Mechanisms and evolutionary consequences of transposon strategies to counteract host silencing

对抗宿主沉默的转座子策略的机制和进化后果

• 批准号: 10331155
• 负责人: Christopher Eugene Ellison
• 金额: $ 6.8万
• 依托单位: RUTGERS, THE STATE UNIV OF N.J.
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-01-01 至 2024-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10331155
• 关键词: Address; Affect; Agreement; Biological Assay; Candidate Disease Gene; Clustered Regularly Interspaced Short Palindromic Repeats; Codon Nucleotides; Conflict (Psychology); DNA Insertion Elements; DNA Transposable Elements; Data; Drosophila genus; Drosophila melanogaster; Elements; Equation; Eukaryota; Event; Evolution; Gene Expression; Gene Silencing; Gene Targeting; Genes; Genetic; Genome; Genomic DNA; Goals; Health; Host Defense; Human; Intervention; Knowledge; Laboratories; Lead; Measures; Mediating; Mendelian disorder; Mission; Modeling; Mutation; Organism; Outcome; Ovary; Pathway interactions; Phenotype; Play; RNA Interference; Race; Repression; Research; Role; Selfish Genes; Side; Small RNA; Sterility; Sulfur; Testing; Transcriptional Silencer Elements; United States National Institutes of Health; Untranslated RNA; Up-Regulation; arm; comparative genomics; fitness; genome editing; histone acetyltransferase; innovation; insight; knock-down; mutant; novel; telomere; theories; transcriptome sequencing

PROJECT SUMMARY Harboring active transposable elements (TEs) imposes a substantial mutational burden on the host genome. To reduce this burden, most organisms have evolved sophisticated, and often multi-layered, mechanisms for identifying and inactivating TEs. In spite of these defenses, active TEs are found in the genomes of almost all eukaryotes. One explanation for the evolutionary persistence of TEs is that they are in an “arms race” with their host genome: TEs are constantly evolving novels ways to block or evade host silencing while the host genome is continuously evolving to re-establish TE suppression. While this theory is appealing, there is a gap in knowledge because the mechanisms by which TEs could block or evade host defenses are largely unknown. The long-term goal of this applicant’s laboratory is to understand the evolutionary dynamics of TE/host co- evolution. The overall objective of this project is to understand and functionally validate a novel TE strategy, discovered in the applicant’s laboratory, that involves TEs using their own piRNAs to target host silencing factors for suppression. Preliminary data produced in the applicant’s laboratory suggests that the Drosophila melanogaster telomeric transposon TART-A captured a portion of the host TE silencing factor nxf2, which allows TART-A to produce piRNAs targeting nxf2 for suppression. The rationale for the proposed research is that it will provide critical insight into the mechanisms of host-TE conflict and how TE counter-defense strategies can impact host gene expression and fitness. The objective of this project will be achieved by pursuing three specific aims: 1) Identify genes acquired by telomeric TEs across Drosophila; 2) Determine whether non-telomeric transposons also use a piRNA-mediated counter-silencing strategy; and 3) Disrupt TE counter-silencing using CRISPR in D. melanogaster. Telomeric TEs will be identified in 28 species of Drosophila and assayed to determine whether they have acquired host gene fragments. The applicant’s laboratory has identified 45 candidate genes in D. melanogaster that share homology with TE-derived piRNAs and are known to play a role in TE suppression. These genes will be tested to determine if they suppress the same TE with which they share homology. Candidate TE/gene pairs will be validated using CRISPR genome editing to erase their shared homology, which should result in upregulation of the gene in question. The proposed research is innovative because it represents a substantial departure from the status quo: instead of the host-centric view of previous studies, which examine how the genome responds to TE activity, this project will study the TE side of the equation by investigating how TEs respond to and counteract host defenses. One of the major goals of the field is to understand why host genes involved in TE silencing are rapidly evolving. The proposed research is significant because it will support this goal by characterizing and functionally validating a specific TE counter-defense strategy, which will provide empirical support for the arms race theory, while also increasing understanding of the co-evolutionary dynamics between host genomes and their TE associates.

项目概要 携带活性转座元件（TE）会给宿主基因组带来巨大的突变负担。 为了减轻这种负担，大多数生物体已经进化出复杂且通常是多层的机制 识别和灭活 TE 尽管存在这些防御，但几乎所有的基因组中都发现了活性 TE。 对 TE 的进化持久性的一种解释是，它们与它们正在进行一场“军备竞赛”。 宿主基因组：TE 不断发展新的方法来阻止或逃避宿主沉默，而宿主基因组 正在不断发展以重新建立 TE 抑制虽然这一理论很有吸引力，但仍存在差距。 因为 TE 阻止或逃避宿主防御的机制在很大程度上是未知的。 该申请人实验室的长期目标是了解 TE/宿主共同的进化动态 该项目的总体目标是理解并在功能上验证一种新颖的 TE 策略， 在申请人的实验室中发现，涉及 TE 使用自己的 piRNA 来靶向宿主沉默因子 申请人实验室产生的初步数据表明果蝇。 黑腹果蝇端粒转座子 TART-A 捕获了宿主 TE 沉默因子 nxf2 的一部分，这使得 TART-A 产生靶向 nxf2 的 piRNA 进行抑制 本研究的基本原理是它会产生抑制作用。 提供对主机与 TE 冲突机制以及 TE 反防御策略如何发挥作用的重要见解 该项目的目标将通过追求三个具体目标来实现。 目标： 1) 鉴定果蝇端粒 TE 获得的基因 2) 确定是否为非端粒； 转座子还使用 piRNA 介导的反沉默策略；3) 使用以下方法破坏 TE 反沉默； 黑腹果蝇中的 CRISPR 端粒转录因子将在 28 种果蝇中被鉴定并进行检测。 确定他们是否获得了宿主基因片段 申请人的实验室已鉴定出45个。 黑腹果蝇中与 TE 衍生的 piRNA 有同源性并已知发挥作用的候选基因 在 TE 抑制中，将测试这些基因以确定它们是否抑制与其共享的相同 TE。 候选 TE/基因对将使用 CRISPR 基因组编辑进行验证，以消除它们的共同点。 同源性，这应该会导致相关基因的上调。拟议的研究是创新的。 因为它代表着对现状的重大背离：而不是以前以主机为中心的观点 研究检查基因组如何响应 TE 活动，该项目将研究等式的 TE 方面 该领域的主要目标之一是研究 TE 如何响应和抵消宿主防御。 了解为什么参与 TE 沉默的宿主基因正在快速进化。这项研究具有重要意义。 因为它将通过表征和功能验证特定的 TE 反防御来支持这一目标 战略，这将为军备竞赛理论提供实证支持，同时也增加对军备竞赛理论的认识 宿主基因组与其 TE 相关基因之间的共同进化动态。