Alternative Splicing: Role of Pseudoexons in Human Genetic Disease

Abstract

In the pre‐mRNA splicing field the term ‘pseudoexons’ has been introduced to describe all those sequences usually localised deep in intronic regions that resemble real exons in appearance but are ignored by the spliceosomal machinery. Although we now know that some of these sequences are important for regulatory purposes it is also true that aberrant pseudoexon activation is increasingly described as one of the major causes of human disease. Several recent studies on pseudoexon inclusion–exclusion mechanisms have allowed researchers to gain further insight with regards to the mechanism that the spliceosome uses to discriminate between true and false exons during the normal splicing process. Most importantly, the newly gained knowledge regarding pseudoexon biology has been extensively exploited to devise novel therapeutic strategies aimed at inhibiting their inclusion in human patients.

Key Concepts:

  • Pseudoexons (also known as ‘false exons’) are very abundant in all eukaryotic genes, especially those harbouring long intronic sequences.

  • In normal conditions, pseudoexon inclusion in mature mRNAs is efficiently inhibited.

  • Mutational events that activate aberrant pseudoexon inclusion are a common source of disease‐causing mutations in humans.

  • A variety of novel therapeutic approaches principally based on antisense oligonucleotide (AON) technology is currently being developed to inhibit their inclusion in human patients.

Keywords: pseudoexons; exons; introns; pre‐mRNA splicing; genetic disease; gene therapy

Figure 1.

Schematic representation of the basic pre‐mRNA splicing process.

Figure 2.

Possible origins and consequences of aberrant pseudoexon insertion in the normal splicing process.

Figure 3.

Use of AON technology to inhibit pseudoexon inclusion in the mature mRNA molecule.

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References

Aartsma‐Rus A and van Ommen GJ (2007) Antisense‐mediated exon skipping: a versatile tool with therapeutic and research applications. RNA 13: 1609–1624.

Alves S, Mangas M, Prata MJ et al. (2006) Molecular characterization of Portuguese patients with mucopolysaccharidosis type II shows evidence that the IDS gene is prone to splicing mutations. Journal of Inherited Metabolic Disease 29: 743–754.

Baralle D, Lucassen A and Buratti E (2009) Missed threads. The impact of pre‐mRNA splicing defects on clinical practice. EMBO Reports 10: 810–816.

Berget SM (1995) Exon recognition in vertebrate splicing. Journal of Biological Chemistry 270: 2411–2414.

Biamonti G and Caceres JF (2009) Cellular stress and RNA splicing. Trends in Biochemical Sciences 34: 146–153.

Black DL (2003) Mechanisms of alternative pre‐messenger RNA splicing. Annual Review of Biochemistry 72: 291–336.

Blaustein M, Pelisch F and Srebrow A (2007) Signals, pathways and splicing regulation. International Journal of Biochemistry & Cell Biology 39: 2031–2048.

Breathnach R, Benoist C, O'Hare K, Gannon F and Chambon P (1978) Ovalbumin gene: evidence for a leader sequence in mRNA and DNA sequences at the exon–intron boundaries. Proceedings of the National Academy of Sciences of the USA 75: 4853–4857.

Buratti E and Baralle D (2010) Novel roles of U1 snRNP in alternative splicing regulation. RNA Biology 7: 412–419.

Buratti E and Baralle FE (2004) Influence of RNA secondary structure on the pre‐mRNA splicing process. Molecular and Cellular Biology 24: 10505–10514.

Buratti E, Chivers M, Kralovicova J et al (2007a) Aberrant 5′ splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Nucleic Acids Research 35: 4250–4263.

Buratti E, Dhir A, Lewandowska MA and Baralle FE (2007b) RNA structure is a key regulatory element in pathological ATM and CFTR pseudoexon inclusion events. Nucleic Acids Research 35: 4369–4383.

Cartegni L, Chew SL and Krainer AR (2002) Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nature Reviews Genetics 3: 285–298.

Catterall JF, O'Malley BW, Robertson MA et al. (1978) Nucleotide sequence homology at 12 intron–exon junctions in the chick ovalbumin gene. Nature 275: 510–513.

Chasin LA (2007) Searching for splicing motifs. Advances in Experimental Medicine and Biology 623: 85–106.

Chen JM, Ferec C and Cooper DN (2010) Revealing the human mutome. Clinical Genetics 78: 310–320.

Chen X, Truong TT, Weaver J et al. (2006) Intronic alterations in BRCA1 and BRCA2: effect on mRNA splicing fidelity and expression. Hum Mutatation 27: 427–435.

Cooper DN, Chen JM, Ball EV et al. (2010) Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics. Hum Mutation 31: 631–655.

Crooke ST (2004) Antisense strategies. Current Molecular Medicine 4: 465–487.

Davis RL, Homer VM, George PM and Brennan SO (2009) A deep intronic mutation in FGB creates a consensus exonic splicing enhancer motif that results in afibrinogenemia caused by aberrant mRNA splicing, which can be corrected in vitro with antisense oligonucleotide treatment. Hum Mutation 30: 221–227.

Dhir A and Buratti E (2010) Alternative splicing: role of pseudoexons in human disease and potential therapeutic strategies. FEBS Journal 277: 841–855.

Dominski Z and Kole R (1993) Restoration of correct splicing in thalassemic pre‐mRNA by antisense oligonucleotides. Proceedings of the National Academy of Sciences of the USA 90: 8673–8677.

