5-Formyluracil (5fU) is a vital DNA marker that is widely distributed in the cells of organisms. A unique feature of 5fU is the possession of a potentially reactive aldehyde group in its structure that could realize addition and condensation reactions. However, the biological functional details of 5fU remain mostly elusive, especially, regarding its relatedness with proteins. In this current study, we show that 5fU bases have a strong affinity toward nucleosome core particles, and that could yield regulable DNA–protein conjugates (DPCs) via chemical interactions between amino and aldehyde groups, and reductants could be applied to stabilize or dissociate the interactions. Besides, we developed a photocaged method to exploit the relationship between 5fU and nucleosomes. Finally, by applying a combination of the existence of 5fU–histone interactions in vivo by ChIP analysis of histone H4 with liquid chromatography–mass spectrometry (LC–MS), we probed further, the DPCs’ influence on nucleosome and enzyme. Collectively, our results showed that the 5fU–protein interactions increase the occupancy and stability of nucleosomes, affect enzyme recognition, and block DNA replication. These might imply that, in vivo, the DPCs between 5fU and nucleosome core particles might play a key role in 5fU-associated pathways such as DNA repair, transcriptional regulation, or development.

中文翻译：

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表观遗传DNA标记在体内和体外可调节的DNA-蛋白质相互作用

5-甲酰尿嘧啶（5fU）是重要的DNA标记，广泛分布于生物体细胞中。5fU的独特之处在于其结构中具有潜在的反应性醛基，可以实现加成和缩合反应。然而，5fU的生物学功能细节仍然难以捉摸，尤其是关于其与蛋白质的相关性。在当前的研究中，我们表明5fU碱基对核小体核心颗粒具有很强的亲和力，并且可以通过氨基和醛基之间的化学相互作用产生可调节的DNA-蛋白质共轭物（DPC），并且还原剂可用于稳定或解离核糖体。互动。此外，我们开发了一种光笼法，以利用5fU和核小体之间的关系。最后，通过应用组蛋白H4的ChIP分析和液相色谱-质谱（LC-MS）结合体内5fU-组蛋白相互作用的存在，我们进一步研究了DPC对核小体和酶的影响。总的来说，我们的结果表明5fU蛋白相互作用增加了核小体的占有率和稳定性，影响酶的识别并阻止DNA复制。这些可能暗示着，在体内，5fU和核小体核心颗粒之间的DPC可能在5fU相关途径（例如DNA修复，转录调控或发育）中发挥关键作用。我们的结果表明5fU蛋白相互作用增加了核小体的占有率和稳定性，影响了酶的识别并阻止了DNA复制。这些可能暗示着，在体内，5fU和核小体核心颗粒之间的DPC可能在5fU相关途径（例如DNA修复，转录调控或发育）中发挥关键作用。我们的结果表明5fU蛋白相互作用增加了核小体的占有率和稳定性，影响了酶的识别并阻止了DNA复制。这些可能暗示着，在体内，5fU和核小体核心颗粒之间的DPC可能在5fU相关途径（例如DNA修复，转录调控或发育）中发挥关键作用。