144 7 Splicing and Alternative Splicing Impact on Gene Design
cells, only 10% of PTC-containing genes were slightly increased in their mRNA
levels [184, 185]. Such a rather minor role is in accordance with a microarray
study, showing uniformly low levels of PTC-containing splice variants across
diverse mammalian cell types and tissues [186].
Although the usage of alternative splicing coupled to nonsense-mediated
mRNA decay (AS-NMD) might be less prevalent than indicated by initial com-
putational surveys, this process is pivotal in regulating the expression of certain
gene families. Among other RNA-binding proteins, AS-NMD was shown to be
prevalent for members of the SR protein and hnRNP families, indicating that it is
an important mechanism for the homeostatic regulation of splicing factors [80,
187, 188].
Further, recent work has shown the function of NMD during cellular differen-
tiation and in response to stress, regulating the expression of certain splicing
isoforms (reviewed in [189]). Coupled to the observation that the deletion of
NMD factors is embryonic lethal in mouse [190–193], these findings emphasize
the importance of this mRNA surveillance mechanism for the maintenance of
physiological processes.7.5.6 Alternative Splicing and Disease
Aberrant splicing has been recognized as the cause of several diseases and also
appears to drive cancer progression [194–196]. 15% of the known disease-caus-
ing single nucleotide polymorphisms (SNPs) are located within splice sites, and
>20% in predicted splicing elements [197, 198]. A comprehensive list of diseases
caused by mutated 5′ and 3′ splice sites including cystic fibrosis, Alzheimer’s
disease, and several types of cancer is available at the database for aberrant splice
sites (DBASS) [199].
Mutations of cis-acting elements can result in several aberrant splicing events:
mutations disrupting exon definition, for example, in ESEs, 5′ or 3′ splice sites,
often lead to exon skipping, resulting in nonfunctional proteins, or in the case of
frame shifting to the introduction of PTCs. One example for disrupted exon defi-
nition is spinal muscular atrophy, which is described later. Similar effects are
seen with mutations that activate cryptic splice sites, resulting in the retention of
intronic sequences. Such activation of cryptic splice sites was already described
in 1982 to cause β-thalassemia [200]. Furthermore, mutations in silencer or
enhancer elements affecting the inclusion ratio of cassette exons do not alter the
encoded mRNA/protein isoforms, but nevertheless can induce pathological
effects as isoform ratios are important cell-type-specific determinants. For
example, several intronic SNPs in the neuregulin receptor erbB4 are associated
with the increased expression of splicing isoforms upregulated in patients with
schizophrenia [201].
Mutations in trans-acting factors can also have a severe impact on splicing
regulation. Consistently, their occurrence in core spliceosomal factors is very
rare, suggesting that mutations with an impact on the basal splicing machinery
are embryonic lethal. The few known examples include mutations in the splicing
factor SF3B1 (a component of the U2 snRNP) that are frequently observed in
leukemia patients [202]. In contrast, mutations in splicing factors important for