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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\u2014a density gradient-based method that uses quantitative mass spectrometry to profile protein sedimentation in the presence and absence of RNA\u2014we 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\u2013protein interactions.<\/jats:p>","DOI":"10.1093\/nar\/gkag799","type":"journal-article","created":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T11:45:46Z","timestamp":1785498346000},"source":"Crossref","is-referenced-by-count":0,"title":["Cross-species R-DeeP profiling reveals a conserved core of RNA-dependent proteins in yeast"],"prefix":"10.1093","volume":"54","author":[{"given":"Nadine Bianca","family":"W\u00e4ber","sequence":"first","affiliation":[{"name":"Institute of Veterinary Physiology and Biochemistry, Justus Liebig University Giessen , Giessen 35392 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johanna Franziska","family":"Seidler","sequence":"additional","affiliation":[{"name":"Institute of Biochemistry, 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