Faa V, Incani F, Meloni A et al. (2009) Characterization of a disease‐associated mutation affecting a putative splicing regulatory element in intron 6b of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Journal of Biological Chemistry 284: 30024–30031.

Fairbrother WG and Chasin LA (2000) Human genomic sequences that inhibit splicing. Molecular and Cellular Biology 20: 6816–6825.

Friedman KJ, Kole J, Cohn JA et al. (1999) Correction of aberrant splicing of the cystic fibrosis transmembrane conductance regulator (CFTR) gene by antisense oligonucleotides. Journal of Biological Chemistry 274: 36193–36199.

Grellscheid SN and Smith CW (2006) An apparent pseudo‐exon acts both as an alternative exon that leads to nonsense‐mediated decay and as a zero‐length exon. Molecular and Cellular Biology 26: 2237–2246.

Gurvich OL, Tuohy TM, Howard MT et al. (2008) DMD pseudoexon mutations: splicing efficiency, phenotype, and potential therapy. Annals of Neurology 63: 81–89.

Hammond SM and Wood MJ (2011) Genetic therapies for RNA mis‐splicing diseases. Trends in Genetics 27: 196–205.

Hertel KJ (2008) Combinatorial control of exon recognition. Journal of Biological Chemistry 283: 1211–1215.

Llorian M and Smith CW (2011) Decoding muscle alternative splicing. Current Opinion in Genetics & Development (in press).

Lucien N, Chiaroni J, Cartron JP and Bailly P (2002) Partial deletion in the JK locus causing a Jk(null) phenotype. Blood 99: 1079–1081.

Luco RF and Misteli T (2011) More than a splicing code: integrating the role of RNA, chromatin and non‐coding RNA in alternative splicing regulation. Current Opinion in Genetics & Development (in press).

Madden HR, Fletcher S, Davis MR and Wilton SD (2009) Characterization of a complex Duchenne muscular dystrophy‐causing dystrophin gene inversion and restoration of the reading frame by induced exon skipping. Hum Mutation 30: 22–28.

Pagani F, Buratti E, Stuani C et al. (2002) A new type of mutation causes a splicing defect in ATM. Nature Genetics 30: 426–429.

Pros E, Fernandez‐Rodriguez J, Canet B et al. (2009) Antisense therapeutics for neurofibromatosis type 1 caused by deep intronic mutations. Human Mutation 30: 454–462.

Raponi M, Buratti E, Llorian M et al. (2008) Polypyrimidine tract binding protein regulates alternative splicing of an aberrant pseudoexon in NF1. FEBS Journal 275: 6101–6108.

Schwartz S, Gal‐Mark N, Kfir N et al. (2009) Alu exonization events reveal features required for precise recognition of exons by the splicing machinery. PLoS Computational Biology 5: e1000300.

Sharma S, Kohlstaedt LA, Damianov A, Rio DC and Black DL (2008) Polypyrimidine tract binding protein controls the transition from exon definition to an intron defined spliceosome. Nature Structural & Molecular Biology 15: 183–191.

Sierakowska H, Sambade MJ, Agrawal S and Kole R (1996) Repair of thalassemic human beta‐globin mRNA in mammalian cells by antisense oligonucleotides. Proceedings of the National Academy of Sciences of the USA 93: 12840–12844.

Sironi M, Menozzi G, Riva L et al. (2004) Silencer elements as possible inhibitors of pseudoexon splicing. Nucleic Acids Research 32: 1783–1791.

Sperling J, Azubel M and Sperling R (2008) Structure and function of the pre‐mRNA splicing machine. Structure 16: 1605–1615.

Sun H and Chasin LA (2000) Multiple splicing defects in an intronic false exon. Molecular and Cellular Biology 20: 6414–6425.

Wang Z and Burge CB (2008) Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA 14: 802–813.

Witten JT and Ule J (2011) Understanding splicing regulation through RNA splicing maps. Trends in Genetics 27: 89–97.

Yamaguchi H, Fujimoto T, Nakamura S et al. (2010) Aberrant splicing of the milk fat globule‐EGF factor 8 (MFG‐E8) gene in human systemic lupus erythematosus. European Journal of Immunology 40: 1778–1785.

Zhang MQ (1998) Statistical features of human exons and their flanking regions. Human Molecular Genetics 7: 919–932.

Zhang XH and Chasin LA (2004) Computational definition of sequence motifs governing constitutive exon splicing. Genes & Development 18: 1241–1250.

Zhang XH, Leslie CS and Chasin LA (2005) Dichotomous splicing signals in exon flanks. Genome Research 15: 768–779.

Further Reading

Buratti E, Baralle M and Baralle FE (2006) Defective splicing, disease and therapy: searching for master checkpoints in exon definition. Nucleic Acids Research 34: 3494–3510.

Stamm S, Ben‐Ari S, Rafalska I et al. (2005) Function of alternative splicing. Gene 344: 1–20.

Stamm S, Smith CW and Lurhmann R (eds) (2011) Alternative pre‐mRNA Splicing: Theory and Protocols. Weinheim: Wiley‐VCH.

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How to Cite close
Emanuele, Buratti(Sep 2011) Alternative Splicing: Role of Pseudoexons in Human Genetic Disease. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0023579]