Skip to main content

Analysis of Alternative Splicing with Microarrays

  • Chapter
Book cover Bioinformatics for Systems Biology

Abstract

Alternative splicing is one of the most important post-transcriptional processing steps that enhances genomic information by generating multiple RNA isoforms from a single gene. Recently, microarrays have been developed that can detect changes in splice site selection. Currently, the biggest challenge for the analysis of alternative splicing with microarrays is the bioinformatics analysis of array data and their low reproducibility by RT-PCR. Despite these problems, microarrays revealed an unexpected number of expressed RNAs, showed changes of alternative splicing in diseases and indicated that a splicing factor regulates a biologically meaningful set of genes.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Suggested Reading

Alternative splicing and gene expression

  1. Kampa, D., Cheng, J., Kapranov, P., Yamanaka, M., Brubaker, S., Cawley, S., Drenkow, J., Piccolboni, A., Bekiranov, S., Helt, G. et al. (2004) Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res, 14, 331–342.

    Article  CAS  PubMed  Google Scholar 

  2. Stamm, S., Ben-Ari, S., Rafalska, I., Tang, Y., Zhang, Z., Toiber, D., Thanaraj, T.A. and Soreq, H. (2005) Function of alternative splicing. Gene, 344C, 1–20.

    Article  Google Scholar 

  3. Hillman, R.T., Green, R.E. and Brenner, S.E. (2004) An unappreciated role for RNA surveillance. Genome Biol, 5, R8.

    Article  PubMed  Google Scholar 

  4. Pan, Q., Saltzman, A.L., Kim, Y.K., Misquitta, C., Shai, O., Maquat, L.E., Frey, B.J. and Blencowe, B.J. (2006) Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression. Genes Dev, 20, 153–158.

    Article  CAS  PubMed  Google Scholar 

  5. Faustino, N.A. and Cooper, T.A. (2003) Pre-mRNA splicing and human disease. Genes Dev, 17, 419–437.

    Article  CAS  PubMed  Google Scholar 

  6. Stoilov, P., Meshorer, E., Gencheva, M., Glick, D., Soreq, H. and Stamm, S. (2002) Defects in pre-mRNA processing as causes of and predisposition to diseases. DNA Cell Biol, 21, 803–818.

    Article  CAS  PubMed  Google Scholar 

  7. Blencowe, B.J. (2006) Alternative splicing: new insights from global analyses. Cell, 126, 37–47.

    Article  CAS  PubMed  Google Scholar 

  8. Bracco, L. and Kearsey, J. (2003) The relevance of alternative RNA splicing to pharmacogenomics. Trends Biotechnol, 21, 346–353.

    Article  CAS  PubMed  Google Scholar 

  9. Hanioka, N., Kimura, S., Meyer, U.A. and Gonzalez, F.J. (1990) The human CYP2D locus associated with a common genetic defect in drug oxidation: a G1934—-A base change in intron 3 of a mutant CYP2D6 allele results in an aberrant 3' splice recognition site. Am J Hum Genet, 47, 994–1001.

    CAS  PubMed  Google Scholar 

  10. Chandrasekharan, N.V., Dai, H., Roos, K.L., Evanson, N.K., Tomsik, J., Elton, T.S. and Simmons, D.L. (2002) COX-3, a cyclooxygenase-1 variant inhibited by acetaminophen and other analgesic/antipyretic drugs: cloning, structure, and expression. Proc Natl Acad Sci U S A., 99, 13926–13931.

    Article  CAS  PubMed  Google Scholar 

  11. Li, H.R., Wang-Rodriguez, J., Nair, T.M., Yeakley, J.M., Kwon, Y.S., Bibikova, M., Zheng, C., Zhou, L., Zhang, K., Downs, T. et al. (2006) Two-dimensional transcriptome profiling: identification of messenger RNA isoform signatures in prostate cancer from archived paraffin-embedded cancer specimens. Cancer Res, 66, 4079–4088.

    Article  CAS  PubMed  Google Scholar 

  12. Srebrow, A. and Kornblihtt, A.R. (2006) The connection between splicing and cancer. J Cell Sci, 119, 2635–2641.

    Article  CAS  PubMed  Google Scholar 

  13. Xing, Y. and Lee, C. (2005) Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences. Proc Natl Acad Sci U S A, 102, 13526–13531.

