The cross-regulation of host DNA replication and LTR Retrotransposons

宿主DNA复制和LTR反转录转座子的交叉调节

• 批准号: 10621925
• 负责人: MIGUEL ANGEL ZARATIEGUI BIURRUN
• 金额: $ 38.85万
• 依托单位: RUTGERS, THE STATE UNIV OF N.J.
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-01 至 2025-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10621925
• 关键词: Affect; Aging; Base Sequence; Biochemistry; Chromatin; Chromosomal Rearrangement; Clustered Regularly Interspaced Short Palindromic Repeats; DNA Transposable Elements; DNA biosynthesis; Defense Mechanisms; Detection; Disease; Eukaryota; Evolution; Fission Yeast; Genetic; Genetic Materials; Genome; Genomics; Goals; Investigation; Lead; Learning; Malignant Neoplasms; Meiosis; Methods; Mutagenesis; Nature; Organism; Parasites; Process; RNA; RNA Interference; RNA Interference Pathway; Regulation; Repetitive Sequence; Research; Retrotransposon; Reverse Transcription; Site; Structure; Work; genetic analysis; genome integrity; homologous recombination; innovation; next generation; novel; pressure

Project summary The proposed work is part of our long-term goal to understand host-transposon interactions that influence eukaryotic genome function and evolution. Retrotransposons are a class of transposable element capable of amplifying their copy number via reverse-transcription of RNA intermediates and insertion in a new locus. Through this transposition activity, they can multiply to the point of making up the majority of genetic material in some genomes, exerting a broad influence in genome structure and regulation. The repetitive nature of TE can also affect genome integrity through homologous recombination between their dispersed copies that can cause chromosomal rearrangements. To counteract their deleterious effects, eukaryotes have evolved multiple genome defense mechanisms that suppress Retrotransposon activity. The most important are RNA interference (RNAi) pathways that are often specifically active in the germline, protecting the genetic material that will make up the next generation. We are investigating these host-Retrotransposon interactions using the LTR Retrotransposons Tf1 and Tf2, endemic to fission yeast. In previous work, we have revealed an intense cross-regulation between the Retrotransposon and the process of host DNA replication, discovering how Retrotransposons select new insertion sites, regulate chromatin silencing, and control homologous recombination. Several aspects of these phenomena are conserved in LTR retrotransposons present in the genomes of other organisms, even while the specific factors involved are not. This suggests that common evolutionary pressures lead to convergent evolution of host-Retrotransposon interactions. As a consequence, these conserved mechanisms may be important for metazoan germline stability. In the present application, we propose a comprehensive line of research combining genetics, biochemistry, and high throughput sequence-based genomics methods to (1) ascertain universal Retrotransposon insertion site selection mechanisms, (2) resolve the determinants of LTR Retrotransposon detection by RNAi, (3) determine the mechanism by which Retrotransposons guide their own homologous recombination, and (4) investigate the effect of Retrotransposon activity in meiosis progression. In pursuit of these goals, we will make use of novel fission yeast strains in which all Retrotransposon copies have been deleted through an innovative CRISPR mutagenesis method. This advance enables us to carry out previously unfeasible genetic analyses of these highly repetitive elements. The proposed studies will provide a novel and comprehensive understanding of host- Retrotransposon interactions, and their consequences on genome regulation and stability.

项目总结 这项拟议的工作是我们了解宿主-转座子相互作用的长期目标的一部分 影响真核生物基因组功能和进化的基因。 反转录转座子是一类能够扩增其拷贝数的转座元件 通过RNA中间体的逆转录和插入新的基因座。通过这件事 转座活性，它们可以繁殖到构成大多数遗传物质的点 一些基因组，对基因组结构和调控产生广泛的影响。重复的本质 也可以通过分散的TE之间的同源重组来影响基因组的完整性 可能导致染色体重排的副本。为了抵消它们的有害影响， 真核生物进化出多种基因组防御机制来抑制反转录转座子 活动。最重要的是RNA干扰(RNAi)途径，通常是特别活跃的 在生殖系中，保护将组成下一代的遗传物质。 我们正在使用LTR反转录转座子研究这些宿主-反转录转座子的相互作用 TF1和TF2，裂殖酵母特有。在之前的工作中，我们揭示了一种强烈的交叉监管 在反转录转座子和宿主DNA复制过程之间，发现如何 反转录转座子选择新的插入位点，调节染色质沉默，并控制同源 重组。这些现象的几个方面在LTR反转录转座子中是保守的 其他生物的基因组，即使涉及的特定因素不是。这表明 共同的进化压力导致宿主-反转录转座子相互作用的收敛进化。 因此，这些保守的机制可能对后生动物种系的稳定性很重要。 在目前的应用中，我们提出了一条综合的研究路线，结合遗传学、 生物化学和高通量基于序列的基因组学方法，以(1)确定普遍性 反转录转座子插入位点选择机制，(2)解决LTR的决定因素 用RNAi技术检测反转录转座子，(3)确定反转录转座子引导的机制 它们自身的同源重组，以及(4)研究反转录转座子活性在 减数分裂进程。为了实现这些目标，我们将利用新的分裂酵母菌株，在这些菌株中 通过一种创新的CRISPR突变方法，所有反转录转座子拷贝都被删除了。 这一进展使我们能够对这些高度重复的基因进行以前不可行的基因分析 元素。建议的研究将提供对寄主的新的和全面的了解- 反转录转座子相互作用及其对基因组调控和稳定性的影响。

项目成果

Transposon Removal Reveals Their Adaptive Fitness Contribution.

• DOI: 10.1093/gbe/evae010
• 发表时间: 2024-02-01
• 期刊: GENOME BIOLOGY AND EVOLUTION
• 影响因子: 3.3
• 作者: Cranz-Mileva, Susanne;Reilly, Eve;Chalhoub, Noor;Patel, Rohan;Atanassova, Tania;Cao, Weihuan;Ellison, Christopher;Zaratiegui, Mikel
• 通讯作者: Zaratiegui, Mikel