AGO2 and LaminB attenuate transcription genome-wide.

<p>A) Western blot analysis showing knockdown efficiencies for each protein analyzed. Tubulin is included as loading control. B) Changes in neuRNA levels upon depletion of AGO2. Statistically significant changes include 710 up-regulated genes (red) and 195 down-regulated genes (blue). (For AGO2 rescue experiments see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007276#pgen.1007276.s001" target="_blank">S1 Fig</a>). Genes containing an AGO2 peak at their promoter are additionally colored orange. FET <i>p</i>-values and odds ratios indicate significance of association between affected genes and presence of AGO2 peak at promoters. C) Scatterplot comparing neuRNA-seq profiles from AGO2 and LaminB knockdowns. Pearson’s R corresponds to correlation coefficient of the two profiles. FET <i>p</i>-values and odds ratios indicate significance of the association between coordinately up-regulated (466, red) or down-regulated (76, blue) genes in both knockdowns. D) Scatterplot comparing neuRNA-seq profiles from Dcr-2 and AGO2 knockdowns. Genes with undetermined log2 fold change (due to zero counts in one condition) are fixed to a minimal value of -1.5 so they can be visually represented on the plots. Genes with zero counts in both conditions are not displayed. E) Scatterplot comparing neuRNA-seq profiles from Dcr-2 and LaminB knockdowns. F) Immunofluorescence analysis for AGO2 and LaminB in mock, AGO2- and LaminB-depleted cells. AGO2 (green, Liu antibody), LaminB (red), and DAPI staining (blue) are shown. Scale bar represents 14 μm.