Delineating the constituents and structural composition of RNA-associated protein complexes is essential to mapping the molecular machinery driving RNA metabolism and its impact on cellular function. Here, we present a comprehensive dataset of RNA-dependent proteins and complexes in the phylogenetically distant yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. Using 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) as a descriptive framework for RNA dependence, enabling the robust comparative analysis of RNA dependence across proteins in both species and relative to existing data from their human counterparts. This identifies a conserved core of RNA-dependent proteins shared across both yeasts, alongside distinct, organism-specific adaptations in complex behaviour. The data further support the analysis of co-sedimentation behaviour of protein complexes with known RNA-directed functions. For instance, we find that the five subunits of the S. cerevisiae THO complex only co-sediment in the absence of RNA, pointing to an underappreciated structural modularity of the well-characterized pentameric complex. The two datasets, available at https://yeast-r-deep.computational.bio/, provide a resource for hypothesis-driven research in RNA biology and establish R-DeeP as a broadly applicable tool for comparative analysis of RNA-protein interactions.

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Journal Article

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Wäber NB, Seidler JF, Thelen F, Kot P, Schreiner S, Timm T, Lochnit G, Sträßer K, Kilchert C

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