Alternative Splicing and Human Disease

Abstract

Almost all human protein coding genes undergo alternative splicing, and an increasing number of diseases is associated with the selection of ‘wrong’ splice sites. Alternative missplicing can be caused by deoxyribonucleic acid point mutations, changes in repetitive sequences or alterations in proteins that regulate splicing. The effect of these mutations can be evaluated by bioinformatic means, but these predictions need to be verified experimentally. With the exception of premature stop codons that are introduced by aberrantly spliced exons, the mechanism of pathological exon usage that leads to a disease is generally poorly understood. A pathological change in the activity of splicing factors typically results in numerous small changes in exon usage. Numerous screening efforts identified oligonucleotides and small molecular weight substances that can be tested as therapeutic approaches for diseases caused by missplicing.

Key Concepts:

  • Alternative splice site selection is regulated by combinatorial control through a network of protein–protein, protein–RNA and RNA–RNA interactions.

  • Mutations in the splice sites, exonic and intronic sequences lead to aberrant exon usage.

  • Mutations can cause exon skipping, a change in the degree of exon usage or activate sequences on the pre‐mRNA to become a new exon.

  • Synonymous mutations in exons can cause their aberrant usage, which can be a disease mechanism.

  • A pathological change in the activity of splicing regulatory proteins results in numerous, individually small changes of alternative exon usage.

  • Aberrant exon usage can be targeted by rationale therapies, several oligonucleotide‐based treatments are tested in clinical trials and small molecules were identified that change splice site selection by high‐throughput screens.

Keywords: alternative splicing; splicing regulatory elements; disease causing mutations; exon enhancer; exon silencer

Figure 1.

Schematic overview of disease mechanisms.

close

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.

Aartsma‐Rus A and van Ommen GJ (2010) Progress in therapeutic antisense applications for neuromuscular disorders. European Journal of Human Genetics 18: 146–153.

Abes R, Arzumanov A, Moulton H et al. (2008) Arginine‐rich cell penetrating peptides: design, structure‐activity, and applications to alter pre‐mRNA splicing by steric‐block oligonucleotides. Journal of Peptide Science 14: 455–460.

Andreadis A (2006) Misregulation of tau alternative splicing in neurodegeneration and dementia. Progress in Molecular and Subcellular Biology 44: 89–107.

Asparuhova MB, Marti G, Liu S et al. (2007) Inhibition of HIV‐1 multiplication by a modified U7 snRNA inducing Tat and Rev exon skipping. Journal of Gene Medicine 9: 323–334.

Boon KL, Grainger RJ, Ehsani P et al. (2007) prp8 mutations that cause human retinitis pigmentosa lead to a U5 snRNP maturation defect in yeast. Nature Structural & Molecular Biology 14: 1077–1083.

Buratti E, Chivers M, Kralovicova J et al. (2007) 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.

Burghes AH and Beattie CE (2009) Spinal muscular atrophy: why do low levels of survival motor neuron protein make motor neurons sick? Nature Reviews. Neuroscience 10: 597–609.

Chen M and Manley JL (2009) Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nature Reviews. Molecular Cell Biology 10: 741–754.

Cooper TA (2005) Use of minigene systems to dissect alternative splicing elements. Methods 37: 331–340.

Cooper TA and Mattox W (1997) The regulation of splice‐site selection, and its role in human disease. American Journal of Human Genetics 61: 259–266.

Dawson HN, Cantillana V, Chen L and Vitek MP (2007) The tau N279K exon 10 splicing mutation recapitulates frontotemporal dementia and parkinsonism linked to chromosome 17 tauopathy in a mouse model. Journal of Neuroscience 27: 9155–9168.

Desmet FO, Hamroun D, Lalande M et al. (2009) Human splicing finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Research 37: e67.

Divina P, Kvitkovicova A, Buratti E and Vorechovsky I (2009) Ab initio prediction of mutation‐induced cryptic splice‐site activation and exon skipping. European Journal of Human Genetics 17: 759–765.

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.

