Figure 3

Depletion of the SWI/SNF core subunits changes the alternative processing of the Gpdh pre-mRNA in S2 cells. S2 cells were treated with dsRNA for Brm, Snr1 or Mor. Mock-treated cells were used as controls for microarray experiments. The control cells in the validation experiments were treated with GFP-dsRNA. (A) The effects of the dsRNA treatments analyzed by Western blotting. (B) The Gpdh mRNAs. The boxes and the thin lines represent exons and introns, respectively. White and dark boxes represent untranslated regions and coding sequences, respectively. The primers used for qPCR are indicated by small arrows on top of each transcript. (C) Results from the microarray data. The histograms show the average ratios between the abundance of each isoform in RNAi-treated cells compared to mock-treated cells (based on data from E-TABM-169). The bars represent average ratios from four mock replicates and three replicates for each of the depletion experiments, respectively. The error bars represent standard deviations. The stars mark transcript ratios that were affected by the depletions according to the selection criteria described in the text. (D), (E) and (F) Validation of the effects of the depletions. Either Brm, Snr1 or Mor was knocked down in S2 cells, and the relative abundance of each transcript was quantified by RT-qPCR. The transcript-specific primer pairs target exon-exon junctions and downstream exons. The abundance of each transcript was calculated relative to the abundance of the first, constitutive exon. The results are expressed as the factor change between RNAi-treated and GFP-treated cells. The bars represent averages from three technical replicates from an RNAi experiment. The error bars represent standard deviations.