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Open Access Research article

Examining the condition-specific antisense transcription in S. cerevisiae and S. paradoxus

Krishna B S Swamy12, Chih-Hsu Lin2, Ming-Ren Yen2, Chuen-Yi Wang2 and Daryi Wang2*

Author Affiliations

1 Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan

2 Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan

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BMC Genomics 2014, 15:521  doi:10.1186/1471-2164-15-521

Published: 25 June 2014

Abstract

Background

Recent studies have demonstrated that antisense transcription is pervasive in budding yeasts and is conserved between Saccharomyces cerevisiae and S. paradoxus. While studies have examined antisense transcripts of S. cerevisiae for inverse expression in stationary phase and stress conditions, there is a lack of comprehensive analysis of the conditional specific evolutionary characteristics of antisense transcription between yeasts. Here we attempt to decipher the evolutionary relationship of antisense transcription of S. cerevisiae and S. paradoxus cultured in mid log, early stationary phase, and heat shock conditions.

Results

Massively parallel sequencing of sequence strand-specific cDNA library was performed from RNA isolated from S. cerevisiae and S. paradoxus cells at mid log, stationary phase and heat shock conditions. We performed this analysis using a stringent set of sense ORF transcripts and non-coding antisense transcripts that were expressed in all the three conditions, as well as in both species. We found the divergence of the condition-specific anti-sense transcription levels is higher than that in condition-specific sense transcription levels, suggesting that antisense transcription played a potential role in adapting to different conditions. Furthermore, 43% of sense-antisense pairs demonstrated inverse expression in either stationary phase or heat shock conditions relative to the mid log conditions. In addition, a large part of sense-antisense pairs (67%), which demonstrated inverse expression, were highly conserved between the two species. Our results were also concordant with known functional analyses from previous studies and with the evidence from mechanistic experiments of role of individual genes.

Conclusions

By performing a genome-scale computational analysis, we have tried to evaluate the role of antisense transcription in mediating sense transcription under different environmental conditions across and in two related yeast species. Our findings suggest that antisense regulation could control expression of the corresponding sense transcript via inverse expression under a range of different circumstances.

Keywords:
Antisense RNA; Evolution; Budding yeast; Stress