Widespread Shortening of 3’ Untranslated Regions and Increased Exon Inclusion Are Evolutionarily Conserved Features of Innate Immune Responses to Infection
(A) Meta-gene distributions of 3’RNA-seq read densities at the upstream polyA sites (core regions, left) and downstream polyA sites (extended regions, right) of Tandem 3’ UTRs after infection with Listeria or Salmonella (top and bottom, respectively). Shown are the read distributions for non-infected samples across all Tandem 3’ UTRs (black) and infected samples at Tandem 3’ UTRs that significantly change after infection (yellow) or show no change after infection (blue), as called by the RNA-seq data. (B) Distribution of ΔΨ values calculated from 3’RNA-seq data for Tandem 3’ UTRs. We observe significant shifts (P < 2.2 × 10−16 for both Listeria and Salmonella) towards negative ΔΨ values in Tandem UTRs that are identified as significantly changing in RNA-seq data (yellow) relative to Tandem UTRs without any change after infection (blue).