AlphaFold-guided structural analyses of nucleosome binding proteins

The nucleosome, as the fundamental unit of chromatin, interacts with a diverse range of proteins, crucially regulating gene expression. In this study, we introduce an AlphaFold-based algorithm designed to analyze nucleosome-binding proteins from a dataset of over 7600 human nuclear proteins. Using proteins that interact with the nucleosome acidic patch as a benchmark, our screening achieves a successful prediction rate of 77% (23 out of 30 proteins). This predictive approach has led to the identification of ARID4A and ARID4B as novel nucleosome-binding proteins. Additionally, this analytical method was used to study RING-family ubiquitin E3 ligase RNF168, demonstrating that RNF168 dimerization enhances its binding to the nucleosome, a finding confirmed by cryogenic-electron microscopy structural analysis. Our findings offer a rapid and effective method for the discovery and characterization of nucleosome-binding proteins and emphasize the significant role of ubiquitin E3 ligase dimerization in epigenetic regulation.