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) .