Fig. 4: Defining the mouse and human CD4⁺ T cell RBPomes.

The RBPomes of Figs. 2 and 3 were inspected for enrichment of abundant proteins, representation of specific RBD, overlapping, and uniquely identified proteins. a Relative abundance (log₂) of proteins identified in a single-shot mouse proteome (orange dots) plotted by their rank from highest to lowest abundant protein. RNA-binding proteins detected by RNA capture (top plots) or by OOPS (bottom plots) are highlighted as blue diamonds. b Same plots as shown in (a) for human data. c, e The recently established database EuRBPDB was used as a reference for eukaryotic RBPs to establish the numbers of canonical and non-canonical RBPs identified by RNA-IC or OOPS on the mouse (c) or human (e) CD4⁺ T cells. d, f The occurrence of RBDs in RNA-IC and OOPS-identified RBPs were analyzed in comparison with the 10 most abundant motifs described for the mouse (d) or human (f) proteome. g Venn diagram using four datasets for RBPs in CD4⁺ T cells as determined by RNA-IC and OOPS in mouse and human cells. We defined the core RBPomes to contain proteins present in at least two datasets. h Result from a four-way Venn diagram comparing published OOPS-identified RBPome data sets²⁹ from the embryonic kidney (HEK 293), mammary epithelial (MCF10A), and bone osteosarcoma epithelial (U2OS) cell lines with the OOPS-derived RBPome from primary human CD4⁺ T cells (left panel). The right panel depicts results obtained by matching 439 T cell-unique identified RBPs against the human EuRBPDB.