Fig. 5: TRA2 proteins are effectors that relocalize multivalent GA-rich mRNAs to nuclear speckles.
From: Collective homeostasis of condensation-prone proteins via their mRNAs
a, Heatmap presenting the CLIP data for RBPs with the greatest preference for multivalent sequences, showing fold enrichment for crosslinks falling within the listed GeRM CDS regions compared with the rest of the same transcript. Datasets in bold are from proteins with known nuclear speckle localization. b, Example CLIP crosslinking profiles for SR proteins across an APP transcript, with the smoothed GeRM score, amino acid entropy and proportion of charged amino acids. The solid lines represent the mean across two samples, whereas the shaded regions represent the standard error. CPM, counts per million. c, Example TRA2B and SC35 immunofluorescence images from two independent experiments showing nuclei containing variable amounts of mScarlet–PPIGLCD. d, Quantification of the enrichment of the TRA2B signal within nuclear speckles (based on the SC35 signal) versus the nucleoplasm per nucleus with respect to PPIGLCD expression. Two independent replicates are plotted in different colours, and the regression lines are plotted in dashed lines. a.u., arbitrary units. e, EIF3A HCR-FISH in nuclei expressing mScarlet–PPIGLCD and treated with either scrambled siRNA or TRA2A-targeting and TRA2B-targeting siRNA for 48 h (three independent replicates). Scale bars, 10 µm. f, Quantification of the enrichment of the EIF3A HCR-FISH signal in the nuclear speckle over the nucleoplasm for cells expressing variable amounts of PPIGLCD and treated with either scrambled siRNA or TRA2A-targeting and TRA2B-targeting siRNA for 48 h. All pairwise statistical comparisons were performed using a Welch t-test with FDR correction for multiple testing, where *P < 0.05. Precise P values can be found in the Source Data.
