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Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant

Al-Balool, Haya H.; Weber, David; Liu, Yilei; Wade, Mark; Guleria, Kamlesh; Nam, Pitsien Lang Ping; Clayton, Jake; Rowe, William; Coxhead, Jonathan; Irving, Julie; Elliott, David J.; Hall, Andrew G.; Santibanez-Koref, Mauro; Jackson, Michael S.

Authors

Haya H. Al-Balool

David Weber

Yilei Liu

Kamlesh Guleria

Pitsien Lang Ping Nam

Jake Clayton

William Rowe

Jonathan Coxhead

Julie Irving

David J. Elliott

Andrew G. Hall

Mauro Santibanez-Koref

Michael S. Jackson



Abstract

In silico analyses have established that transcripts from some genes can be processed into RNAs with rearranged exon order relative to genomic structure (post-transcriptional exon shuffling, or PTES). Although known to contribute to transcriptome diversity in some species, to date the structure, distribution, abundance, and functional significance of human PTES transcripts remains largely unknown. Here, using high-throughput transcriptome sequencing, we identify 205 putative human PTES products from 176 genes. We validate 72 out of 112 products analyzed using RT-PCR, and identify additional PTES products structurally related to 61% of validated targets. Sequencing of these additional products reveals GT-AG dinucleotides at >95% of the splice junctions, confirming that they are processed by the spliceosome. We show that most PTES transcripts are expressed in a wide variety of human tissues, that they can be polyadenylated, and that some are conserved in mouse. We also show that they can extend into 5′ and 3′ UTRs, consistent with formation via trans-splicing of independent pre-mRNA molecules. Finally, we use real-time PCR to compare the abundance of PTES exon junctions relative to canonical exon junctions within the transcripts from seven genes. PTES exon junctions are present at 90% of the levels of canonical junctions, with transcripts from MAN1A2, PHC3, TLE4, and CDK13 exhibiting the highest levels. This is the first systematic experimental analysis of PTES in human, and it suggests both that the phenomenon is much more widespread than previously thought and that some PTES transcripts could be functional.

Journal Article Type Article
Publication Date Nov 1, 2011
Journal Genome Research
Print ISSN 1088-9051
Publisher Cold Spring Harbor Laboratory Press
Peer Reviewed Peer Reviewed
Volume 21
Issue 11
Pages 1788-1799
APA6 Citation Al-Balool, H. H., Weber, D., Liu, Y., Wade, M., Guleria, K., Nam, P. L. P., …Jackson, M. S. (2011). Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant. Genome research, 21(11), 1788-1799. doi:10.1101/gr.116442.110
DOI https://doi.org/10.1101/gr.116442.110
Publisher URL https://genome.cshlp.org/content/21/11/1788
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