146 7 Splicing and Alternative Splicing Impact on Gene Design
Mer1 is transcribed only during meiosis and activates splicing by binding to an
intronic enhancer sequence (AYACCCUY) near the 5′ splice site. Splicing activa-
tion by MER1 is further dependent on a reduced basal splicing efficiency of the
introns (e.g., a non-consensus 5′ splice site) and on the NAM8 protein, which is
part of the U1 snRNP [212].
Further on, intron retention can be regulated by a negative feedback loop of
the encoded protein: overexpression of the RNA export factor YRA1 is toxic to
cells. Therefore, its expression has to be tightly regulated. YRA1 restricts its own
expression by inhibiting the splicing of a highly unusual intron in its ORF. With
766 nucleotides, this intron is very large: it is located 300 nucleotides down-
stream of the AUG and contains a non-consensus branch point (GACUAAC).
All these unusual features seem to be important for autoregulation, which relies
on a suboptimal splicing efficiency and co-transcriptional binding of YRA1
[213, 214]. The unspliced pre-mRNA is exported to the cytoplasm, where its
degra dation is initiated by EDC3-activated decapping and completed by XRN1
digestion.
In addition to these cases, in which a specific protein regulates one (or four)
specific transcripts, the spliceosome itself might differentiate between different
introns. Genome-wide studies of changes in splicing efficiency after the intro-
duction of mutations in 18 core spliceosomal components revealed several
transcript specific effects [215]. This implies that not only specialized factors
but also the core spliceosome machinery itself can influence differential splicing
decisions.7.6.2 Regulated Splicing
Instead of alternative splicing, “regulated splicing” is predominantly found in
S. cerevisiae. There, nonfunctional introns are retained in the mature mRNA,
introducing PTCs that ultimately lead to mRNA decay. The degradation of
unspliced pre-mRNAs can occur in the nucleus involving the exosome.
Additionally, intron-containing mRNAs can be exported to the cytoplasm, where
they are degraded by either the 5′ to 3′ exonuclease XRN1 or the NMD pathway.
The decision, if an intron-containing mRNA is directed to the NMD pathway,
depends on the intron’s identity [216].
The most prominent example of regulated splicing in S. cerevisiae occurs dur-
ing meiosis. All 13 of the intron-containing genes related to meiosis are spliced
inefficiently during exponential growth in rich medium, but splicing is dramati-
cally induced during sporulation [217]. This regulation mechanism seems to
depend on the competition of meiosis-related genes with intron-containing
ribosomal proteins for the splicing machinery [218]. During meiosis, the expres-
sion of ribosomal proteins is temporary repressed. During this time period, the
global splicing efficiency, including splicing of meiosis-related genes, is improved.
Ribosomal proteins comprise ~90% of all splicing substrates during vegetative
growth, outcompeting other intron-containing pre-mRNAs for the splicing
apparatus. Therefore transcriptional repression of ribosomal proteins leads to an
overall change in the composition of nuclear pre-mRNAs, ultimately allowing for
efficient splicing of otherwise inefficiently spliced meiosis-related pre-mRNAs.