Fig. 1.

“Feature-level” analysis of microarray data identifies a role for Aire in releasing paused Pol-II. (A) Expression values for individual microarray features were analyzed relative to whole-transcript averages, and “imbalanced” exons in datasets from MECs from Aire-KO and Aire-WT mice were flagged (PLATA t test P < 0.05). The proportion of imbalanced exons is shown for 420 transcripts most strongly induced by Aire, or an equal number of expression-matched Aire-neutral genes, or 84 transcripts repressed by Aire (Table S1). (B) Exon-level expression was normalized to the whole-transcript average in either WT or Aire KO datasets. Transcripts with imbalanced exon1 representation are shown in red (Left) or imbalanced representation of internal exons in purple (Right). (C) The expression level of each feature for transcripts showing an exon1 imbalance was plotted relative to its distance from the TSS for Aire-induced genes, in Aire KO or WT MECs. (D) Expression level of each feature for all Aire-induced (Left; overall WT/KO ratio >3) or Aire-neutral genes (Right) plotted as a function of distance from the TSS, either individually (Upper) or grouped in 25-bp bins (Lower). (E) The expression level of each feature for transcripts showing an exon1 imbalance was plotted relative to its distance from the TSS for Klf4-induced genes, in Klf4 KO or WT cells (data from ref. 35). A “TSS proximal–distal” index was calculated in the KO samples as the ratio of the medians of expression values in proximal (<200 bp from TSS) vs. distal features.