Collaborative Research: RNA-guided DNA recombination through assembly graphs

基因组重排发生在进化的规模，以及在发展的规模，在广泛的真核生物。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。本计画以某些种类的纤毛虫为模式系统，研究基因重排。这些微生物在档案生殖细胞微核分化为能够表达基因的体细胞大核的过程中发生大量重组。 该项目的目标是增加对组装过程的理解，从分子DNA - RNA -酶相互作用的基本原理开始，通过对导致最终产品的可能途径和中间步骤的一般知识。 通过相互加强，该项目将生物实验与数学发现交织在一起。理论模型利用具有4价顶点的空间图作为重组时DNA的物理表示，并且顶点的平滑模拟实际的重组。 具体目标包括：（a）检查重组时模板RNA的相互作用和可能的切割和剪接酶的参与，（B）通过在解扰多种基因期间精确定位推定的中间分子来鉴定该过程中的步骤，并且理论上分析通向这些中间体的指针组（c）理论上表征和实验上确认基因子集的所有可能的基因解扰途径，（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，它们可以导致物种特异性差异，甚至创建物种边界。在发育尺度上，基因组重排出现在广泛的分化真核细胞中。该项目的研究结果将提供深入了解纤毛虫基因解扰的过程，也可能更普遍地扩展到其他模型系统。 本计画旨在从理论与实验两方面探讨以RNA为模板的DNA重组机制如何塑造纤毛虫的遗传资讯组合。这种模板介导的DNA重排机制可以被视为控制和编程细胞内某些类型遗传信息的支架。这种对信息处理的控制可以促进体内的生物分子计算，以及用于发育的表观遗传控制的方法。

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.