Báo cáo khoa học: Alternative splicing: role of pseudoexons in human disease and potential

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: [email protected]

(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 ª 2010 ICGEB Trieste (Italy) Journal compilation ª 2010 FEBS 841