DNA mutagenesis driven by transcription factor competition with mismatch repair

The distribution of somatic mutations across the genome is not uniform. Recently, an unexpected pattern of hyper-mutation was reported at binding sites of transcriptional regulatory factors (TFs). In some human cells, a decrease in DNA repair activity was also observed at TF binding sites, leading to the hypothesis that TFs may increase mutagenesis by interfering with the recognition of DNA lesions by repair enzymes, and thus inhibiting repair. However, direct proof of this surprising TF-induced mutagenesis mechanism is lacking. Here, we show that TF binding to DNA mismatch lesions leads to increased mutation rates at TF binding sites by reducing the efficiency of lesion recognition by MutSα, the main enzyme that initiates mismatch repair in eukaryotic cells. We developed a yeast mutagenesis assay to directly observe the accumulation of mutations in a TF binding site. Upon TF overexpression, the binding site exhibited an increased mutation rate, specifically for mutations resulting from mismatches where the TF strongly reduced MutSα binding in vitro. This trend was amplified in cells with an increased rate of misincorporation errors, and it was not observed in mismatch repair-deficient cells. Analyses of human cancer somatic mutation data revealed a pattern similar to that observed in yeast, with mutations resulting from TF-bound mismatches being specifically enriched in mismatch repair-proficient tumors. Taken together, our results demonstrate that in addition to their well-known roles in gene regulation, TFs also play a role in DNA mutagenesis, by directly interfering with the repair of replication errors. Since a majority of cancer mutations originate from unrepaired replication errors, most commonly mismatches, our results suggest that TF interference with mismatch repair will shape the mutation landscape of regulatory DNA in cancer genomes.基因组中体细胞突变的分布并非均匀一致。近期有研究报道，转录调控因子（transcriptional regulatory factors, TFs）的结合位点处存在一种异常的高突变模式。在部分人类细胞中，研究人员同时观测到转录因子结合位点的DNA修复活性出现下降，据此提出假说：转录因子可通过干扰修复酶对DNA损伤的识别过程，抑制DNA修复，进而提升突变发生概率。但目前仍缺乏直接验证这一转录因子诱导突变机制的实验证据。 本研究证实，转录因子与DNA错配损伤结合后，会通过降低MutSα的损伤识别效率，提升转录因子结合位点的突变率；而MutSα是启动真核细胞错配修复的核心酶类。我们建立了酵母诱变实验（yeast mutagenesis assay）体系，以直接观测转录因子结合位点的突变积累情况。当转录因子过表达时，该结合位点的突变率显著升高，且这类突变多源于碱基错配——体外实验证实，转录因子可大幅削弱MutSα与这类错配的结合能力。在碱基掺入错误发生率升高的细胞中，这一趋势更为显著；而在错配修复缺陷的细胞中，则未观测到该现象。 对人类癌症体细胞突变数据的分析显示，其突变模式与酵母实验结果高度相似：在错配修复功能正常的肿瘤中，由转录因子结合的错配所导致的突变呈现特异性富集。 综上，本研究证实，转录因子除了在基因调控中发挥已知的核心作用外，还可通过直接干扰复制错误的修复过程，参与DNA突变的发生。由于绝大多数癌症突变源于未被修复的复制错误（其中最常见的类型为碱基错配），本研究结果提示，转录因子对错配修复过程的干扰，将塑造癌症基因组中调控区域的突变图景。