Retrotransposon expression within ribosomal gene loci

描述（由申请人提供）：只有一小部分真核生物基因组编码蛋白质或参与基因表达的调控。这些基因组中更大的一部分几乎没有功能，并且来自RNA的逆转录。例如，至少40%的人类基因组是由这些逆转录本组成的。随着时间的推移，这种插入的逐渐积累在塑造我们基因组的大小、结构和功能方面发挥了重要作用。被称为LINEs的逆转录转座元件家族产生了负责大多数这些插入的蛋白质机制。研究LINEs的最佳模型系统之一是R2，这是一种以特定序列方式插入所有高等生物中发现的数百个串联重复的28S rRNA基因中的一小部分的元件。R2整合反应高度的序列特异性使得对其机制进行详细的生化研究成为可能。这种整合机制的一个关键但鲜为人知的方面是R2蛋白如何结合用于逆转录的R2 RNA模板的两端。本提案中的一系列实验是对R2蛋白中影响其结合这些RNA区域能力的氨基酸取代的详细研究。这些研究将有助于更好地理解LINE元素如何负责在整个人类基因组中以更随机的方式发生的许多插入。本提案的另一个目标是了解R2元素是如何被调节的。串联重复的rRNA基因（rDNA位点）形成核核、rRNA合成位点和核糖体亚基组装。虽然每次R2插入都会破坏一个28S rRNA基因的功能，但只要有足够数量的rRNA基因未插入，生物体就可以存活。因此，第二个系列的实验旨在确定生物体如何能够从未插入的基因中产生高水平的rRNA，同时最大限度地减少从其他相同的插入rRNA基因中表达R2元素。插入的rRNA基因转录产生新的R2插入。利用监测特定R2元件转录并将这些元件定位在rDNA位点内的方法，将定义rDNA位点的转录区域，并随着时间的推移监测这些转录区域，以确定它们如何受到重组和R2元件活性的影响。最后，参与染色体结构和rRNA基因调控的一些基因的突变将在第三系列实验中进行测试，以确定它们是否影响生物体区分插入和未插入的28S基因的能力。这些实验将揭示整个rDNA位点及其R2元件的转录如何受到差异调控的新见解。

DESCRIPTION (provided by applicant): Only a small fraction of eukaryotic genomes encode protein or is involved in the regulation of gene expression. A far larger fraction of these genomes has little or no function and is derived from the reverse transcription of RNA. For example, at least 40% of the human genome is composed of these reverse transcripts. The gradual accumulation of such insertions over time has played a significant role in shaping the size, structure and function of our genome. The family of retrotransposable elements known as LINEs generates the protein machinery responsible for most of these insertions. One of the best model systems in which to study LINEs is R2, an element that inserts in a sequence specific manner into a fraction of the hundreds of tandemly repeated 28S rRNA genes found in all higher organisms. The high degree of sequence specificity of the R2 integration reaction has enabled detailed biochemical studies of its mechanism. A critical but poorly understood aspect of this integration mechanism is how the R2 protein binds the two ends of the R2 RNA template used for reverse transcription. One series of experiments in this proposal is a detailed study of amino acid substitutions in the R2 protein that influence its ability to bind these RNA regions. These studies will contribute to a better understanding of how LINE elements are responsible for many of the insertions that occur in a more random manner throughout the human genome. Another goal of this proposal is to understand how R2 elements are regulated. The tandemly repeated rRNA genes (rDNA locus) form the nucleolus, the site of rRNA synthesis and ribosomal subunit assembly. While each R2 insertion disrupts the function of one 28S rRNA gene, an organism can survive as long as sufficient numbers of rRNA genes remain uninserted. Thus a second series of experiments is designed to determine how organisms are able to generate high levels of rRNA from uninserted genes while minimizing the expression of R2 elements from the otherwise identical inserted rRNA genes. Transcription of inserted rRNA genes gives rise to new R2 insertion. Using methods to monitor the transcription of specific R2 elements and to position these elements within the rDNA locus, the regions of the rDNA locus that are transcribed will be defined, and these transcribed regions monitored over time to determine how they are influenced by recombination and R2 element activity. Finally, mutations in a number of genes involved in chromosome structure and rRNA gene regulation will be tested in a third series of experiments to determine whether they affect the ability of the organism to differentiate between inserted and uninserted 28S genes. These experiments should reveal new insights into how transcription of the entire rDNA locus and its R2 elements are differentially regulated. PUBLIC HEALTH RELEVANCE: Transposable elements are extremely abundant in human genomes and are responsible directly or indirectly for many mutations associated with various genetic diseases and the onset of cancer. This research studies a model system that enables detailed studies of the insertion mechanism likely to be used by the most abundant, and only active, transposable element in humans. This research also studies the regulated expression of the many ribosomal RNA genes, genes that play a key role in all aspects of cellular metabolism.