Molecular Medicine

, Volume 18, Issue 2, pp 314–319 | Cite as

Biomedical Impact of Splicing Mutations Revealed through Exome Sequencing

  • Bahar Taneri
  • Esra Asilmaz
  • Terry Gaasterland


Splicing is a cellular mechanism, which dictates eukaryotic gene expression by removing the noncoding introns and ligating the coding exons in the form of a messenger RNA molecule. Alternative splicing (AS) adds a major level of complexity to this mechanism and thus to the regulation of gene expression. This widespread cellular phenomenon generates multiple messenger RNA isoforms from a single gene, by utilizing alternative splice sites and promoting different exon-intron inclusions and exclusions. AS greatly increases the coding potential of eukaryotic genomes and hence contributes to the diversity of eukaryotic proteomes. Mutations that lead to disruptions of either constitutive splicing or AS cause several diseases, among which are myotonic dystrophy and cystic fibrosis. Aberrant splicing is also well established in cancer states. Identification of rare novel mutations associated with splice-site recognition, and splicing regulation in general, could provide further insight into genetic mechanisms of rare diseases. Here, disease relevance of aberrant splicing is reviewed, and the new methodological approach of starting from disease phenotype, employing exome sequencing and identifying rare mutations affecting splicing regulation is described. Exome sequencing has emerged as a reliable method for finding sequence variations associated with various disease states. To date, genetic studies using exome sequencing to find disease-causing mutations have focused on the discovery of nonsynonymous single nucleotide polymorphisms that alter amino acids or introduce early stop codons, or on the use of exome sequencing as a means to genotype known single nucleotide polymorphisms. The involvement of splicing mutations in inherited diseases has received little attention and thus likely occurs more frequently than currently estimated. Studies of exome sequencing followed by molecular and bioinformatic analyses have great potential to reveal the high impact of splicing mutations underlying human disease.


