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.

项目摘要 携带活性转座因子（TE）对宿主基因组施加了大量的突变负担。到 为了减轻这种负担，大多数生物体已经进化出复杂的，通常是多层的， 鉴定和灭活TE。尽管有这些防御措施，活跃的TE在几乎所有的基因组中都被发现。 真核生物对TE进化持久性的一种解释是，它们与它们的竞争对手进行“军备竞赛”。 宿主基因组：TE是不断进化的新方法，以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，但在 因为TE可以阻止或逃避宿主防御的机制在很大程度上是未知的。 本申请人的实验室的长期目标是了解TE/宿主共表达的进化动力学。 进化本项目的总体目标是了解并在功能上验证一种新的TE策略， 在申请人的实验室中发现的，其涉及TE使用其自身的piRNA靶向宿主沉默因子 为了镇压。在申请人的实验室中产生的初步数据表明， 黑腹果蝇端粒转座子TART-A捕获了宿主TE沉默因子nxf 2的一部分，这使得 TART-A产生靶向nxf 2的piRNA用于抑制。拟议研究的理由是， 提供关键的洞察主机TE冲突的机制，以及TE反防御战略如何可以 影响宿主基因表达和适应性。该项目的目标将通过以下三个具体方面来实现： 目的：1）鉴定果蝇端粒末端转移酶获得的基因; 2）确定非端粒末端转移酶是否与果蝇端粒末端转移酶有关。 转座子还使用piRNA介导的反沉默策略;以及3）使用 CRISPR在D.黑腹菌将在28种果蝇中鉴定端粒TE，并进行测定， 确定它们是否获得了宿主基因片段。申请人的实验室已确定45个 候选基因D.与TE衍生的piRNA共享同源性并且已知在转录过程中发挥作用的黑腹菌的基因。 TE抑制。这些基因将被测试，以确定它们是否抑制与它们共享的相同的TE。 同源性候选TE/基因对将使用CRISPR基因组编辑进行验证，以删除它们的共享基因。 同源性，这应该导致所讨论的基因的上调。该研究具有创新性 因为它代表了对现状的实质性偏离：而不是以前以主机为中心的观点， 研究，研究基因组如何响应TE活动，该项目将研究方程的TE方面 通过研究TE如何应对和抵消宿主的防御。该领域的主要目标之一是 了解为什么参与TE沉默的宿主基因正在迅速进化。所提出的研究是有意义的 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，同时也增加了对 宿主基因组与其TE关联基因之间的协同进化动力学。