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: 10321244
• 负责人: Christopher Eugene Ellison
• 金额: $ 31.4万
• 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/10321244
• 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; Repression; Research; Role; Selfish Genes; Side; Small RNA; Sterility; Testing; Transcriptional Silencer Elements; United States National Institutes of Health; Untranslated RNA; Up-Regulation; arms race; 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.

项目摘要 携带主动转座元件（TES）不可能在宿主基因组上大量突变燃烧。到 减少这种燃烧，大多数生物已经进化出了复杂的，并且通常是多层的机制 识别和灭活TE。尽管有这些防御，但在几乎所有的基因组中都发现了主动TE 真核生物。 TES进化持久性的一种解释是，他们与自己的 宿主基因组：TE不断发展小说，以阻止或逃避主机沉默，而主机基因组 不断发展以重新建立TE抑制。尽管这个理论出现了，但存在差距 知识是因为TES可以阻止或逃避宿主防御的机制在很大程度上未知。 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 进化。该项目的总体目的是了解并在功能上验证一种新型的TE策略， 在申请人的实验室中发现，其中涉及使用自己的piRNA来针对宿主沉默因素 用于抑制。申请人实验室中产生的初步数据表明果蝇 Melanogaster远程固定转座子TART-A捕获了宿主TE沉默因子NXF2的一部分，该系数允许 TART-A产生靶向NXF2的PIRNA进行抑制。拟议研究的理由是 对主机 - TE冲突的机制以及对抗防卫策略的批判性见解 撞击宿主基因表达和适应性。该项目的目标将通过追求三个特定的 目的：1）识别远程果蝇中远程测量的基因； 2）确定是否非tellomeric 转座子还使用PIRNA介导的反沉降策略； 3）使用使用 D. Melanogaster的CRISPR。端粒TE将在28种果蝇中鉴定，并测定为 确定它们是否获得了宿主基因片段。申请人的实验室已经确定了45 D. melanogaster中的候选基因与Tedered Pirnas共享同源性，众所周知 在TE抑制中。这些基因将经过测试以确定它们是否抑制与他们共享的相同的TE 同源性。候选TE/基因对将使用CRISPR基因组编辑验证，以消除其共享 同源性，这应该导致有关基因的上调。拟议的研究是创新的 因为它代表了与现状的实质性不同：而不是以前的以主机为中心的观点 研究，研究基因组对TE活动的反应，该项目将研究方程的TE侧 通过调查TE的反应和抵消宿主防御。该领域的主要目标之一是 了解为什么涉及沉默的宿主基因正在迅速发展。拟议的研究很重要 因为它将通过表征和功能验证特定的TE反防卫来支持这一目标 策略将为军备竞赛理论提供经验支持，同时也越来越多地理解 宿主基因组与其TE同伴之间的共同进化动力学。