Ribosomal gene loci dynamics and specific retrotransposons

核糖体基因位点动力学和特异性逆转录转座子

• 批准号: 0544071
• 负责人: Thomas Eickbush
• 金额: $ 62.15万
• 依托单位: University of Rochester
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-06-01 至 2010-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0544071&HistoricalAwards=false
• 关键词: Ribosomal; gene; loci; dynamics; specific

All higher eukaryotic genomes are composed to a large measure of transposable elements that continually attempt to expand their numbers even further. These elements can be thought of as intracellular parasites. While it is generally assumed that transposable elements insert more or less at random, a growing number of elements have been shown to minimize their effects on the host by evolving site-specificity. The model systems used in this research are the R1 and R2 non-LTR retrotransposable elements, which insert specifically into the 28S rRNA genes of many animals but have been studied most extensively in insects. The hundreds of tandemly arranged rRNA genes (the rDNA loci) of eukaryotes undergo dynamic processes of recombination to eliminate variation within the locus. Yet throughout their history, R1 and R2 have stably maintained their presence in the rRNA genes indicating they are well-adapted to exploit the recombinational and regulatory mechanisms devised by the cell to synthesize rRNA. The objectives of this research are to study the rDNA genes and their R1and R2 insertions in several Drosophila species at three levels. The first objective is to define the changes that have occurred in specific rDNA loci over defined periods of time. Large segments of the rDNA loci from two replicate lines of D. melanogaster that have been separated by over 400 generations will be recovered on a series of overlapping recombinant DNA clones assembled using the 5' marked R1 and R2 elements as reference points. Detailed comparisons of the extended regions will enable a first view of the specific patterns of recombination and of the distribution of the retrotransposition events that have given rise to the many changes known to have occurred between these lines. Second, natural populations of D. simulans will be screened to determine the frequency with which R2 elements are active as well as to characterize the size and structure of the rDNA loci. These studies will be conducted in D. simulans because this sister species of D. melanogaster has no rDNA units on the Y chromosome and populations with active R2 elements are readily obtained. Third, public data made available through whole genome shot-gun sequencing efforts of 12 Drosophila species as well as those of other insects will be used to score the nucleotide variation within the rDNA loci of various animals. The goal will be to establish the approaches that can be used to compare the mechanism and efficiency of concerted evolution of the rDNA loci. These studies will enable a greater understanding of the fluctuation in size, the regulation of expression, and the recombinational processes that give rise to both the sequence uniformity and the segmental changes that occur in the rDNA locus over time. They will also increase our understanding of the delicate balance that is reached between higher organisms and these intracellular parasites. The genomes of all higher organisms are in a constant battle with internal parasites called mobile or transposable elements. Between 10% and 90% of total genomic DNA from different organisms is composed of these elements. This research focuses on a model system that has the advantage that the mobile elements specifically insert into one location of the genome: the tandemly repeated ribosomal RNA genes (rDNA locus). The model organisms are several fruit fly species (Drosophila). The studies include short term laboratory experiments, population experiments, and the utilization of genomic sequence data to follow the mobile elements being inserted into and deleted from the rDNA locus, as well as how the rDNA locus changes as a result of these insertions. This knowledge will help researchers both control and exploit these elements for the advantage of mankind. The project will also serve to further the education of high school science teachers, undergraduates, and graduate students.

所有高等真核生物的基因组都是由大量的转座因子组成的，这些转座因子不断地试图进一步扩大它们的数量。这些元素可以被认为是细胞内的寄生虫。虽然一般认为转座因子或多或少是随机插入的，但越来越多的转座因子已被证明通过进化位点特异性来最小化它们对宿主的影响。本研究中使用的模型系统是R1和R2非LTR反转录转座元件，它们特异性地插入许多动物的28S rRNA基因中，但在昆虫中研究得最广泛。真核生物的数百个串联排列的rRNA基因（rDNA基因座）经历动态重组过程以消除基因座内的变异。然而，在它们的整个历史中，R1和R2稳定地保持了它们在rRNA基因中的存在，表明它们很好地适应了利用细胞设计的重组和调节机制来合成rRNA。本研究的目的是从三个水平上研究果蝇的rDNA基因及其R1和R2插入。第一个目标是确定特定rDNA基因座在特定时间段内发生的变化。 两个重复系的rDNA基因座的大片段。已经分离超过400代的黑腹果蝇将在一系列重叠的重组DNA克隆上回收，所述重组DNA克隆使用5 ′标记的R1和R2元件作为参考点组装。对延伸区域的详细比较将使我们能够初步了解重组的具体模式和逆转录转座事件的分布，这些事件引起了已知在这些细胞系之间发生的许多变化。第二，D.将筛选simulans以确定R2元件具有活性的频率以及表征rDNA基因座的大小和结构。这些研究将在D. simulans是D.黑腹果蝇在Y染色体上没有rDNA单位，因此很容易获得具有活性R2元件的种群。第三，通过12种果蝇以及其他昆虫的全基因组鸟枪测序工作获得的公共数据将用于对各种动物rDNA基因座内的核苷酸变异进行评分。 我们的目标将是建立方法，可以用来比较的机制和效率的协同进化的rDNA基因座。这些研究将使我们能够更好地理解大小的波动、表达的调节以及重组过程，这些过程导致rDNA基因座随时间推移发生的序列均匀性和片段变化。它们还将增加我们对高等生物和这些细胞内寄生虫之间达成的微妙平衡的理解。 所有高等生物的基因组都在与称为移动的或转座因子的内部寄生虫进行持续的斗争。来自不同生物体的总基因组DNA的10%至90%由这些元素组成。本研究的重点是一个模型系统，具有的优势，移动的元件专门插入到一个位置的基因组：串联重复的核糖体RNA基因（rDNA位点）。模式生物是几种果蝇物种（果蝇）。这些研究包括短期实验室实验、群体实验和利用基因组序列数据来跟踪插入和删除rDNA位点的移动的元件，以及rDNA位点如何由于这些插入而改变。 这些知识将帮助研究人员控制和利用这些元素，为人类造福。 该项目还将进一步促进高中科学教师、本科生和研究生的教育。