Báo cáo khoa học: Alternative splicing: global insights potx

MINIREVIEW

Alternative splicing: global insights

Martina Hallegger*, Miriam Llorian* and Christopher W. J. Smith

Department of Biochemistry, University of Cambridge, UK

Introduction

Alternative splicing allows individual genes to produce

two or more variant mRNAs, which in many cases

encode functionally distinct proteins. With the progres￾sive generation of ever larger sequence datasets, the

proportion of multi-exon human genes that are known

to be alternatively spliced has expanded to 92–94%, of

which 85% have a minor isoform frequency of at least

15% [1,2]. Despite some debate about the extent to

which all of this alternative splicing is functionally

important [3], there is no disputing that alternative

splicing is a major contributor to the diverse repertoire

of transcriptomes and proteomes. Its importance is

underscored by the fact that misregulated alternative

splicing can lead to human disease [4,5]. As part of the

overarching effort to understand how the information

encrypted within genomes is used to generate fully

functional organisms, it is therefore necessary to deci￾pher the ‘RNA codes’ underlying regulated patterns of

alternative splicing.

Traditionally, research on alternative splicing regula￾tion focused on the study of minigene models in vitro

or in vivo. The picture that emerged is that regulation

of alternative splicing occurs via the action of numer￾ous RNA binding proteins expressed at variable levels

between tissues. These activators and repressors often

mediate their effects by binding to enhancer and silen￾cer elements within or surrounding alternatively spliced

exons (reviewed in [6]). Although much progress has

been made using model systems, a drawback is that

even when a model alternative splicing event has been

thoroughly characterized it is not immediately obvi￾ous which of its features are generally shared by

Keywords

alternative splicing; microarray; RNA-Seq

Correspondence

C. W. J. Smith, Department of

Biochemistry, University of Cambridge, 80

Tennis Court Road, Cambridge CB2 1GA,

UK

Fax: +44 1223 766002

Tel: +44 1223 333655

E-mail: [email protected]

*These authors contributed equally to this

work

(Received 26 August 2009, accepted

22 October 2009)

doi:10.1111/j.1742-4658.2009.07521.x

Following the original reports of pre-mRNA splicing in 1977, it was

quickly realized that splicing together of different combinations of splice

sites – alternative splicing– allows individual genes to generate more than

one mRNA isoform. The full extent of alternative splicing only began to

be revealed once large-scale genome and transcriptome sequencing projects

began, rapidly revealing that alternative splicing is the rule rather than the

exception. Recent technical innovations have facilitated the investigation of

alternative splicing at a global scale. Splice-sensitive microarray platforms

and deep sequencing allow quantitative profiling of very large numbers of

alternative splicing events, whereas global analysis of the targets of RNA

binding proteins reveals the regulatory networks involved in post-transcrip￾tional gene control. Combined with sophisticated computational analysis,

these new approaches are beginning to reveal the so-called ‘RNA code’

that underlies tissue and developmentally regulated alternative splicing, and

that can be disrupted by disease-causing mutations.

Abbreviations

CLIP, UV cross-linking and immunoprecipitation; CELF, CUGBP and ETR3 like family (of RNA binding proteins); CUGBP, CUG binding

protein; miRNA, micro-RNA; RNP, ribonucleoprotein; MBNL, muscleblind like; PTB, polypyrimidine tract binding protein; SELEX, selective

evolution of ligands by exponential enrichment; SR protein, serine-arginine rich protein.

856 FEBS Journal 277 (2010) 856–866 ª 2010 The Authors Journal compilation ª 2010 FEBS