The diverse influences of Alu elements on human genetic instability

Alu元素对人类遗传不稳定性的多种影响

• 批准号: 9982379
• 负责人: Prescott L. Deininger
• 金额: $ 32.36万
• 依托单位: TULANE UNIVERSITY OF LOUISIANA
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-01 至 2023-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9982379
• 关键词: Affect; Alu Elements; Back; Cells; Characteristics; Colon Carcinoma; Common Neoplasm; Complex; DNA; DNA Damage; DNA Repair; DNA Repair Pathway; DNA Sequence Rearrangement; DNA biosynthesis; Data; Development; Direct Repeats; Disease; Elements; Environment; Event; Genes; Genetic; Genetic Diseases; Genetic Recombination; Genetic Variation; Genome; Genomic Instability; Genomic Segment; Genomics; Goals; Haploidy; Human; Human Genetics; Human Genome; Individual; Lead; Length; Lesion; Location; MLL gene; Malignant Neoplasms; Mismatch Repair; Mutation; Nature; Nonhomologous DNA End Joining; Primates; Process; Reporter; Reporter Genes; Role; Series; Somatic Cell; Source; System; TP53 gene; Testing; Therapeutic; Time; Tissues; Transgenic Mice; Variant; base; cell type; deep sequencing; density; design; genetic variant; genomic predictors; high risk; human disease; mouse model; repaired; replication stress; tumor

Alu elements represent one of the biggest sources of intrinsic instability in the human genome. The human genome contains over 1,000,000 Alu elements, making up about 11% of the human genome. These approximately 300 bp elements contain variable levels of mismatch relative to one another and are dispersed throughout the genome in all orientations. They are also enriched in genes and many genes are densely populated with these elements in the genome. Thus, non-allelic homology between different Alu elements has the ability to confuse many DNA replication and repair processes leading to higher rates of various genetic instabilities and Alu elements represent one of the major sources of intrinsic genomic instability. Almost 0.5% of new human genetic diseases are the result of non-allelic recombination between nearby (1-50 kb) Alu pairs. In some genes this type of instability is one of the major sources of genetic defects. In addition, both inverted Alu pairs and direct repeat Alu pairs seem to contribute an intrinsic instability that leads to a concentration of NHEJ events in the vicinity of Alu elements. Their length, mismatch and high copy number make Alu elements a relatively unique substrate that leads to genetic variation in humans in primates in ways not experienced in most other genomes and which are therefore understudied. We have developed a powerful reporter gene system that allows us to explore the features of Alu elements that contribute to different forms of genetic instability. In this proposal we use adaptations of that reporter gene to understand Alu orientation, spacing and mismatch influences on deletions caused with both I-Sce1 to create targeted double-strand breaks, as well as replication stress. We will then use a series of very deep sequencing studies, and human tumor deep sequencing studies to provide an overall picture of the factors that lead to higher instability around different Alu variants and how Alu-influenced rearrangements compete with other DNA repair processes. These studies will allow us to develop rules that will predict which regions of the human genome are prone to which types of Alu-influenced genetic instability (NAR vs. NHEJ for instance). Furthermore, we adapt our reporter system to a transgenic mouse reporter system that will, for the first time, allow us to determine whether the germline, somatic cells, and tumors are subject to similar instabilities associated with their Alu elements and begin the process of understanding how genetic variants, particularly in DNA repair may alter how Alus contribute to genetic instability. These data are likely to help design better ways to influence Alu-related genetic instability, perhaps by guiding better designed synthetic lethality therapeutics.

Alu元件是人类基因组内在不稳定性的最大来源之一。的 人类基因组包含超过1，000，000个Alu元件，约占人类基因组的11%。这些 大约300 bp的元件含有相对于彼此的可变水平的错配， 在基因组的各个方向。它们也富含基因，许多基因密集地 在基因组中充满了这些元素。因此，不同Alu元件之间的非等位基因同源性具有 这种能力能够混淆许多DNA复制和修复过程，导致各种遗传缺陷的发生率更高， 不稳定性和Alu元件代表内在基因组不稳定性的主要来源之一。几乎0.5% 新的人类遗传疾病的结果是相邻的（1-50 kb）Alu对之间的非等位基因重组。 在某些基因中，这种不稳定性是遗传缺陷的主要来源之一。此外，两个倒置 Alu对和直接重复Alu对似乎有助于内在的不稳定性，导致浓度 Alu元素附近的NHEJ事件。 它们的长度、错配和高拷贝数使Alu元件成为相对独特的底物， 导致人类和灵长类动物的遗传变异，这种变异在大多数其他基因组中都没有经历过， 因此被低估了。我们已经开发了一个强大的报告基因系统，使我们能够探索 Alu元素的特征有助于不同形式的遗传不稳定性。在本提案中，我们使用 报告基因的适应性，以了解Alu方向，间距和错配对缺失的影响 I-Sce 1引起的靶向双链断裂以及复制应激。然后我们将使用 一系列非常深入的测序研究，以及人类肿瘤深度测序研究， 导致不同Alu变体周围更高不稳定性的因素以及Alu变体如何影响 重组与其他DNA修复过程竞争。这些研究将使我们能够制定规则， 将预测人类基因组的哪些区域容易受到哪种类型的基因不稳定性的影响 (NAR例如，与NHEJ相比）。此外，我们调整我们的报告系统的转基因小鼠报告 该系统将首次允许我们确定生殖系，体细胞和肿瘤是否 受到与其Alu元素相关的类似不稳定性的影响，并开始了解如何 遗传变异，特别是在DNA修复中，可能会改变Alus对遗传不稳定性的贡献。这些数据 可能有助于设计更好的方法来影响与遗传相关的遗传不稳定性，也许是通过指导更好的设计， 合成致命疗法