    Article  CAS  PubMed  Google Scholar 

  14. Johnson, J.M., Castle, J., Garrett-Engele, P., Kan, Z., Loerch, P.M., Armour, C.D., Santos, R., Schadt, E.E., Stoughton, R. and Shoemaker, D.D. (2003) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science, 302, 2141–2144.

    Article  CAS  PubMed  Google Scholar 

  15. Stamm, S., Riethoven, J.J., Le Texier, V., Gopalakrishnan, C., Kumanduri, V., Tang, Y., Barbosa-Morais, N.L. and Thanaraj, T.A. (2006) ASD: a bioinformatics resource on alternative splicing. Nucleic Acids Res., 34, D46–55.

    Article  CAS  PubMed  Google Scholar 

Detection of splicing variants with microarrays

  1. Moore, M.J. (2005) From birth to death: the complex lives of eukaryotic mRNAs. Science, 309, 1514–1518.

    Article  CAS  PubMed  Google Scholar 

  2. Yeakley, J.M., Fan, J.B., Doucet, D., Luo, L., Wickham, E., Ye, Z., Chee, M.S. and Fu, X.D. (2002) Profiling alternative splicing on fiber-optic arrays. Nat Biotechnol, 20, 353–358.

    Article  CAS  PubMed  Google Scholar 

  3. Gardina, P.J., Clark, T.A., Shimada, B., Staples, M.K., Yang, Q., Veitch, J., Schweitzer, A., Awad, T., Sugnet, C., Dee, S. et al. (2006) Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics, 7, 325.

    Article  PubMed  Google Scholar 

  4. Carninci, P. and Kasukawa, T. and Katayama, S. and Gough, J. and Frith, M.C. and Maeda, N. and Oyama, R. and Ravasi, T. and Lenhard, B. and Wells, C. et al. (2005) The transcriptional landscape of the mammalian genome. Science, 309, 1559–1563.

    Article  CAS  PubMed  Google Scholar 

  5. Hughes, T.R., Hiley, S.L., Saltzman, A.L., Babak, T. and Blencowe, B.J. (2006) Microarray analysis of RNA processing and modification. Methods Enzymol, 410, 300–316.

    Article  CAS  PubMed  Google Scholar 

  6. Relogio, A., Schwager, C., Richter, A., Ansorge, W. and Valcarcel, J. (2002) Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Res, 30, e51.

    Article  PubMed  Google Scholar 

  7. Hiller, M., Nikolajewa, S., Huse, K., Szafranski, K., Rosenstiel, P., Schuster, S., Backofen, R. and Platzer, M. (2007) TassDB: a database of alternative tandem splice sites. Nucleic Acids Res, 35, D188192.

    Article  Google Scholar 

  8. Cheng, J., Kapranov, P., Drenkow, J., Dike, S., Brubaker, S., Patel, S., Long, J., Stern, D., Tammana, H., Helt, G. et al. (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science, 308, 1149–1154.

    Article  CAS  PubMed  Google Scholar 

Analysis tools

  1. Cleveland, W.S. and Devlin, S.J. (1988) Locally Weighted Regression: An Approach to Regression Analysis by Local Fitting. J. Ameri. Stat. Asso., 83, 596–610.

    Article  Google Scholar 

  2. Yang, Y.H., Dudoit, S., Luu, P., Lin, D.M., Peng, V., Ngai, J. and Speed, T.P. (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res, 30, e15.

    Article  PubMed  Google Scholar 

  3. Ule, J., Ule, A., Spencer, J., Williams, A., Hu, J.S., Cline, M., Wang, H., Clark, T., Fraser, C., Ruggiu, M. et al. (2005) Nova regulates brain-specific splicing to shape the synapse. Nat Genet, 37, 844–852.

    Article  CAS  PubMed  Google Scholar 

  4. Shai, O., Morris, Q.D., Blencowe, B.J. and Frey, B.J. (2006) Inferring global levels of alternative splicing isoforms using a generative model of microarray data. Bioinformatics, 22, 606–613.

    Article  CAS  PubMed  Google Scholar 

  5. Cuperlovic-Culf, M., Belacel, N., Culf, A.S. and Ouellette, R.J. (2006) Data analysis of alternative splicing microarrays. Drug Discov Today, 11, 983–990.

