Background Short tandem repeats (STRs) contribute significantly to de novo mutagenesis, driving phenotypic diversity and genetic disease. Although highly diverse, their repetitive sequences induce DNA polymerase slippage and stalling, leading to length and sequence variation. However, current studies of DNA synthesis through STRs are restricted to a handful of selected sequences, limiting our broader understanding of their evolutionary behaviour and hampering the characterisation of the determinants of their abundance and stability in eukaryotic genomes. Results We perform a comprehensive analysis of DNA synthesis at all STR permutations and interrogate the impact of STR sequence and secondary structure on their genomic representation and mutability. To do this, we developed a high-throughput primer extension assay that allows monitoring of the kinetics and fidelity of DNA synthesis through 20,000 sequences comprising all STR permutations in different lengths. By combining these measurements with population-scale genomic data, we show that the response of a model replicative DNA polymerase to variously structured DNA is sufficient to predict the complex genomic behaviour of STRs, including abundance and mutational constraints. We demonstrate that DNA polymerase stalling at DNA structures induces error-prone DNA synthesis, which constrains STR expansion. Conclusions Our data support a model in which STR length in eukaryotic genomes results from a balance between expansion due to polymerase slippage at repeated DNA sequences and point mutations caused by error-prone DNA synthesis at DNA structures.

中文翻译：

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DNA 聚合酶在结构化 DNA 上停滞限制了短串联重复序列的扩展

背景 短串联重复序列 (STR) 对从头突变、驱动表型多样性和遗传疾病有显着贡献。尽管高度多样化，但它们的重复序列会导致 DNA 聚合酶滑动和停滞，从而导致长度和序列变异。然而，目前通过 STR 进行 DNA 合成的研究仅限于少数选定的序列，限制了我们对其进化行为的更广泛理解，并阻碍了对其在真核基因组中丰度和稳定性的决定因素的表征。结果我们对所有 STR 排列的 DNA 合成进行了全面分析，并探讨了 STR 序列和二级结构对其基因组表征和突变性的影响。为此，我们开发了一种高通量引物延伸测定，可通过包含不同长度的所有 STR 排列的 20,000 个序列监测 DNA 合成的动力学和保真度。通过将这些测量结果与群体规模的基因组数据相结合，我们表明模型复制 DNA 聚合酶对不同结构 DNA 的响应足以预测 STR 的复杂基因组行为，包括丰度和突变限制。我们证明 DNA 聚合酶在 DNA 结构上停滞会导致容易出错的 DNA 合成，从而限制 STR 扩展。结论 我们的数据支持一个模型，其中真核基因组中的 STR 长度是由于重复 DNA 序列聚合酶滑移引起的扩展与 DNA 结构中容易出错的 DNA 合成引起的点突变之间的平衡所致。