Fig. 3
Temporal changes in the mRNA binding proteome after MMS treatment. A–C ANOVA p-values (−log10) plotted against median SILAC ratios (log2) at 0 h (A), 4 h (B) or 15 h (C). D–F Volcano plots showing t-test p-values (−log10) versus median SILAC ratios (log2) of oligo(dT)/input extract at 0 h (D), 4 h (E) and 15 h (F). Significantly altered proteins after Benjamini Hochberg FDR correction (< 0.05) are shown in red. G-I Verification of SILAC data by western analysis. HeLa cells were treated as indicated with either PBS (control) or MMS for 1 h, lysed and subjected to oligo(dT) enrichment. G SND1 and SERBP1 show reduced binding to m RNA, while HNRNPA1 does not alter its binding. H Input of extracts utilized for oligo(dT) enrichment in G. Note that the protein levels in lanes 1–3 remain the same. I Reduced mRNA binding is not caused by cross-linking bias. As in G, but MMS-treated cells were irradiated with either 25 mJ/cm2 (standard) or 100 mJ/cm2 (4 × standard dose). Note that increasing the UVC dose does not lead to increased cross-linking (lane 3 vs. lane 4)