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

Authors

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

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.

Document Type

Article

Publication Date

12-29-2015

Notes/Citation Information

Published in PLOS One, v. 10, no. 12, article e0144302, p. 1-14.

© 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

Digital Object Identifier (DOI)

http://dx.doi.org/10.1371/journal.pone.0144302

Funding Information

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.

Repository Citation

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.
https://uknowledge.uky.edu/gerc_facpub/7