A census of RNA-dependent proteins in yeast

Understanding the roles of RNA-associated protein complexes is essential to uncovering the mechanisms driving RNA metabolism and its impact on cellular function. Here, we present a comprehensive dataset of RNA-dependent proteins and complexes in the distantly related yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. For this, we adapt R-DeeP--a density gradient-based method that uses quantitative mass spectrometry to profile protein sedimentation in the presence and absence of RNA. We introduce an RNA dependence index (RDI) to provide a descriptive framework for RNA dependence. This approach enables the comparative analysis of RNA dependence across hundreds of proteins in both species. Furthermore, the data support the analysis of co-sedimentation of protein complexes with known RNA-directed functions. For instance, we find that the five subunits of the THO complex only co-sediment in the absence of RNA, implying that the well-characterized pentameric complex might not represent the RNA-bound state. The two datasets, available at https://yeast-r-deep.computational.bio/, support hypothesis-driven research in RNA biology, expanding the utility of R-DeeP to uncover conserved and organism-specific features of RNA-protein interactions across different biological systems.