7.5 Alternative Splicing in ammals 143The kinetic model proposes that the rate of transcription elongation affects
the outcome of alternative splicing. One possibility is that upon Pol II pausing or
slowing down, inclusion of alternative exons increases. An upstream exon with
a weak 3′ splice site can be defined, before the downstream exon is synthesized,
resulting in exon inclusion at slow transcription rates but exclusion at fast tran-
scription kinetics. Other mechanisms include a Pol II “roadblock” upon DNA
binding by proteins, like the CCCTC-binding factor (CTCF), which stalls the
Pol II complex and therefore promotes inclusion of the alternative exon 5 in
cd45 [175].
As histone modifications directly affect Pol II extension speed, they can also
have an impact on alternative splicing. Exons show increased nucleosome occu-
pancy, probably caused by their higher GC content compared with the flanking
intronic regions [176–178]. Furthermore, the histones associated with exons are
enriched in certain modifications, which influence alternative splicing decisions
(reviewed in [179]). Trimethylation of histone H3 lysine 9 (H3K9me3) is corre-
lated with transcriptional repression. Enrichment of H3K9me3 marks on alter-
native exons in the cd44 gene has been shown to increase exon inclusion [171].
The H3K9me3 modification is recognized by the chromodomain protein HP1γ,
which reduces the local elongation rate of Pol II. Conversely, an increase in the
Pol II transcription rate by increased histone 3 lysine 9 acetylation (H3K9ac)
leads to skipping of the ncam exon 18 [172].
Similar to the recruitment model discussed earlier, proteins recognizing spe-
cific histone modifications have been shown to modulate alternative splicing by
recruitment of splicing factors. One example is trimethylation of histone 3 lysine
36 (H3K36me3). This mark can be recognized by the Mrg15 (MORF-related
gene 15) protein, which recruits PTB to an ISS near a mutually exclusive exon in
fgfr2 (fibroblast growth factor 2), repressing its inclusion in mesenchymal cells
[169]. Furthermore, it has been proposed that the short isoform of Psip1 (PC4
and SF2 interacting protein 1) enhances exon inclusion by recruitment of the
splicing factor SRSF1 to H3K36me3 marks [170].
7.5.5 Alternative Splicing and Nonsense-Mediated Decay
Apart from increasing protein diversity, alternative splicing can also result in
mRNA degradation via the nonsense-mediated mRNA decay (NMD) pathway.
NMD is one of several RNA surveillance mechanisms to ensure the accuracy
of gene expression by degrading mRNAs that contain a premature termination
codon (PTC). At first, it was thought that NMD only removes defective mRNAs
arising from errors in gene expression to avoid accumulation of truncated, non-
functional proteins [180]. Nowadays, it is known that alternative splicing can
introduce PTCs and exploit NMD to achieve quantitative posttranscriptional
regulation [181]. In mammals, a stop codon is recognized as premature if it is
located >50–55 nucleotides upstream of an exon–exon junction, which is marked
by an accumulation of several proteins and called an exon junction complex
(EJC) [182]. According to this rule, one third of the human alternative mRNA
isoforms in the RefSeq database were predicted to be subject to NMD [183].
However, upon siRNA-mediated depletion of the NMD factor UPF1 in HeLa