Intron retention rates (IR)
Intron retention is a specific type of AS that is not
necessarily captured by JunctionSeq and can have different
biological implications for the control of gene expression. An intron
can be retained in the final mature mRNA, coding for a new
function (Jacob and Smith, 2017; Monteuuis et al., 2019) or a
nonfunctional transcript that is degraded by the nonsense-mediated
decay (NMD) (Farlow et al., 2010). We investigated whether DE
changes due to WGP and TGP involve mechanisms of IR using theIRFinder pipeline (Middleton et al., 2017). A new reference
annotation was built by removing all overlapping features present in the
same strain sense of individual introns and then unique identifiers were
assigned to each flattened exon. Only regions with high mapping scores
as estimated through simulated reads across the genome were identified
and included in the flattened annotation file. A read count matrix with
all reads overlapping splice junctions was generated and IR rates were
estimated as: IR rate = junction reads / (junction reads +intronic reads) for each sample using the IRFinder R
package (Middleton et al., 2017).