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Widespread Shortening of 3’ Untranslated Regions and Increased Exon Inclusion Are Evolutionarily Conserved Features of Innate Immune Responses to Infection

Fig 4

Directed shifts in RNA processing persist across time, stimulus conditions, and closely related species.

(A) Correlations between ΔΨ values after 2 hours of infection (x-axis) and ΔΨ values after 24 hours of infection (y-axis), presented as density plots per RNA processing category in contrasting colors. Plotted are events that are significant after 2 hours of either Listeria or Salmonella infection. (B) Distributions of ΔΨ values for skipped exons (purple) and TandemUTRs (blue) following infection of whole blood cells with lipopolysaccharide, assessed in human (top), chimpanzee (middle) and rhesus macaque (bottom) individuals (N = 6 per species). We observe prominent global shifts in isoform distributions in human and macaque (SEhuman P = 0.003, TandemUTRhuman P = 2.4×10−13; SEmacaque P = 0.05, TandemUTRmacaque P = 8.8×10−6) with a more modest trend observed in chimpanzee, potentially due to poor transcript annotations in the chimpanzee genome (SEchimpanzee P = 0.26, TandemUTRchimpanzee P = 0.002). All p-values were calculated using a Student’s t-test testing deviation from a mean of zero.

Fig 4