Collaborative Research: RNA-guided DNA recombination through assembly graphs

合作研究：通过组装图进行 RNA 引导的 DNA 重组

• 批准号: 0900544
• 负责人: Laura Landweber
• 金额: $ 84.19万
• 依托单位: Princeton University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-01 至 2013-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0900544&HistoricalAwards=false
• 关键词: Collaborative; Research; RNA; guided; DNA

Genome rearrangements occur on an evolutionary scale, as well as on a developmental scale, in a wide range of eukaryotes. Even in cancer cells, dramatic DNA rearrangements are frequently observed in somatic cell lineages. This project uses certain species of ciliates as a model system to study gene rearrangements. These organisms undergo massive recombination during differentiation of an archival germline micronucleus into a somatic macronucleus capable of gene expression. The objective of this project is to increase the understanding of this process of assembly, starting from the basic principles of molecular DNA - RNA - enzyme interactions, through general knowledge of the possible pathways and intermediate steps that lead to the final product. Through mutual reinforcement, the project interlaces biological experiments with mathematical findings. The theoretical model utilizes spatial graphs with 4-valent vertices as a physical representation of the DNA at the time of recombination, and smoothing of the vertices models the actual recombination. Specific aims include: (a) examine the interactions of the template RNA and the involvement of possible cutting and splicing enzymes at the moment of recombination, (b) identify steps in the process by pinpointing putative intermediate molecules during unscrambling a variety of genes, and theoretically analyze sets of pointers leading to these intermediates (c) characterize theoretically and confirm experimentally all possible gene unscrambling pathways for a subset of genes, and (d) develop mathematical techniques based on methods from knot theory and formal languages to study the theoretical model.Our understanding of genome-wide DNA rearrangements is still very limited. These processes appear on an evolutionary scale, where they can lead to species-specific differences and even the creation of species boundaries. On a developmental scale, genome rearrangements appear in a wide range of differentiating eukaryotic cells. The findings of this project will offer insight into the process of gene descrambling in ciliates and may also extend more generally to other model systems. This project seeks to learn from both theory and experiments how a mechanism for RNA-templated DNA recombination sculpts the assembly of genetic information in ciliates. This mechanism of template-mediated DNA rearrangement can be visualized as a scaffold for controlling and programming certain types of genetic information within a cell. Such control of information processing could facilitate biomolecular computing in vivo, as well as methods for epigenetic control of development.

在广泛的真核生物中，基因组重排发生在进化规模上，也发生在发育规模上。即使在癌细胞中，在体细胞谱系中也经常观察到戏剧性的DNA重排。该项目使用某些种类的纤毛虫作为研究基因重排的模型系统。这些生物在将档案种系微核分化为能够表达基因的体细胞大核的过程中经历了大规模的重组。这个项目的目标是从分子DNA-RNA-酶相互作用的基本原理出发，通过对导致最终产品的可能途径和中间步骤的一般知识，增加对这一组装过程的理解。通过相互加强，该项目将生物实验与数学结果交织在一起。理论模型使用具有4价顶点的空间图作为重组时DNA的物理表示，而顶点的平滑模拟了实际的重组。具体目标包括：(A)检查模板RNA的相互作用以及重组时可能的切割和剪接酶的参与；(B)通过在解读各种基因的过程中精确定位假定的中间分子来确定过程中的步骤，并从理论上分析通向这些中间分子的指针集；(C)从理论上表征并实验证实基因子集的所有可能的基因解读途径；以及(D)发展基于纽结理论和形式语言方法的数学技术来研究理论模型。我们对全基因组DNA重排的理解仍然非常有限。这些过程出现在进化的尺度上，它们可能导致特定物种的差异，甚至造成物种边界的形成。在发育规模上，基因组重排出现在广泛的分化真核细胞中。这个项目的发现将提供对纤毛虫基因解扰过程的洞察，也可能更广泛地扩展到其他模型系统。该项目试图从理论和实验中了解RNA模板DNA重组的机制如何塑造纤毛虫中遗传信息的组装。这种模板介导的DNA重排机制可以被视作控制和编程细胞内某些类型的遗传信息的支架。这种对信息处理的控制可以促进体内的生物分子计算，以及对发育的表观遗传控制方法。