Numerous anti-cancer drugs perturb thymidylate biosynthesis and lead to genomic uracil incorporation contributing to their antiproliferative effect. Still, it is not yet characterized if uracil incorporations have any positional preference. Here, we aimed to uncover genome-wide alterations in uracil pattern upon drug treatments in human cancer cell line models derived from HCT116. We developed a straightforward U-DNA sequencing method (U-DNA-Seq) that was combined with in situ super-resolution imaging. Using a novel robust analysis pipeline, we found broad regions with elevated probability of uracil occurrence both in treated and non-treated cells. Correlation with chromatin markers and other genomic features shows that non-treated cells possess uracil in the late replicating constitutive heterochromatic regions, while drug treatment induced a shift of incorporated uracil towards segments that are normally more active/functional. Data were corroborated by colocalization studies via dSTORM microscopy. This approach can be applied to study the dynamic spatio-temporal nature of genomic uracil.

中文翻译：

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化疗后人类 DNA 中尿嘧啶分布模式的全基因组改变


许多抗癌药物扰乱胸苷酸生物合成并导致基因组尿嘧啶掺入，从而发挥抗增殖作用。尽管如此，目前还不清楚尿嘧啶掺入是否有任何位置偏好。在这里，我们的目标是在源自 HCT116 的人类癌细胞系模型中发现药物治疗后尿嘧啶模式的全基因组变化。我们开发了一种与原位超分辨率成像相结合的简单 U-DNA 测序方法 (U-DNA-Seq)。使用新颖的稳健分析流程，我们发现在处理和未处理的细胞中尿嘧啶出现概率较高的广泛区域。与染色质标记和其他基因组特征的相关性表明，未处理的细胞在晚期复制组成型异染色质区域中具有尿嘧啶，而药物处理诱导掺入的尿嘧啶向通常更活跃/功能性更强的片段转移。数据通过 dSTORM 显微镜的共定位研究得到证实。该方法可用于研究基因组尿嘧啶的动态时空性质。