Ribonucleoside triphosphate (rNTP) incorporation in DNA by DNA polymerases is a frequent phenomenon that results in DNA structural change and genome instability. However, it is unclear whether the rNTP incorporation into DNA follows any specific sequence patterns. We analyzed multiple datasets of ribonucleoside monophosphates (rNMPs) embedded in DNA, generated from three rNMP-sequencing techniques. These rNMP libraries were obtained from Saccharomyces cerevisiae cells expressing wild-type or mutant replicative DNA polymerase and ribonuclease H2 genes. We performed computational analyses of rNMP sites around early and late-firing autonomously replicating sequences (ARSs) of the yeast genome, where leading and lagging DNA synthesis starts bidirectionally. We found the preference of rNTP incorporation on the leading strand in wild-type DNA polymerase yeast cells. The leading/lagging-strand ratio of rNTP incorporation changes dramatically within the first 1,000 nucleotides from ARSs, highlighting the Pol δ - Pol ϵ handoff during early leading-strand synthesis. Furthermore, the pattern of rNTP incorporation is markedly distinct between the leading and lagging strands not only in mutant but also in wild-type polymerase cells. Such specific signatures of Pol δ and Pol ϵ provide a new approach to track the labor of these polymerases.

中文翻译：

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酵母中自主复制序列周围核糖核苷酸掺入的频率和模式揭示了复制性 DNA 聚合酶的分工

核糖核苷三磷酸 (rNTP) 通过 DNA 聚合酶掺入 DNA 是一种常见现象，会导致 DNA 结构变化和基因组不稳定。然而，尚不清楚 rNTP 掺入 DNA 是否遵循任何特定的序列模式。我们分析了嵌入在 DNA 中的多个核糖核苷单磷酸 (rNMP) 数据集，这些数据集由三种 rNMP 测序技术生成。这些 rNMP 文库是从表达野生型或突变型复制 DNA 聚合酶和核糖核酸酶 H2 基因的酿酒酵母细胞中获得的。我们对酵母基因组的早期和晚期自主复制序列 (ARS) 周围的 rNMP 位点进行了计算分析，其中领先和落后的 DNA 合成双向开始。我们发现 rNTP 优先掺入野生型 DNA 聚合酶酵母细胞的前导链上。rNTP 掺入的前导/滞后链比率在来自 ARS 的前 1,000 个核苷酸内发生显着变化，突出了早期前导链合成期间的 Pol δ - Pol ε 切换。此外，不仅在突变体中而且在野生型聚合酶细胞中，rNTP 掺入的模式在前导链和滞后链之间明显不同。Pol δ 和 Pol ε 的这种特定特征为跟踪这些聚合酶的作用提供了一种新方法。不仅在突变体中而且在野生型聚合酶细胞中，rNTP 掺入的模式在前导链和滞后链之间明显不同。Pol δ 和 Pol ε 的这种特定特征为跟踪这些聚合酶的作用提供了一种新方法。不仅在突变体中而且在野生型聚合酶细胞中，rNTP 掺入的模式在前导链和滞后链之间明显不同。Pol δ 和 Pol ε 的这种特定特征为跟踪这些聚合酶的作用提供了一种新方法。