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: 10275297
• 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/10275297
• 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)

项目总结 转座元件已经产生了人类基因组中的大部分序列，以及所有人类 生物学已经在由这些自我复制的片段制造的DNA、RNA和蛋白质中进化 自私的DNA。可转座元件的复制构成了人类新突变的主要来源 这会导致基因组不稳定和各种遗传性疾病。我们小组之前发现了快速的 内源逆转录因子最多的长散布因子-1(L1)的几个制约因素的演化 活跃在人类身上。这种进化模式表明，L1进化是为了逃避这些限制因素， 推动宿主快速进化以跟上步伐。然而，L1S中的序列变异如何影响尚不清楚 它们在寄主限制因素存在的情况下逃避和复制的能力。 我们特别感兴趣的是了解--有没有进化出可转座的成分来逃避防御 人类基因组的机制？转座元件逃避的机制是什么？什么是 在时间和地点复制的可躲避转座元件对人类健康的影响 正常情况下被压抑？为了回答这些问题，我们的实验室采用了非传统的方法组合 包括对基因组的回顾分析，以了解发生了什么，并进行预期的实验 问一问可能会发生什么。我们建议利用实验室最近生成的由130多个人组成的多样化小组 年轻人在L1中寻找变异的L1的复制能力，否则有效 寄主限制因素。这种变异可能表明L1适应以逃避寄主限制或适应 用于限制规避L1的主机。除了对进化史的回顾分析外，我们还建议 通过建立体外进化系统来选择逃避特定限制的L1，从而加速进化 因素。对这些历史和未来进化方法的比较将有助于我们破译 推动L1和人类进化的选择性压力。这项研究将解决一个引人入胜的基础 面对宿主固有免疫系统的冲击，L1进化机制的科学问题 关于我们对没有明确遗传因素的散发性自身免疫性疾病的理解。 我们的实验室将致力于指导和科学推广与努力建立一个 并容纳空间，以实现创造性的、大胆的科学。我们多元化且经验丰富的科学家团队 整合比较基因组学、基因组进化、L1生物学、体外进化和蛋白质方面的专业知识 发展和功能，为拟议的项目带来以发展为驱动的方法。以我们的推搡记录 概念和技术界限为蛋白质进化和蛋白质进化领域带来新的理解 限制因素生物学，我们的团队独一无二地准备对L1进化和 与基因组进化有关的生物学，以及与L1明显相关的众多疾病状态。(30行)