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）结合位点处存在一种出人意料的超突变模式。在部分人类细胞中，研究人员同时观测到TF结合位点的DNA修复活性出现下降，由此提出假说：TF可通过干扰修复酶对DNA损伤的识别、抑制修复过程，进而提升突变发生率。然而，这一由TF诱导的突变机制尚未有直接实验证据支撑。 本研究证实，TF与DNA错配损伤的结合，会通过降低MutSα的损伤识别效率——该酶是真核细胞中启动错配修复的核心酶——从而提升TF结合位点的突变率。我们构建了酵母诱变检测实验体系，以直接观测TF结合位点处的突变积累情况。当TF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；体外实验显示，TF可大幅削弱MutSα与这类错配的结合能力。在碱基错配掺入错误率升高的细胞中，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此现象。 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：在错配修复功能完整的肿瘤中，由TF结合错配所产生的突变呈现特异性富集。 综上，本研究结果表明，除了已被广泛认知的基因调控功能外，TF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（最常见的类型即为碱基错配），我们的研究结果提示，TF对错配修复的干扰将会塑造癌症基因组中调控区域的突变景观。