Synthetic Biology Parts, Devices and Applications

138 7 Splicing and Alternative Splicing Impact on Gene Design

In certain cases, multiple cassette exons can be mutually exclusive, producing

mRNAs that always include one of several possible exon choices, but not more.

Additionally, the use of alternative 5′ or 3′ splice sites can lengthen or shorten

exons, a mechanism that accounts for 25% of all alternative splicing events [50].

Finally, the failure to remove an intron leads to a splicing pattern called intron

retention. All four types can occur in the translated or untranslated regions

(UTRs) of any given pre-mRNA [51].

Many genes show multiple splicing patterns, often in conjunction with the

usage of alternative promoters or polyadenylation sites. One striking example is

the fast skeletal troponin T (tnnt3) gene, which is part of the troponin complex

and undergoes extensive alternative splicing. The tnnt3 gene encodes 19 exons,

including five alternatively spliced exons (exons 4–8) and a pair of mutually

exclusive exons (exons 16 and 17) [52]. While isoforms including exon 17 (or β)

are predominantly expressed throughout development, exon 16 (or α)-containing

isoforms are mostly abundant in adult muscles [53, 54]. In addition, the tnnt3

gene contains a developmentally regulated fetal exon F located between exons 8

and 9 [55, 56].

Cassette exons

Mutually exclusive exons

Alternative 5′ splice site

Alternative 3′ splice site

Intron retention

Figure 7.2 Alternative splicing events in mammalian transcripts. The main types of alternative

splicing, which are responsible for the generation of different transcripts, are depicted. Dark

gray indicate constitutive, and light gray cylinders alternative exons.