Abstract
BackgroundRNA sequencing (RNA-seq) has revolutionized the detection of transcriptomic signatures due to its high-throughput sequencing ability. Therefore, genomic annotations on different animal species have been rapidly updated using information from tissue-enriched novel transcripts and novel exons.Results34 putative novel transcripts and 236 putative tissue-enriched exons were identified using RNA-Seq datasets representing six tissues available in mouse databases. RT-PCR results indicated that expression of 21 and 2 novel transcripts were enriched in testes and liver, respectively, while 31 of the 39 selected novel exons were detected in the testes or heart. The novel isoforms containing the identified novel exons exhibited more dominant expression than the known isoforms in heart and testes. We also identified an example of pathology-associated exclusion of heart-enriched novel exons such as Sorbs1 and Cluh during pressure-overload cardiac hypertrophy.ConclusionThe present study depicted tissue-enriched novel transcripts, a tissue-specific isoform switch, and pathology-associated alternative splicing in a mouse model, suggesting tissue-specific genomic diversity and plasticity.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-592) contains supplementary material, which is available to authorized users.
Highlights
RNA sequencing (RNA-seq) has revolutionized the detection of transcriptomic signatures due to its high-throughput sequencing ability
The present study employed RNA-seq data to identify novel exons and novel transcripts enriched in different tissues in mice, leading to the discovery of novel transcripts expressed in testes or liver, and recognition that the novel isoforms containing the novel exons were dominantly expressed in testes or heart
We found that testes-enriched novel 5′UTRs have abundant upstream open reading frames (uORFs) (n = 56, 50%) with some of 197 novel exons in the testes, suggesting a testes-specific regulatory role in translation
Summary
RNA sequencing (RNA-seq) has revolutionized the detection of transcriptomic signatures due to its high-throughput sequencing ability. The present study employed RNA-seq data to identify novel exons and novel transcripts enriched in different tissues in mice (here “novel” means “new” exons or “new” transcripts not identified in mice so far), leading to the discovery of novel transcripts expressed in testes or liver, and recognition that the novel isoforms containing the novel exons were dominantly expressed in testes or heart. These results should contribute to a more sophisticated annotation of the mouse genome, as well as improved understanding of tissue-specific gene regulation
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