Ghigna C, Giordano S, Shen H et al. (2005) Cell motility is controlled by SF2/ASF through alternative splicing of the Ron protooncogene. Molecular Cell 20: 881–890.

Hasler J, Samuelsson T and Strub K (2007) Useful ‘junk’: Alu RNAs in the human transcriptome. Cellular and Molecular Life Sciences 64: 1793–1800.

Huang HY, Chien CH, Jen KH and Huang HD (2006) RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Research 34: W429–W434.

Kalbfuss B, Mabon SA and Misteli T (2001) Correction of alternative splicing of tau in frontotemporal dementia and parkinsonism linked to chromosome 17. Journal of Biological Chemistry 276: 42986–42993.

Karni R, de Stanchina E, Lowe SW et al. (2007) The gene encoding the splicing factor SF2/ASF is a proto‐oncogene. Nature Structural & Molecular Biology 14: 185–193.

Kishore S, Khanna A and Stamm S (2008) Rapid generation of splicing reporters with pSpliceExpress. Gene 427: 104–110.

Kishore S, Khanna A, Zhang Z et al. (2010) The snoRNA MBII‐52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. Human Molecular Genetics 19: 1153–1164.

Kuyumcu‐Martinez NM, Wang GS and Cooper TA (2007) Increased steady‐state levels of CUGBP1 in myotonic dystrophy 1 are due to PKC‐mediated hyperphosphorylation. Molecular Cell 28: 68–78.

Lacerra G, Sierakowska H, Carestia C et al. (2000) Restoration of hemoglobin A synthesis in erythroid cells from peripheral blood of thalassemic patients. Proceedings of the National Academy of Sciences of the USA 97: 9591–9596.

Lebleu B, Moulton HM, Abes R et al. (2008) Cell penetrating peptide conjugates of steric block oligonucleotides. Advanced Drug Delivery Reviews 60: 517–529.

Lev‐Maor G, Sorek R, Shomron N and Ast G (2003) The birth of an alternatively spliced exon: 3′ splice‐site selection in Alu exons. Science 300: 1288–1291.

Licatalosi DD and Darnell RB (2010) RNA processing and its regulation: global insights into biological networks. Nature Reviews. Genetics 11: 75–87.

Liu S, Asparuhova M, Brondani V et al. (2004) Inhibition of HIV‐1 multiplication by antisense U7 snRNAs and siRNAs targeting cyclophilin A. Nucleic Acids Research 32: 3752–3759.

Lopez‐Bigas N, Audita B, Ouzounis C, Parra G and Guigo R (2005) Are splicing mutations the most frequent cause of hereditary disease? FEBS Letters 579: 1900–1903.

Lunn MR and Wang CH (2008) Spinal muscular atrophy. Lancet 371: 2120–2133.

Mann CJ, Honeyman K, Cheng AJ et al. (2001) Antisense‐induced exon skipping and synthesis of dystrophin in the mdx mouse. Proceedings of the National Academy of Sciences of the USA 98: 42–47.

Meyer K, Marquis J, Trub J et al. (2009) Rescue of a severe mouse model for spinal muscular atrophy by U7 snRNA‐mediated splicing modulation. Human Molecular Genetics 18: 546–555.

van Ommen GJ, van Deutekom J and Aartsma‐Rus A (2008) The therapeutic potential of antisense‐mediated exon skipping. Current Opinion in Molecular Therapy 10: 140–149.

Pan Q, Shai O, Lee LJ, Frey BJ and Blencowe BJ (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high‐throughput sequencing. Nature Genetics 40: 1413–1415.

Ranum LP and Cooper TA (2006) RNA‐mediated neuromuscular disorders. Annual Review of Neuroscience 29: 259–277.

Raponi M, Upadhyaya M and Baralle D (2006) Functional splicing assay shows a pathogenic intronic mutation in neurofibromatosis type 1 (NF1) due to intronic sequence exonization. Human Mutation 27: 294–295.

Romero PR, Zaidi S, Fang YY et al. (2006) Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms. Proceedings of the National Academy of Sciences of the USA 103: 8390–8395.

