Abstract
We carried out the first analysis of alternative splicing complexity in human tissues using mRNA-Seq data. New splice junctions were detected in ∼20% of multiexon genes, many of which are tissue specific. By combining mRNA-Seq and EST-cDNA sequence data, we estimate that transcripts from ∼95% of multiexon genes undergo alternative splicing and that there are ∼100,000 intermediate- to high-abundance alternative splicing events in major human tissues. From a comparison with quantitative alternative splicing microarray profiling data, we also show that mRNA-Seq data provide reliable measurements for exon inclusion levels.
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28 April 2009
Addendum: The GEO accession number for the mRNA-Seq datasets is GSE13652.
References
Matlin, A.J., Clark, F. & Smith, C.W. Nat. Rev. Mol. Cell Biol. 6, 386–398 (2005).
Blencowe, B.J. Cell 126, 37–47 (2006).
Ben-Dov, C., Hartmann, B., Lundgren, J. & Valcarcel, J. J. Biol. Chem. 283, 1229–1233 (2008).
Johnson, J.M. et al. Science 302, 2141–2144 (2003).
Sorek, R., Dror, G. & Shamir, R. BMC Genomics 7, 273 (2006).
Calarco, J.A. et al. Adv. Exp. Med. Biol. 623, 64–84 (2007).
Bainbridge, M.N. et al. BMC Genomics 7, 246 (2006).
Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Nat. Methods 5, 621–628 (2008).
Cloonan, N. et al. Nat. Methods 5, 613–619 (2008).
Sultan, M. et al. Science 321, 956–960 (2008).
Su, A.I. et al. Proc. Natl. Acad. Sci. USA 101, 6062–6067 (2004).
Zhang, W. et al. J. Biol. 3, 21 (2004).
Yeo, G., Holste, D., Kreiman, G. & Burge, C.B. Genome Biol. 5, R74 (2004).
Schiaffino, S. & Reggiani, C. Physiol. Rev. 76, 371–423 (1996).
Pan, Q. et al. Mol. Cell 16, 929–941 (2004).
Acknowledgements
We thank S. Luo, I. Khrebtukova and G. Schroth of Illumina Inc. for providing some of the mRNA-Seq datasets used in this analysis. We also thank M. Brudno, Y. Barash, J. Calarco and S. Ahmad for helpful suggestions and comments on the manuscript. B.J.B and B.J.F. acknowledge support from the Canadian Institutes of Health Research and from Genome Canada through the Ontario Genomics Institute.
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Q.P. created the exon and splice junction libraries and performed analyses of the mRNA-Seq, cDNA-EST and microarray data. O.S., L.J.L. and B.J.F. designed and implemented the logistic regression classifier and contributed to the analyses of tissue-specific alternative splicing events. The study was coordinated by B.J.B. The manuscript was prepared by B.J.B. and Q.P., with the participation of O.S., L.J.L. and B.J.F.
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Supplementary Methods, Supplementary Table 1 and Supplementary Figures 1 and 2 (PDF 329 kb)
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Pan, Q., Shai, O., Lee, L. et al. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40, 1413–1415 (2008). https://doi.org/10.1038/ng.259
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DOI: https://doi.org/10.1038/ng.259
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