Fig. 2.

Validation of the microarray-based detection of stalled polymerases. (A) RT-PCR analysis of the effect of flavopiridol on AIRE-transfected 4D6 cells for a panel of AIRE-sensitive or -insensitive genes. Relative expression levels are shown as the mean ± SD from three replicates. (B) 4D6 epithelial cells were treated with flavopiridol for 24 h before expression profiling. The expression level of each microarray feature for flavopiridol sensitive transcripts showing an exon1 imbalance is plotted vs. its distance from the TSS, in flavopiridol-treated and control 4D6 cells. (C) A “TSS proximal–distal” index was calculated in KO samples for several transcription factors from plots such as those of Fig. 1C as the ratio of the medians of expression values in proximal (<200 bp from TSS) vs. distal features. TSS “proximal–distal” indices calculated for sensitive genes, in expression datasets of KO of factors involved in the release of stalled Pol-II (black) or of classic transcription factors impacting initiation (gray).