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. 2014 Jun 25;15(1):521.
doi: 10.1186/1471-2164-15-521.

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

Krishna B S Swamy, Chih-Hsu Lin, Ming-Ren Yen, Chuen-Yi Wang, Daryi Wang  1
Affiliations

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

Krishna B S Swamy et al. BMC Genomics. .

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.

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Figures

Figure 1
Figure 1
Toy diagram for the estimation of conservation score. Here L i and O i, where i = Sc or Sp are the total length of the sense region and length of the overlapping region between sense and antisense transcripts respectively. In this ORF, conservation score is computed by employing the fraction of region O sp.
Figure 2
Figure 2
Histogram of sense and antisense transcription levels in Sc and Sp from the three culture conditions. (a) Sc-ML, (b) Sp-ML, (c) Sc-ES, (d) Sp-ES, (e) Sc-HS, and (f) Sp-HS conditions. (See Methods for details on Density and Expression).
Figure 3
Figure 3
The correlation of expression levels between sense and antisense transcription in ML, ES and HS conditions in Sc and Sp. Expression is derived from logarithm of sense and antisense BPKM values from our selected dataset. For both species the ES and HS conditions have slight positive correlation between antisense and sense transcript levels, which is not evident in Sc-ML condition. Here (a) Sc-ML, (b) Sp-ML, (c) Sc-ES, (d) Sp-ES, (e) Sc-HS, and (f) Sp-HS conditions.
Figure 4
Figure 4
Significant inverse expression patterns of sense-antisense pairs conserved in Sc and Sp . (a) Sense-antisense pairs that show inverse expression patterns conserved in Sc and Sp from ML to (I) both ES and HS, (II) only ES, (III) only HS. (b&c) Sense-antisense pairs that show inverse expression patterns only in (b) Sc or (c) Sp from ML to (I) both ES and HS, (II) only ES, (III) only HS.
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