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Open Access Research article

Identification of tissue-enriched novel transcripts and novel exons in mice

Seong-Eui Hong, Hong Ki Song and Do Han Kim*

Author Affiliations

School of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro (Oryong-dong), Buk-gu, Gwangju 500-712, Korea

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BMC Genomics 2014, 15:592  doi:10.1186/1471-2164-15-592

Published: 13 July 2014

Abstract

Background

RNA 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.

Results

34 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.

Conclusion

The 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.

Keywords:
Next generation sequencing; Novel transcript; Novel exon; Tissue-specificity