The role of intron retention (IR) in transcriptional plasticity
Since alternatively spliced genes significantly associated with transcriptional plasticity are WGP-specific, we next investigated a more general role of splicing in the regulation of gene expression by estimating rates of intron retention (IR). Transcripts with retained introns often contain premature stop codons, and these transcripts are degraded by the nonsense-mediated decay (NMD) pathway (Farlow et al., 2010). This mechanism has also been associated with the control of gene expression, as an increase in the rate of retained introns results in higher transcript degradation (Jacob and Smith, 2017; Hadar et al., 2022). We tested this hypothesis as a possible mechanism of gene regulation in transcriptional plasticity by estimating IR changes between acclimated vs. control samples (IR change) and then compared the IR change between up and down-regulated genes (Figure 2b). IR changes were consistently higher for down-regulated genes when compared to up-regulated genes in both WGP and TGP (Figure 2b). This finding implicates IR as one mechanism for the control of gene expression in thermal plasticity and is consistent with increased IR rates in response to stress conditions in other species (Jacob and Smith, 2017; Hadar et al., 2022) .