Alternative isoform regulation in human tissue transcriptomes

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Abstract

Through alternative processing of pre-messenger RNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes on the basis of deep sequencing of complementary DNA fragments, yielding a digital inventory of gene and mRNA isoform expression. Analyses in which sequence reads are mapped to exon–exon junctions indicated that 92–94% of human genes undergo alternative splicing, 86% with a minor isoform frequency of 15% or more. Differences in isoform-specific read densities indicated that most alternative splicing and alternative cleavage and polyadenylation events vary between tissues, whereas variation between individuals was approximately twofold to threefold less common. Extreme or ‘switch-like’ regulation of splicing between tissues was associated with increased sequence conservation in regulatory regions and with generation of full-length open reading frames. Patterns of alternative splicing and alternative cleavage and polyadenylation were strongly correlated across tissues, suggesting coordinated regulation of these processes, and sequence conservation of a subset of known regulatory motifs in both alternative introns and 3′ untranslated regions suggested common involvement of specific factors in tissue-level regulation of both splicing and polyadenylation.

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Figure 1: Frequency and relative abundance of alternative splicing isoforms in human genes.
Figure 2: Pervasive tissue-specific regulation of alternative mRNA isoforms.
Figure 3: The extent of individual-specific differences in alternative isoform expression.
Figure 4: Conservation and function of switch-like alternative splicing exons.
Figure 5: Evidence for coordination between splicing and polyadenylation.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

The reported sequence read data have been deposited to the Short Read Archive section of GEO at NCBI under accession numbers GSE12946 and SRA002355.1.

Change history

  • 27 November 2008

    The AOP version of this paper contained a typo in the legend for Figure 1. This was corrected for print on 27 November 2008.

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Acknowledgements

We thank E. Anderson, D. Black, B. Friedman, and members of the Burge laboratory for comments on the manuscript, N. Spies for analyses, J. Mudge, G. D. May, N. A. Miller, E. Vermaas, T. Kerelska, J. Yan and V. Quijano for assistance in generating the mRNA-Seq data, and R. C. Roberts and N. Perrone-Bizzozero for supplying cerebellar cortex RNA samples. This research was supported by an NIH training grant (E.T.W.), and by grants from the Knut & Alice Wallenberg Foundation and the Swedish Foundation for Strategic Research (R.S.) and from the NIH (C.B.B.).

Author Contributions E.W. and R.S. designed and performed the computational analyses of sequencing reads, prepared figures, tables and methods and contributed to manuscript text. S.L. developed protocols and created libraries, L.Z. contributed to sequencing development, and I.K., S.L. and L.Z. did primary data analysis. G.P.S. contributed to study design and manuscript preparation. C.M. and S.F.K. provided RNA samples and contributed to manuscript preparation. C.B.B. designed the study and prepared the manuscript, with input from other authors.

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Correspondence to Christopher B. Burge.

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Competing interests

S.L., I.K., L.Z. and G.P.S. are employees of Illumina, Inc.

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This file contains Supplementary Methods, Supplementary References, Supplementary Figures S1-S9 with Legends and Supplementary Tables S1-S9. (PDF 9256 kb)

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Wang, E., Sandberg, R., Luo, S. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470–476 (2008) doi:10.1038/nature07509

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