  1. 1.
    Wang ET, et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature. 456:470–6.CrossRefGoogle Scholar
  2. 2.
    Cartegni L, Chew SL, Krainer AR. (2002) Listening to silence and understanding nonsense: Exonic mutations that affect splicing. Nat. Rew. Genet. 3:285–98.CrossRefGoogle Scholar
  3. 3.
    Kim E, Goren A, Ast G. (2007) Alternative splicing: current perspectives. BioEssays. 30:38–47.CrossRefGoogle Scholar
  4. 4.
    Darnell RB. (2007) Developing global insight into RNA regulation. Cold Spring Harbor Symposia on Quantitative Biology. LXXI:1–7.Google Scholar
  5. 5.
    Taneri B, Snyder B, Novoradovsky A, Gaasterland T. (2004) Alternative splicing of mouse transcription factors affects their DNA-binding domain architecture and is tissue specific. Gen. Biol. 5:R75.CrossRefGoogle Scholar
  6. 6.
    Nilsen TW, Graveley BR. (2010) Expansion of the eukaryotic proteome by alternative splicing. Nature. 463:457–462.CrossRefGoogle Scholar
  7. 7.
    Black DL. (2003) Mechanisms of alternative pre-mRNA splicing. Annu. Rew. Biochem. 72:291–336.CrossRefGoogle Scholar
  8. 8.
    Marden JH. (2006) Quantitative and evolutionary biology of alternative splicing: how changing the mix of alternative transcripts affects phenotypic plasticity and reaction norms. Heredity. 100:111–20.CrossRefGoogle Scholar
  9. 9.
    Luco RF, Allo M, Schor IE, Kornblihtt AR, Misteli T. (2011) Epigenetics in alternative pre-mRNA splicing. Cell. 144:16–26.CrossRefGoogle Scholar
  10. 10.
    Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 40:1413–15.CrossRefGoogle Scholar
  11. 11.
    Tazi J, Bakkour N, Stamm S. (2008) Alternative splicing and disease. Biochim. Biophys. Acta. 1792:14–25.CrossRefGoogle Scholar
  12. 12.
    McGlincy NJ, Smith CWJ. (2008) Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense? Trends Biochem. Sci. 33:385–93.CrossRefGoogle Scholar
  13. 13.
    Iida K, Akashi H. (2000) A test of translational selection at ‘silent’ sites in the human genome: base composition comparisons in alternatively spliced genes. Gene. 261:93–105.CrossRefGoogle Scholar
  14. 14.
    Parmley JL, Chamary JV, Hurst LD. (2006) Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol. Biol. Evol. 23:301–9.CrossRefGoogle Scholar
  15. 15.
    Ermakova EO, Mal’ko DB, Gelfand MS. (2006) Evolutionary differences between alternative and constitutive protein-coding regions of alternatively spliced genes of Drosophila. Mol. Biophys. 51:515–22.CrossRefGoogle Scholar
  16. 16.
    Caceres JF, Kornblihtt AR. (2002). Alternative splicing: Multiple control mechanisms and involvement in human disease. Trends Gene. 18:186–93.CrossRefGoogle Scholar
  17. 17.
    Venables JP, et al. (2009) Cancer-associated regulation of alternative splicing. Nature Struct. Mol. Biol. 16:670–6.CrossRefGoogle Scholar
  18. 18.
    Sanz DJ, et al. (2010) A high proportion of DNA variant of BRCA1 and BRCA2 is associated with aberrant splicing in breast/ovarian cancer patients. Clin. Cancer Res. 16:1957–67.CrossRefGoogle Scholar
  19. 19.
    Karni R, et al. (2010) The gene encoding the splicing factor SF2/ASF is a proto-oncogene. Nature Struct. Mol. Bio. 14:185–93.CrossRefGoogle Scholar
  20. 20.
    Garcia-Blanco MA, Baraniak AP, Lasda EL. (2004) Alterantive splicing in disease and theraphy. Nat. Biotechnol. 22:535–46.CrossRefGoogle Scholar
  21. 21.
    Wang G-S, Cooper TA. (2007) Splicing in disease: disruption of the splicing code and the decoding machinery. Nature Rev. Genet. 8:749–61.CrossRefGoogle Scholar
  22. 22.
    Biesecker LG. (2010) Exome sequencing makes medical genomics a reality. Nature Gen. 42:13–4.CrossRefGoogle Scholar
  23. 23.
    Lehne B, Lewis CM, Schlitt T. (2011) Exome localization of complex disease association signals. BMC Genom. 12:92.CrossRefGoogle Scholar
  24. 24.
    Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, Shendure J. (2011) Exome sequencing as a tool for Mendelian disease gene discovery. Nature Rev. Gen. 12:745–55.CrossRefGoogle Scholar
  25. 25.
    Singleton AB. (2011) Exome sequencing: a transformative technology. Lancet Neurol. 10:942–6.CrossRefGoogle Scholar
  26. 26.
    Ng SB, et al. (2009) Targeted capture and massively parallel sequencing of twelve human exons. Nature. 461:272–6.CrossRefGoogle Scholar
  27. 27.
    Kryukov GV, Shpunt A, Stamatoyannopoulos JA, Sunyaev SR. (2009). Power of deep, all-exon resequencing for discovery of human trait genes. PNAS. 106:3871–6.CrossRefGoogle Scholar
