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: 10634618
• 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/10634618
• 关键词: Autoimmune Diseases; Autoimmunity; Automobile Driving; Basic Science; Binding; Biology; Creativeness; 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; Repression; Research; Retroelements; Retrotransposon; Science; Scientist; Selfish DNA; Source; Speed; System; 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 转座因子产生了人类基因组中的大部分序列，并且所有人类基因组序列都是由转座因子产生的。 生物学在这些自我复制的片段所制造的永远存在的DNA、RNA和蛋白质中进化。 自私的DNA转座因子的复制构成了人类新突变的主要来源 导致基因组不稳定和各种遗传疾病。我们小组先前发现了 长散布元件-1（L1）的几个限制因子的进化， 活跃于人类。这种进化模式表明，L1已经进化到逃避这些限制因素， 推动宿主快速进化以跟上步伐然而，L1序列变异如何影响 它们在宿主限制因子存在下逃避和复制的能力。 我们特别感兴趣的是了解-转座因子是否进化成逃避防御 人类基因组的机制转座因子逃避的机制是什么？有哪些 逃避性转座因子在它们所处的时间和地点复制对人类健康的后果 正常压抑？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性分析，以了解发生了什么，以及前瞻性实验， 问问会发生什么我们建议利用实验室最近产生的130多个多样化的小组， 年轻的人类L1寻找L1在其他有效的存在下复制能力的变化， 宿主限制因素这种变异可能表明L1适应逃避宿主限制或适应 来限制L1的躲避除了对进化历史的回顾性分析外，我们还建议 通过建立一个体外进化系统来“加速”进化，以选择逃避限定限制的L1 因子比较这些历史和未来的进化方法将有助于我们解码 选择性压力驱动了L1和人类的进化。这项研究将解决一个有趣的基本问题， 关于L1进化机制的科学问题，面对宿主先天免疫系统的影响 我们对散发性自身免疫性疾病的理解没有明确的遗传贡献。 我们的实验室结合了致力于指导和科学推广，努力建立一个沟通的 和容纳空间来实现创造性的、大胆的科学。我们多元化且经验丰富的科学家团队 整合了比较基因组学、基因组进化、L1生物学、体外进化和蛋白质方面的专业知识 演变和功能，为拟议项目带来一种演变驱动的方法。以我们的记录 概念和技术界限，为蛋白质进化领域带来新的理解， 限制因子生物学，我们的团队是独一无二的准备带来一个新的理解L1进化， 生物学与基因组进化的影响和许多疾病状态与明确的L1参与。(30行）