Molecular Mechanisms for DNA Damage Processing by Transcription Machinery

描述（由申请人提供）：所有细胞和生物体不断面临的一个重要挑战是由内源性和环境因子引起的基因组中大量有害的DNA损伤。重要的是，高度转录基因组内的DNA病变以特定和有效的方式处理，以防止转录机制的停滞和细胞死亡。大量证据表明，RNA聚合酶II （Pol II）是一种高度选择性的DNA损伤传感器，因为它在转录过程中不断扫描转录的基因组。生物化学和遗传学研究表明，Pol II在遇到DNA损伤时的作用因DNA损伤的不同而有显著差异，可归纳为以下三大类：Pol II转录旁路；Pol II回溯和tfiis介导的裂解Pol II的停滞和转录偶联修复（TCR）的启动。然而，关于Pol II感知不同DNA损伤和信号不同下游加工途径的分子机制知之甚少。我们假设DNA损伤经常改变碱基，导致模板DNA、传入底物和Pol II残基之间的相互作用模式发生变化。这些相互作用模式的变化，加上DNA损伤的化学性质，引导Pol II进入不同的过程：绕过、回溯和停滞。清楚地了解相关蛋白质-核酸和蛋白质-蛋白质相互作用的分子细节将揭示DNA损伤加工途径的机制。本研究项目的目标是通过结合结构生物学、化学生物学、生物物理学、生物化学、计算生物学和遗传学的多学科方法来了解转录机制如何对DNA损伤做出反应。

DESCRIPTION (provided by applicant): A vital challenge that all cells and organisms constantly have to face is numerous harmful DNA lesions in the genome caused by endogenous and environmental agents. It is important that DNA lesions within the highly transcribed genome are dealt with in a specific and efficient manner to prevent stalling of the transcriptional machinery and cell death. A body of evidence indicates RNA polymerase II (Pol II) is a highly selective DNA damage sensor, since it constantly scans the transcribed genome during transcription. Biochemical and genetic studies indicate that the actions of Pol II when encountering DNA damage vary dramatically for different DNA lesions and can be summarized in the following three major categories: Pol II transcription bypass; Pol II backtracking and TFIIS-mediated cleavage; Pol II stalling and initiation of transcription-coupled repair (TCR). However, little is known about the molecular mechanisms by which Pol II senses different DNA damage and signals different downstream processing pathways. We hypothesize that DNA lesions frequently modify bases leading to changes in the interaction patterns between the template DNA, incoming substrate, and Pol II residues. These changes in the interaction patterns, coupled with the chemical nature of DNA lesions, direct Pol II to different processes: bypass, backtracking, and stalling. A clear understanding of the molecular details of the relevant protein-nucleic acid and protein-protein interactions will uncover the mechanisms underlying DNA damage processing pathways. The goal of this research project is to understand how the transcription machinery responds to DNA damage through a multidisciplinary approach that combines structural biology, chemical biology, biophysics, biochemistry, computational biology, and genetics.