergraduates, including women, underrepresented minorities, and students from primarily undergraduate institutions. The methods and molecular resources developed will be of interest to the larger scientific community, as has been the case for other techniques previously developed by these principal investigators. Furthermore, contributing to the understanding of evolutionary processes is a benefit to science and society. Specifically, rapid evolution of a highly conserved process is an under-­studied phenomenon, and the results are likely to shed light on the natural variation found in other essential cellular processes.

染色体的忠实复制是每个分裂细胞的中心使命。虽然DNA复制的机制是整个生命树中最保守的，但复制起始的染色体区域“复制起点”在其结构和位置上都因物种而异。染色体复制在模式生物面包酵母中得到了最好的研究。酵母中的复制起点由短段DNA序列定义，每条染色体上分散着十到五十个起点。相比之下，人类染色体有数百至数千个起源，每个染色体的DNA序列未指定。尽管在起源结构上存在这些惊人的差异，但人们对复制起点如何进化以及它们如何与进化过程中发生的染色体重排有关知之甚少。面包酵母和它的其他芽殖酵母亲戚提供了一个无与伦比的优势，在解决这些差距，在我们的知识：许多菌株和物种已经测序，并服从实验首先在面包酵母。这项研究将利用一套染色体范围的测定来发现酵母复制起点，描绘它们的基本序列，并在其天然染色体背景下测量每个位点的调控。此外，将经历过全基因组复制（WGD）的多个酵母物种与其他没有经历过该事件的物种进行比较的机会可以为面对大规模基因组剧变时塑造复制和染色体组织的力量提供独特的见解。这项工作将集中在起源如何演变超过5亿年的时间尺度。这些目标基于测试以下广泛假设的背景：首先，由于在WGD事件后的基因组丢失期间选择的放松，后WGD物种将显示出比前WGD物种更大的起源序列和位置多样性。第二，与此相反，密切相关的物种将共享共同的起源序列，但不是染色体位置。最后，识别起源的蛋白质机制发生的变化是驱动起源DNA序列多样化的原因。考虑到起源在维持染色体完整性方面的作用日益受到重视，研究结果将为了解染色体结构的进化增加一个重要的缺失元素。更广泛的影响：这项工作将在本科生和公共科学教育、纳入代表性不足的群体和科学理解方面产生广泛的影响。与海岸线社区学院的一个新的伙伴关系已被提议专门用于这个项目，特别是将导致获得研究和学生驱动的，基于探究的学习，为更广泛的跨学科的学生比否则可能。特别是，实习经验将建立信心，并为学生在大学或生物技术研究实验室担任技术人员做好准备，并可能激发他们继续深造的兴趣。这三位主要研究人员都有良好的本科生教育记录，包括女性，代表性不足的少数民族，以及主要来自本科院校的学生。开发的方法和分子资源将引起更大科学界的兴趣，就像这些主要研究人员以前开发的其他技术一样。此外，有助于理解进化过程对科学和社会都有好处。具体而言，高度保守过程的快速进化是一种未充分研究的现象，其结果可能揭示在其他基本细胞过程中发现的自然变异。