Figure 3.

Impact of Drosha and Dicer deficiencies on the proteome. Shown are ratios of individual protein expression levels in in vitro activated CD4⁺ T cells (A) and MEFs (B) as determined by SILAC analysis. Drosha-deficient cells were cultured in L-Lys/L-Arg-deficient medium supplemented with the light isotopes L-Lys ¹²C₆¹⁴N₂ and L-Arg ¹²C₆¹⁴N₄, Dicer-deficient cells were cultured in medium supplemented with the intermediate isotopes L-Lys 4,4,5,5-D4 and L-Arg ¹³C₆¹⁴N₄, and control cells were cultured in medium supplemented with the heavy isotopes L-Lys ¹³C₆¹⁵N₂ and L-Arg ¹³C₆¹⁵N₄. The labels were then inverted for repeat experiments. Labeling was performed for at least five cell divisions to label all proteins before analysis by quantitative mass spectrometry. In CD4⁺ T cells, deletion was achieved with CD4-cre, and in MEFs, deletion was achieved with Gt(Rosa)26Sor^CreER. Only data for proteins that were quantified in all three genotypes are shown. Indicated are the proteins that were found to be significantly different (P < 0.05 by ANOVA) in Drosha- and/or Dicer-deficient cells compared with controls. r = Pearson's correlation coefficient.