The role of DE and AS in transcriptional plasticity
In addition to differential gene expression (DE), we found evidence for
differential alternative splicing with substantial consequences for
transcriptional plasticity not reflected in DE. Moreover, we detected
the functional specialization of alternatively spliced genes (AS)
relative to DE genes in response to thermal acclimation. AS genes are
only linked to WGP, while DE genes are associated with WGP and TGP.Our results of transcriptional WGP show that the number of AS
genes often exceeded that of the DE genes, demonstrating that AS is an
important mechanism of transcriptional regulation in response to thermal
acclimation in D. mojavensis . These mechanisms appear mutually
exclusive, with only 4 % of overlapping genes between DE and AS. The
role of AS in transcriptional plasticity following acclimation is well
supported in multiple organisms (Anduaga et al., 2019; Dikaya et al.,
2021; John et al., 2021; Steward et al., 2022). The great majority of
this evidence comes from studies of WGP, while the evidence for TGP is
more limited. Our results suggest that differential AS may have little
or no role in TGP (Ryu et al., 2018). However, we provide evidence for a
more general role of intron retention (IR), which is a particular case
of AS, being likely linked to negative gene regulation (Farlow et al.,
2010). An increased rate of retained introns, which often contain
premature stop codons, has been associated with higher transcript
degradation that might result from the nonsense-mediated mRNA decay
(NMD) pathway (Jacob and Smith, 2017; Hadar et al., 2022). We found that
IR rates are significantly higher for down-regulated genes than for
up-regulated genes, suggesting IR is a mechanism for regulating gene
expression in response to thermal acclimation within and across
generations. This finding is consistet with increased IR rates in
response to stress conditions in other species (Jacob and Smith, 2017;
Hadar et al., 2022).