    Article  CAS  PubMed  Google Scholar 

Experiments with splice-site sensitive microarrays

  1. Le, K., Mitsouras, K., Roy, M., Wang, Q., Xu, Q., Nelson, S.F. and Lee, C. (2004) Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data. Nucleic Acids Res, 32, e180.

    Article  PubMed  Google Scholar 

  2. Ule, J., Stefani, G., Mele, A., Ruggiu, M., Wang, X., Taneri, B., Gaasterland, T., Blencowe, B.J. and Darnell, R.B. (2006) An RNA map predicting Nova-dependent splicing regulation. Nature.

    Google Scholar 

  3. Sugnet, C.W., Srinivasan, K., Clark, T.A., O'Brien, G., Cline, M.S., Wang, H., Williams, A., Kulp, D., Blume, J.E., Haussler, D. et al. (2006) Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLoS Comput Biol, 2, e4.

    Article  PubMed  Google Scholar 

  4. Relogio, A., Ben-Dov, C., Baum, M., Ruggiu, M., Gemund, C., Benes, V., Darnell, R.B. and Valcarcel, J. (2005) Alternative splicing microarrays reveal functional expression of neuron-specific regulators in Hodgkin lymphoma cells. J Biol Chem, 280, 4779–4784.

    Article  CAS  PubMed  Google Scholar 

  5. Hu, G.K., Madore, S.J., Moldover, B., Jatkoe, T., Balaban, D., Thomas, J. and Wang, Y. (2001) Predicting splice variant from DNA chip expression data. Genome Res, 11, 1237–1245.

    Article  CAS  PubMed  Google Scholar 

  6. Ni, J.Z., Grate, L., Donohue, J.P., Preston, C., Nobida, N., O'Brien, G., Shiue, L., Clark, T.A., Blume, J.E. and Ares, M., Jr. (2007) Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev, 21, 708–718.

    Article  CAS  PubMed  Google Scholar 

  7. Clark, T.A., Schweitzer, A.C., Chen, T.X., Staples, M.K., Lu, G., Wang, H., Williams, A. and Blume, J.E. (2007) Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biol, 8, R64.

    Article  PubMed  Google Scholar 

  8. Pan, Q., Shai, O., Misquitta, C., Zhang, W., Saltzman, A.L., Mohammad, N., Babak, T., Siu, H., Hughes, T.R., Morris, Q.D. et al. (2004) Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol Cell, 16, 929–941.

    Article  CAS  PubMed  Google Scholar 

  9. Ip, J.Y., Tong, A., Pan, Q., Topp, J.D., Blencowe, B.J. and Lynch, K.W. (2007) Global analysis of alternative splicing during T-cell activation. Rna, 13, 563–572.

    Article  CAS  PubMed  Google Scholar 

  10. Blanchette, M., Green, R.E., Brenner, S.E. and Rio, D.C. (2005) Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila. Genes Dev, 19, 1306–1314.

    Article  CAS  PubMed  Google Scholar 

  11. Boutz, P.L., Stoilov, P., Li, Q., Lin, C.H., Chawla, G., Ostrow, K., Shiue, L., Ares, M., Jr. and Black, D.L. (2007) A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev, 21, 1636–1652.

    Article  CAS  PubMed  Google Scholar 

  12. Clark, T.A., Sugnet, C.W. and Ares, M., Jr. (2002) Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science, 296, 907–910.

    Article  CAS  PubMed  Google Scholar 

  13. Stolc, V., Gauhar, Z., Mason, C., Halasz, G., van Batenburg, M.F., Rifkin, S.A., Hua, S., Herreman, T., Tongprasit, W., Barbano, P.E. et al. (2004) A gene expression map for the euchromatic genome of Drosophila melanogaster. Science, 306, 655–660.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Stefan Stamm .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Humana Press, a part of Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Hui, J., Kishore, S., Khanna, A., Stamm, S. (2009). Analysis of Alternative Splicing with Microarrays. In: Krawetz, S. (eds) Bioinformatics for Systems Biology. Humana Press. https://doi.org/10.1007/978-1-59745-440-7_14

Download citation

Publish with us

Policies and ethics