The role of transcription factor proteins in mutagenesis at regulatory sites

摘要 超过90%的癌症体细胞突变落在基因组的非编码区。虽然绝大多数人 这些突变预计将是乘客，其中一小部分可能会通过扰乱监管来充当司机 转录因子与DNA相互作用，导致基因表达失调。尽管 提高全基因组癌症体细胞突变数据的可用性，识别非编码驱动因素 Tf结合位点的突变仍然是一个挑战，可能是因为我们对Tf结合位点的理解存在差距 作用于调控DNA的诱变过程。越来越多的证据表明，转铁蛋白与基因组结合 会干扰正常的DNA复制和修复，从而可能导致突变率增加。然而， 这些相互作用的确切分子机制还知之甚少。当前项目将解决 通过使用新的实验技术和新的实验技术，我们对TF结合位点的突变的理解存在差距 直接研究转铁蛋白结合的分子机制的计算模型 基因突变。我们的主要假设是，结合到包含DNA损伤的基因组位置的转录因子可以 导致损伤的修复/矫正效率低下，从而导致突变率增加。在DNA中 我们将把重点放在碱基错配上，这是大多数癌症突变的重要先兆， 在DNA复制、重组甚至修复其他基因的过程中，经常在基因组中产生 损伤。因此，由于被转铁蛋白结合而保留在癌症基因组中的错配有望 对观察到的Tf结合位点的高突变信号有很大贡献。因此，至关重要的是 在存在DNA错配的情况下表征TF-DNA结合情况(目标1)，并彻底 研究转铁蛋白与错配结合可导致基因突变的机制(目标2)。总的来说， 我们提议的工作是朝着确定癌症突变的丰富是否在 Tf结合位点至少部分归因于DNA结合的Tf，它们是DNA错配纠正的障碍 并进行修复。从长远来看，彻底了解转录因子在调节DNA突变中的作用将是 有助于开发准确的方法来识别癌症中的调控驱动突变。

ABSTRACT More than 90% of cancer somatic mutations fall in non-coding regions of the genome. While the vast majority of these mutations are expected to be passengers, a small fraction could act as drivers by disrupting regulatory interactions between transcription factors (TFs) and DNA, leading to dysregulation of gene expression. Despite the increased availability of whole-genome cancer somatic mutation data, identifying non-coding driver mutations in TF binding sites remains a challenge, likely because of gaps in our understanding of the mutagenic processes acting on regulatory DNA. There is increasing evidence that TFs bound to the genome can interfere with normal DNA replication and repair, which could lead to increased mutation rates. However, the precise molecular mechanisms of these interactions are poorly understood. The current project will address this gap in our understanding of mutagenesis in TF binding sites by using new experimental techniques and computational models to directly investigate the molecular mechanisms by which TF binding can lead to genetic mutations. Our overarching hypothesis is that TFs bound to genomic sites containing DNA lesions can lead to inefficient repair/correction of the lesions, and consequently to increased mutation rates. Among DNA lesions we will focus on base mismatches, which are important precursors for a majority of cancer mutations, and are frequently generated in the genome during DNA replication, recombination, and even repair of other lesions. Thus, mismatches retained in cancer genomes due to being bound by TF proteins are expected to have a large contribution to the hyper-mutation signal observed at TF binding sites. It is therefore critical to characterize the TF-DNA binding landscape in the presence of DNA mismatches (Aim 1), and to thoroughly investigate the mechanisms by which TF binding to mismatches can lead to genetic mutations (Aim 2). Overall, our proposed work represents a first step toward determining whether the enrichment of cancer mutations in TF binding sites is due, at least in part, to DNA-bound TFs that act as roadblocks for DNA mismatch correction and repair. Longer term, a thorough understanding of the role of TFs in mutagenesis at regulatory DNA will be instrumental for developing accurate methods to identify regulatory driver mutations in cancer.