Leveraging natural and directed evolution to dissect the functional consequences of sequence variation in human L1 retrotransposons

利用自然和定向进化来剖析人类 L1 逆转录转座子序列变异的功能后果

• 批准号: 10470839
• 负责人: Richard Noel McLaughlin
• 金额: $ 46万
• 依托单位: PACIFIC NORTHWEST RESEARCH INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-01 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10470839
• 关键词: Address; Autoimmune Diseases; Autoimmunity; Automobile Driving; Basic Science; Biology; DNA; DNA Transposable Elements; Dedications; Defense Mechanisms; Directed Molecular Evolution; Disease; Elements; Evolution; Genetic; Genetic Diseases; Genome; Genomic Instability; Health; Human; Human Biology; Human Genome; In Vitro; Infertility; Innate Immune System; Long Interspersed Elements; Malignant Neoplasms; Mentorship; Mutation; Pattern; Prevalence; Proteins; RNA; Recording of previous events; Research; Retroelements; Retrotransposon; Science; Scientist; Selfish DNA; Source; Speed; System; Time; Variant; comparative genomics; experience; experimental study; fascinate; genome analysis; interest; outreach; pressure; prospective

PROJECT SUMMARY Transposable elements have generated the majority of the sequence in the human genome, and all of human biology has evolved in the ever-present DNA, RNA, and protein made by these self-replicating pieces of selfish DNA. The replication of transposable elements constitutes a major source of new mutations in humans which drive genome instability and a variety of genetic diseases. Our group previously discovered the rapid evolution of several restriction factors of Long Interspersed Element-1 (L1), the endogenous retroelements most active in humans. This pattern of evolution suggests that L1s have evolved to evade these restriction factors, driving rapid host evolution to keep pace. However, it is unknown how sequence variation in L1s impacts their ability to evade and replicate in the presence of host restriction factors. We are specifically interested in understanding – have transposable elements evolved to evade the defense mechanisms of the human genome? What are the mechanisms of transposable element evasion? What are the consequences to human health of evasive transposable elements replicating at times and places they are normally repressed? To answer these questions, our lab employs non-traditional combinations of approaches including retrospective analyses of genomes to understand what has happened and prospective experiments to ask what could happen. We propose to leverage the lab’s recently generated, diverse panel of more than 130 young human L1s to search for variation in the ability of L1s to replicate in the presence of otherwise effective host restriction factors. This variation could indicate adaptation of an L1 to evade host restriction or adaptation of the host to restrict evasive L1s. In addition to this retrospective analysis of evolutionary history, we propose to ‘speed up’ evolution by building an in vitro evolution system to select for L1s that evade a defined restriction factor. Comparison of these historical and prospective evolutionary approaches will help us decode the selective pressures that drove L1 and human evolution. This research will address a fascinating basic science question about the mechanisms of L1 evolution in the face of the host innate immune system with impact on our understanding of sporadic autoimmune diseases without a clear genetic contribution. Our lab combines a dedication to mentorship and scientific outreach with effort to build a communicative and accommodating space to enable creative, daring science. Our diverse and experienced team of scientists integrates expertise in comparative genomics, genome evolution, L1 biology, in vitro evolution, and protein evolution and function to bring an evolution-driven approach to the proposed projects. With our record of pushing conceptual and technical boundaries to bring new understanding to the fields of protein evolution and restriction factor biology, our team is uniquely poised to bring about a new understanding of L1 evolution and biology with implications for genome evolution and numerous disease states with clear L1 involvement. (30 lines)

项目摘要 转座元素已经产生了人类基因组和所有人类的大部分序列 生物学已经在这些自我复制的碎片制造的永远存在的DNA，RNA和蛋白质中发展 自私的DNA。 驱动基因组不稳定性和多种遗传疾病。 长期相互元素1（L1）的严重程度限制因子的演变，内源性重新元素最多 活跃于人类。 驱动快速宿主的演变以保持步伐。 他们在存在宿主限制因素的情况下逃避和复制的能力。 我们对理解特别感兴趣 - 转移元素进化以逃避辩护 人类基因组的机制？ 对人类健康的后果的后果，在有时和地点复制它们 通常压制这些问题，我们的实验室扩展非传统组合 纳入基因组的回顾性分析，以了解WHA具有有效的实验 询问我们可能会发生什么。 年轻的人类L1搜索L1在有效的存在下复制能力的变化 宿主限制因素。 除了对进化史的回顾性分析外，宿主限制了逃避的L1。 通过建立一个体外演化系统来选择逃避定义限制的L1来加快演变 因素的比较。 选择性提出了L1和人类进化。 科学问题，面对宿主免疫系统的L1进化机制 关于我们对零星自身免疫性疾病的理解，没有明确的遗传贡献。 我们的努力致力于建立交流的指导和科学宣传 并容纳我们的多样化和经验丰富的科学团队 整合了比较基因组学，基因组进化，L1生物学和蛋白质的专业知识 进化和功能，将进化驱动的方法带入拟议的项目。 概念和技术界限将新的净资金带入蛋白质进化领域和 限制性因素生物学，我们的团队独一无二，以对L1进化和 生物学对基因组进化和众多疾病状态具有明显的L1涉及。