Fig. 2: The T helper cell RBPome of polyadenylated RNAs.

T_H0 cultures from three mice or three human donors were used as biologic replicates (n = 3) to investigate proteins interacting with mRNA. a Schematic illustration of the RNA-interactome capture (RNA-IC) method that was carried out to identify RBPs from mouse and human CD4⁺ T cells. b, c Volcano plots from two-sided Student’s T-test analysis using a permutation-based FDR method for multiple hypothesis corrections showing the −log10 p-value plotted against the log2 fold-change comparing the RNA-capture from crosslinked (CL) mouse CD4⁺ T cells (b) or human CD4⁺ T cells (c) versus the non-crosslinked (nCL) control. Red dots represent proteins significant at a 5% FDR cut-off level in both mouse and human RNA-capture experiments and blue dot proteins were significant only in mice or humans, respectively. d Enrichment analysis of GO molecular function terms of significant proteins in mouse or human RNA capture data. The 10 most enriched terms in mouse (dark blue) and the respective terms in human (light blue) are shown. The y-axis represents the number of proteins matching the respective GO term. p-values were calculated using the hypergeometric distribution and were adjusted by Benjamini–Hochberg multiple testing correction. Numbers above each term depict the adjusted p-value. e Distribution of IDRs in all Uniprot reviewed protein sequences (black line), in proteins of the mouse EuRBPDB database (green line), and in proteins significant in the mouse RNA-IC experiment (red line). The same plot is shown for human data at the bottom. According to two-sided Kolmogorov–Smirnov testing, the IDR distribution differences between RNA-IC (red lines) and all proteins (black lines) are highly significant in mice and man and reach the smallest possible p-value (p < 2.2 × 10⁻¹⁶).