Fig 1: Many R-loop–binding proteins are enriched within the nucleolus.A, immunofluorescence staining of three R-loop–associated DEAD-box proteins, DDX18, DDX24, and DDX27, costained with FBRL to mark the nucleolus. DNA was stained by DAPI. The scale bar represents 10 μm. B, comparison of rRNA-related and rRNA-unrelated proteins enriched by S9.6. R-loop–associated proteins were classified as rRNA related or unrelated by GO term analysis, using the biological process term “ribosomebiogensis,” “rRNAmetabolicprocess,” and “rRNAprocessing.” Boxes of the box plot represent the first and third quartiles, the band represents the median, and the whiskers depict 1.5 times the interquartile range. C, Venn diagram of the overlap between the R-loop interactomes (with and without filtering) and the nucleolar proteome from Kar et al. (80). The upper diagram includes the 335 proteins enriched in S9.6 co-IP samples with the 76 most enriched (corresponding to the orange dots in Fig. 1B) depicted in the lower diagram. p Values were calculated using hypergeometric tests. DAPI, 4′,6-diamidino-2-phenylindole; FBRL, fibrillarin; GO, Gene Ontology; IP, immunoprecipitation.