Fig. 3: Comparative analysis of RBPs from mouse brain, kidney, and liver.
From: The RNA-binding protein landscapes differ between mammalian organs and cultured cells
a Venn diagram showing the number of shared and organ-specific RBPs identified. b Normalized signal sum of identified RBPs in ex vivo eRIC eluates (upper panel) and the corresponding input samples (middle panel) for each organ analyzed. Blue, brain; red, kidney; orange, liver. Center lines indicate the median, box borders represent the interquartile range (IQR), and whiskers extend to ±1.5 time the IQR; outliers are shown as black dots (pairwise comparisons using two-sided t-test with FDR correction, ***p.adj <2e-16; n.s.: not significant). Bottom panel: amount of poly(A) RNA isolated from each organ by eRIC. Note that the retrieved mass of protein (upper panel) differs extensively across the tissues analyzed (with kidney > liver > brain) and does not correlate with the mass of RNA recovered (bottom panel) (see also Supplementary Data 2). For each organ, four +UV eRIC eluates were generated, each derived from a single mouse; eRIC eluates from two mice were combined, rendering n = 2. Organ sections from four mice were pooled to generate one -UV eRIC eluate per organ (n = 1). c Hierarchical clustering and heatmap of the RBPs identified in the brain, kidney, and liver, showing protein abundance in eRIC eluates (left columns) and inputs (right columns) across the three organs (shown as the Log.2 ratio of protein abundance in each eRIC or input sample relative to the average protein abundance in corresponding eRIC and input samples). d Representative images of three biologically independent experiments of the proximity ligation assay (PLA) for interactions of ENO1 and poly(A) RNA, nuclear staining (DAPI), and ENO1 immunofluorescence in the brain, kidney, and liver. Scale bar, 20 µM. See quantification in Supplementary Fig. 2b. e poly(A) (green) and total RNA (violet) levels, in the brain, kidney, and liver, expressed as µg of RNA per mg of total protein. non-poly(A) RNA, n = 4 biologically independent experiments. Poly(A) RNA, n = 3, 4, 5 biologically independent experiments for liver, kidney, and brain, respectively. **p.adj < 0.01, ***p.adj < 0.001, ****p.adj < 0.0001, n.s.: not significant (one-way ANOVA with Tukey post hoc test). Poly(A) RNA: BvsK, p.adj = 2.76e-4; BvsL, p.adj = 9e-6; KvsL, p.adj = 9.36e-3. Total RNA: BvsK, p.adj = 6.34e-2; BvsL, p.adj = 1.0e-5; KvsL, p.adj = 1.24e-4. Source data are provided as a Source Data file.
