Cellular mechanisms that achieve protein diversity in eukaryotes are multifaceted, including transcriptional components such as RNA splicing. Through alternative splicing, a single protein-coding gene can generate multiple mRNA transcripts and protein isoforms, some of which are tissue-specific. We have conducted qualitative and quantitative analyses of the Bodymap 2.0 messenger RNA-sequencing data from 16 human tissue samples and identified 209,363 splice junctions. Of these, 22,231 (10.6%) were not previously annotated and 21,650 (10.3%) were expressed in a tissue-restricted pattern. Tissue-restricted alternative splicing was found to be widespread, with approximately 65% of expressed multi-exon genes containing at least one tissue-specific splice junction. Interestingly, we observed many tissue-specific splice junctions not only in genes expressed in one or a few tissues, but also from gene loci with a broad pattern of expression.
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This work was supported by the National Science Foundation (Crosscut-EF-0850237 to J.L. and J.N.M. and 1054631 to J.L.) and a Kentucky Infrastructure for Biomedical Research Excellence award (KY-INBRE, 5P20RR016481-09) from the National Institutes of Health. Additional financial support was received from the Lourie Foundation and through endowments at the Gluck Equine Research Center, University of Kentucky. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Hestand, Matthew S.; Zeng, Zheng; Coleman, Stephen J.; Liu, Jinze; and MacLeod, James N., "Tissue Restricted Splice Junctions Originate Not Only from Tissue-Specific Gene Loci, but Gene Loci with a Broad Pattern of Expression" (2015). Maxwell H. Gluck Equine Research Center Faculty Publications. 7.
S1 File. Bed track of novel human splice junctions.
journal.pone.0144302.s002.BED (2065 kB)
S2 File. Bed track of human tissue restricted splice junctions.
journal.pone.0144302.s003.PNG (89 kB)
S1 Fig. Heat map of GO biological processes in relation to genes containing tissue restricted splice junctions.
journal.pone.0144302.s004.PDF (16 kB)
S1 Table. Ratio of detectable junctions to detectable genes.