MINIREVIEW
Alternative splicing: role of pseudoexons in human disease
and potential therapeutic strategies
Ashish Dhir and Emanuele Buratti
International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
Introduction
Towards the end of the 1970s, in the beginning of
pre-mRNA splicing research [1,2], defining exons and
introns was essentially based on observing the final
composition of the mature mRNA molecule. In 1978,
any sequence that was included in a mature mRNA
became tagged as an ‘exon’, whereas all the intervening
genomic sequences that were left out during the splic-
ing process became defined as ‘introns’ [3]. However,
this way of thinking did not explain what makes an
exon an exon or an intron an intron. The discovery of
the basic splice site consensus sequences during the
same years [4,5], and later on of enhancer and repres-
sor elements, has taken us a long way in the direction
of discovering exon- and intron-definition complexes
[6–8]. Nowadays, the splicing signals that define ex-
ons ⁄introns have been greatly aided by basic research,
bioinformatic approaches and advanced sequencing
tools [9,10]. In this regard, we certainly know much
more about splicing regulation than we did 20 years
ago. Considering that several reviews have been writ-
ten recently on the subject, the reader is referred to
them for further information on the latest discoveries
[11–14]. Most important, in this respect, have been the
initial observations that in alternative splicing pro-
cesses the same nucleotide sequence could be defined
by the spliceosome as an intron or an exon in response
to specific signals [15,16]. It is now clear that these
kinds of decision (What is an exon? What is an
intron?) are of paramount importance in explaining
genome complexity and evolutionary pathways
[17–20]. However, the sum of this new knowledge does
not necessarily mean that we are near the goal of
Keywords
alternative splicing; antisense
oligonucleotides; mRNA; pseudoexons;
splicing therapy
Correspondence
E. Buratti, Padriciano 99, 34012 Trieste, Italy
Fax: +39 040 226555
Tel: +39 040 3757316
E-mail: buratti@icgeb.org
(Received 26 August 2009, revised 15
October 2009, accepted 5 November 2009)
doi:10.1111/j.1742-4658.2009.07520.x
What makes a nucleotide sequence an exon (or an intron) is a question
that still lacks a satisfactory answer. Indeed, most eukaryotic genes are full
of sequences that look like perfect exons, but which are nonetheless
ignored by the splicing machinery (hence the name ‘pseudoexons’). The
existence of these pseudoexons has been known since the earliest days of
splicing research, but until recently the tendency has been to view them as
an interesting, but rather rare, curiosity. In recent years, however, the
importance of pseudoexons in regulating splicing processes has been stea-
dily revalued. Even more importantly, clinically oriented screening studies
that search for splicing mutations are beginning to uncover a situation
where aberrant pseudoexon inclusion as a cause of human disease is more
frequent than previously thought. Here we aim to provide a review of the
mechanisms that lead to pseudoexon activation in human genes and how
the various cis- and trans-acting cellular factors regulate their inclusion.
Moreover, we list the potential therapeutic approaches that are being tested
with the aim of inhibiting their inclusion in the final mRNA molecules.
Abbreviations
3¢ss, 3¢splice site; 5¢ss, 5¢splice site; AON, antisense oligonucleotide; LINE, long interspersed elements; NMD, nonsense-mediated decay;
PTB, polypyrimidine tract binding protein; SINE, short interspersed elements.
FEBS Journal 277 (2010) 841–855 ª2010 ICGEB Trieste (Italy) Journal compilation ª2010 FEBS 841
