Aire promotes the generation of long transcripts in TEC. (A) The numbers of protein-coding genes (x-axis) in which significant differential splicing events (y-axis) were detected; comparisons of immature versus mature mTEC (blue), immature mTEC versus Aire-knockout mTEC (red) and Aire-knockout versus Aire-positive mature mTEC (yellow) (n = 2 replicates per sample). (B) Breakdown of identified splicing events by event type and promiscuous expression status. (SE) skipped exon; (RI) retained intron; (MXE) mutually exclusive exon; (A3SS/A5SS) alternative 3′/5′ splice site. (C) MA plot of differential transcript expression in Aire-knockout compared to Aire-positive mTEC. Transcripts regulated by Aire are shown in red (sleuth, Wald test, Qval < 0.05, fc ≳ 2, n = 2 replicates per sample). Transcripts from housekeeping genes are shown in blue. (D) The length distributions of Aire-regulated and non-Aire-regulated transcripts in Aire-regulated genes (analysis limited to genes that contained at least one significantly Aire-regulated transcript as defined in C).
