Phosphosite-Centric Association of MBD3 and NuRD Complex Based on Meta-Analysis of Global Human Phosphoproteome

Methyl-CpG-binding domain protein 3 (MBD3) is a member of the methyl-CpG-binding domain (MBD) family, which functions as a scaffold within the nucleosome remodeling and histone deacetylase complex (NuRD). MBD3 has been studied extensively in pluripotency and gene regulation, particularly through chromatin remodeling. Emerging evidence indicates the role MBD3 in cancer-related signaling pathways. Although MBD3 is detected to be highly phosphoregulated in various phosphoproteomic studies, the phosphoregulatory network of MBD3 remains largely unknown. To address this gap, a comprehensive analysis of MBD3 was performed using publicly available human cellular phosphoproteome datasets. Our study identified two phosphosites, S85 and S56, as the most frequently detected and differentially regulated across datasets. The S56 is situated within its MBD while the S85 site resides within the MBDa. Co-occurrence analysis revealed co-ordinated regulation between these predominant phosphosites. Focusing on the phosphoregulation of the NuRD complex proteins and their binary interactors that co-regulated with MBD3-predominant phosphosites, we constructed a protein-protein interaction network that highlights co-ordinated interactions between MBD3 phosphoregulated proteins with the NuRD complex. These findings provide the first phosphosite-centric view on MBD3 regulation, establishing a basis for future investigations into MBD3 phosphorylation and its implications in cancer.