Sazani P and Kole R (2003) Therapeutic potential of antisense oligonucleotides as modulators of alternative splicing. Journal of Clinical Investigation 112: 481–486.

Scaffidi P and Misteli T (2005) Reversal of the cellular phenotype in the premature aging disease Hutchinson‐Gilford progeria syndrome. Nature Medicine 11: 440–445.

Schwartz S, Hall E and Ast G (2009) SROOGLE: webserver for integrative, user‐friendly visualization of splicing signals. Nucleic Acids Research 37: W189–W192.

Singh NN, Shishimorova M, Cao LC, Gangwani L and Singh RN (2009) A short antisense oligonucleotide masking a unique intronic motif prevents skipping of a critical exon in spinal muscular atrophy. RNA Biology 6: 341–350.

Singh R N (2007) Evolving concepts on human SMN pre‐mRNA splicing. RNA Biology 4: 7–10.

Smith CW and Valcarcel J (2000) Alternative pre‐mRNA splicing: the logic of combinatorial control. Trends in Biochemical Sciences 25: 381–388.

Smith PJ, Zhang C, Wang J et al. (2006) An increased specificity score matrix for the prediction of SF2/ASF‐specific exonic splicing enhancers. Human Molecular Genetics 15: 2490–2508.

Sorek R, Ast G and Graur D (2002) Alu‐containing exons are alternatively spliced. Genome Research 12: 1060–1067.

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

Stoilov P, Lin CH, Damoiseaux R, Nikolic J and Black DL (2008) A high‐throughput screening strategy identifies cardiotonic steroids as alternative splicing modulators. Proceedings of the National Academy of Sciences of the USA 105: 11218–11223.

Sumanasekera C, Watt DS and Stamm S (2008) Substances that can change alternative splice‐site selection. Biochemical Society Transactions 36: 483–490.

Tang Y, Novoyatleva T, Benderska N et al. (2005) Analysis of alternative splicing in vivo using minigenes. In: Hartmann RK, Bindereif A, Schön A and Westhof E (eds) Handbook of RNA Biochemistry, pp. 755–782. Weinheim, Germany: Wiley‐VCH.

Varon R, Gooding R, Steglich C et al. (2003) Partial deficiency of the C‐terminal‐domain phosphatase of RNA polymerase II is associated with congenital cataracts facial dysmorphism neuropathy syndrome. Nature Genetics 35: 185–189.

Vithana EN, Abu‐Safieh L, Allen MJ et al. (2001) A human homolog of yeast pre‐mRNA splicing gene, PRP31, underlies autosomal dominant retinitis pigmentosa on chromosome 19q13.4 (RP11). Molecular Cell 8: 375–381.

Vorechovsky I (2006) Aberrant 3′ splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Nucleic Acids Research 34: 4630–4641.

Watermann DO, Tang Y, zur Hausen A et al. (2006) Splicing factor Tra2‐β1 is specifically induced in breast cancer and regulates alternative splicing of the CD44 gene. Cancer Research 66: 4774–4780.

Wilkie SE, Vaclavik V, Wu H et al. (2008) Disease mechanism for retinitis pigmentosa (RP11) caused by missense mutations in the splicing factor gene PRPF31. Molecular Vision 14: 683–690.

Zhang Z, Lotti F, Dittmar K et al. (2008) SMN deficiency causes tissue‐specific perturbations in the repertoire of snRNAs and widespread defects in splicing. Cell 133: 585–600.

Further Reading

Cooper TA, Wan L and Dreyfuss G (2009) RNA and disease. Cell 136: 777–793.

Jeanteur P (ed.) (2006) Alternative Splicing and Disease, Progress in Molecular and Subcelluar Biology. Berlin, Heidelberg: Springer.

Tazi J, Bakkour N and Stamm S (2009) Alternative splicing and disease. Biochimica Biophysica Acta 1792: 14–26.

Web Links

www.eurasnet.info

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Stamm, Stefan(Mar 2011) Alternative Splicing and Human Disease. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0021435]