  28. 28.
    Shi Y, et al. (2011). Exome sequencing identifies ZNF644 mutations in high myopia. PLOS Gen. 7:e1002084.CrossRefGoogle Scholar
  29. 29.
    Kumar A, et al. (2011). Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers. PNAS. 108:17087–92.CrossRefGoogle Scholar
  30. 30.
    Ng SB, et al. (2010) Exome sequencing identifies the cause of a mendelian disorder. Nature Gen. 42:30–5.CrossRefGoogle Scholar
  31. 31.
    Ku CS, Naidoo N, Pawitan Y. (2011) Revisiting Mendelian disorders through exome sequencing. Human Gen. 129:351–70.CrossRefGoogle Scholar
  32. 32.
    Cirulli ET, et al. (2010) Screening the human exome: a comparison of whole genome and whole transcriptome sequencing. Gen. Biol. 11:R57.CrossRefGoogle Scholar
  33. 33.
    Montgomery SB, et al. (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature. 464:773–9.CrossRefGoogle Scholar
  34. 34.
    Choi M, et al. (2009) Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. PNAS. 106:19096–101.CrossRefGoogle Scholar
  35. 35.
    Montenegro G, et al. (2011) Exome sequencing allows for rapid gene identification in a Charcot-Marie-Tooth family. Ann. Neurol. 69:464–70.CrossRefGoogle Scholar
  36. 36.
    Caliskan M, et al. (2011) Exome sequencing reveals a novel mutation for autosomal recessive nonsyndromic mental retardation in the TECR gene on chromosome 19p13. Hum. Mol. Genet. 20:1285–9.CrossRefGoogle Scholar
  37. 37.
    Worthey EA, et al. (2011) Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet. Med. 13:255–62.CrossRefGoogle Scholar
  38. 38.
    Johnson JO, et al. (2010). Exome sequencing reveals VCP mutations as a cause of familial ALS. Neuron. 68:857–64.CrossRefGoogle Scholar
  39. 39.
    Wang JL, et al. (2010). TGM6 identified as a novel causative gene of spinocerebellar ataxias using exome sequencing. Brain. 133:3510–8.CrossRefGoogle Scholar
  40. 40.
    Musunuru K, et al. (2010) Exome sequencing, ANGPTL3 mutations, and familial combined hypolipidemia. N. Eng. J. Med. 363:2220–7.CrossRefGoogle Scholar
  41. 41.
    Johnson JO, Gibbs JR, van Maldergern L, Houlden H, Singleton AB. (2010) Exome sequencing in Brown-Vialetto-van Laere Syndrome. Am. J. Hum. Genet. 87:567–9.CrossRefGoogle Scholar
  42. 42.
    Simpson MA, et al. (2011) Mutations in NOTCH2 cause Hajdu-Cheney Syndrome, a disorder of severe and progressive bone loss. Nat. Genet. 43:303–5.CrossRefGoogle Scholar
  43. 43.
    Becker J, et al. (2011). Exome sequencing indentifies truncating mutations in human SERPINF1 in autosomal-recessive Osteogenesis Imperfecta. Am. J. Hum. Genet. 88:362–71.CrossRefGoogle Scholar
  44. 44.
    ElSharawy A, et al. (2009) Systematic evaluation of the effect of common SNPs on pre-mRNA splicing. Hum. Mutat. 30:625–32.CrossRefGoogle Scholar
  45. 45.
    Krawczak M, et al. (2007) Single base-pair substitutions in exon-intron junctions of human genes: nature, distribution, and consequences for mRNA splicing. Human Mutat. 28:150–8.CrossRefGoogle Scholar
  46. 46.
    Byun M, et al. (2010) Whole exome sequencing-based discovery of STIM1 deficiency in a child with fatal classic Kaposi sarcoma. J. Exp. Med. 207:2307–12.CrossRefGoogle Scholar
  47. 47.
    Gilissen C, et al. (2010) Exome sequencing identifies WDR35 variants involved in Sensenbrenner syndrome. Am. J. Hum. Genet. 87:418–23.CrossRefGoogle Scholar

Copyright information

© The Author(s) 2012

Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, and provide a link to the Creative Commons license. You do not have permission under this license to share adapted material derived from this article or parts of it.

The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.

To view a copy of this license, visit (

Authors and Affiliations

  • Bahar Taneri
    • 1
    • 2
  • Esra Asilmaz
    • 3
  • Terry Gaasterland
    • 4
  1. 1.Institute of Public Health Genomics, Department of Genetics and Cell Biology, Research Institutes CAPHRI and GROW, Faculty of Health, Medicine and Life SciencesMaastricht UniversityMaastrichtThe Netherlands
  2. 2.Department of Biological Sciences, Faculty of Arts and SciencesEastern Mediterranean UniversityFamagusta, North CyprusTurkey
  3. 3.King’s College LondonGuy’s and St. Thomas’ Hospital NHS Foundation TrustLondonUK
  4. 4.University of California San Diego, Scripps Genome CenterScripps Institution of OceanographyLa JollaUSA

Personalised recommendations