Tissue Restricted Splice Junctions Originate Not Only from Tissue-Specific Gene Loci, but Gene Loci with a Broad Pattern of Expression

Matthew S. Hestand; Zheng Zeng; Stephen J. Coleman; Jinze Liu; James N. MacLeod

doi:10.1371/journal.pone.0144302

Tissue Restricted Splice Junctions Originate Not Only from Tissue-Specific Gene Loci, but Gene Loci with a Broad Pattern of Expression

Matthew S. Hestand, Zheng Zeng, Stephen J. Coleman, Jinze Liu, James N. MacLeod

Research output: Contribution to journal › Article › peer-review

4 Scopus citations

Abstract

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.

Original language	English
Article number	0144302
Journal	PLoS ONE
Volume	10
Issue number	12
DOIs	https://doi.org/10.1371/journal.pone.0144302
State	Published - Dec 1 2015

Bibliographical note

Publisher Copyright:
©2015 Hestand et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding

We thank members of the Liu laboratory for assistance using MapSplice. 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.

Funders	Funder number
KY-INBRE	5P20RR016481-09
National Science Foundation Arctic Social Science Program	Crosscut-EF-0850237, 1054631
National Science Foundation Arctic Social Science Program
National Institutes of Health (NIH)
National Human Genome Research Institute	R01HG006272
National Human Genome Research Institute
University of Kentucky
Lourie Family Foundation

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abstract = "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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AU - MacLeod, James N.

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Tissue Restricted Splice Junctions Originate Not Only from Tissue-Specific Gene Loci, but Gene Loci with a Broad Pattern of Expression

Abstract

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