Conserved abundance and topological features in chromatin-remodeling protein interaction networks

The study of conserved protein interaction networks seeks to better understand the evolution and regulation of protein interactions. Here, we present a quantitative proteomic analysis of 18 orthologous baits from three distinct chromatin-remodeling complexes in Saccharomyces cerevisiae and Homo sapiens. We demonstrate that abundance levels of orthologous proteins correlate strongly between the two organisms and both networks have highly similar topologies. We therefore used the protein abundances in one species to cross-predict missing protein abundance levels in the other species. Lastly, we identified a novel conserved low-abundance subnetwork further demonstrating the value of quantitative analysis of networks. Synopsis Quantitative proteomic analysis of a yeast and human chromatin remodeling protein interaction network demonstrates the conservation of protein content, abundance, and topology in this network. This allowed cross-species prediction of missing values and led to the discovery of a conserved low-abundance subnetwork. The abundance of proteins within INO80, TIP60/NuA4, and SRCAP/SWR complexes are conserved between S. cerevisiae and H. sapiens. The yeast and human chromatin remodeling networks have a similar network topology. Affinity purifications of new associations of orthologous yeast and human proteins pulled down components of multiple chromatin remodeling complexes. Quantitative proteomic analysis of a yeast and human chromatin remodeling protein interaction network demonstrates the conservation of protein content, abundance, and topology in this network. This allowed cross-species prediction of missing values and led to the discovery of a conserved low-abundance subnetwork.