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Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines

Nature Genetics volume 40, pages 1416–1425 (2008)Cite this article

Abstract

Alternative pre–messenger RNA splicing influences development, physiology and disease, but its regulation in humans is not well understood, partially because of the limited scale at which the expression of specific splicing events has been measured. We generated the first genome-scale expression compendium of human alternative splicing events using custom whole-transcript microarrays monitoring expression of 24,426 alternative splicing events in 48 diverse human samples. Over 11,700 genes and 9,500 splicing events were differentially expressed, providing a rich resource for studying splicing regulation. An unbiased, systematic screen of 21,760 4-mer to 7-mer words for cis-regulatory motifs identified 143 RNA 'words' enriched near regulated cassette exons, including six clusters of motifs represented by UCUCU, UGCAUG, UGCU, UGUGU, UUUU and AGGG, which map to trans-acting regulators PTB, Fox, Muscleblind, CELF/CUG-BP, TIA-1 and hnRNP F/H, respectively. Each cluster showed a distinct pattern of genomic location and tissue specificity. For example, UCUCU occurs 110 to 35 nucleotides preceding cassette exons upregulated in brain and striated muscle but depleted in other tissues. UCUCU and UGCAUG seem to have similar function but independent action, occurring 5′ and 3′, respectively, of 33% of the cassette exons upregulated in skeletal muscle but co-occurring for only 2%.

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Figure 1: Interrogation of A2BP1 (Fox-1) isoforms on the alternative splicing microarrays.
Figure 2: Alternative splicing characteristics.
Figure 3
Figure 4: Motif identification and enrichment.
Figure 5: Motif enrichment upstream of cassette exons upregulated in human tissues and cell lines.
Figure 6: Motif enrichment downstream of cassette exons upregulated in human tissues and cell lines.
Figure 7: Higher-resolution enrichment of UGCAUG adjacent heart-regulated cassette exons.
Figure 8: Higher-resolution enrichment of UCUCU adjacent regulated cassette exons.

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Gene Expression Omnibus

NCBI Reference Sequence

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Acknowledgements

We thank C. Armour, C. Raymond, D. Haynor, V. Emilsson, P. Garrett-Engele, F. Roth, P. Loerch, R. Chen, C. Rohl, M. Tompa, E. Schadt and L. Lim for input, Rosetta's Gene Expression Laboratory microarray hybridization facility for microarray data, and S. Carlson for project management. Funding for T.A.C. provided by R01GM076493.

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Authors and Affiliations

  1. Rosetta Inpharmatics LLC, Seattle, 98109, Washington, USA

    John C Castle, Jyoti K Shah, Amit V Kulkarni & Jason M Johnson

  2. Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, 11724, New York, USA

    Chaolin Zhang

  3. Departments of Pathology, Baylor College of Medicine, Houston, 77030, Texas, USA

    Auinash Kalsotra & Thomas A Cooper

  4. Molecular and Cellular Biology, Baylor College of Medicine, Houston, 77030, Texas, USA

    Thomas A Cooper

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Contributions

J.M.J. conceived the experiment; J.C.C. and J.M.J. executed the experiment and wrote the paper; J.C.C. designed the microarrays and analyzed the data; J.C.C. and C.Z. identified motifs; J.K.S. and A.V.K. processed and managed data; and A.K. and T.A.C. provided validation experiments.

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Correspondence to John C Castle or Jason M Johnson.

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Castle, J., Zhang, C., Shah, J. et al. Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nat Genet 40, 1416–1425 (2008). https://doi.org/10.1038/ng.264

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