Regulable DNA–Protein Interactions in Vitro and Vivo at Epigenetic DNA Marks

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.