Investigating the dynamic nature of the interactions between nuclear proteins and histones upon DNA damage using an immobilized peptide chemical proteomics approach.

As a result of the complexity and dynamic range of the cellular proteome, including mutual interactions and interactions with other molecules, focused proteomic approaches are important to study subsets of physiologically important proteins. In one such approach, a small molecule or part of a protein is immobilized on a solid phase and used as bait to fish out interacting proteins from complex mixtures such as cellular lysates. Here, such a chemical proteomics experiment is presented to explore the range of proteins that interact with the N-terminal tail of core histones. Therefore, a core histone consensus N-terminal tail (NTT) peptide was synthesized and immobilized on agarose. Interactions between histone NTTs and proteins are extremely important as they regulate chromatin structure, which is important in many DNA-related processes, like transcription and DNA repair. Induction of DNA damage, like DNA double strand breaks, is known to trigger chromatin remodeling events through interactions between histone NTTs and so-called histone chaperones. Therefore, we set out to investigate specific changes in interactions of nuclear proteins before and shortly after DNA double strand break induction. Over 700 proteins were found to bind specifically to the NTT peptide, which makes our study the most comprehensive proteomic survey of the broad spectrum of nuclear proteins interacting with the NTT of core histones in nucleosomes. Apart from a few exceptions, the abundance of the majority of NTT binding proteins was found to be unchanged following DNA damage. However, an in-depth analysis of protein phosphorylation (we detected more than 90 unique sites in about 60 proteins) revealed that the phosphorylation status of several proteins involved in chromatin remodeling changes upon DNA damage. We observed that in these differentially phosphorylated chaperones are part of closely interacting protein complexes involved in regulatory mechanisms at the crossroads of nucleosome assembly, DNA replication, transcription, and the early onset of DNA damage repair.