Abstract
BackgroundRecent 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.ResultsMassively 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.ConclusionsBy 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-521) contains supplementary material, which is available to authorized users.
Highlights
Recent studies have demonstrated that antisense transcription is pervasive in budding yeasts and is conserved between Saccharomyces cerevisiae and S. paradoxus
Growth conditions and treatments To study the evolutionary characteristics of antisense transcription with respect to the change in environmental conditions, the strand-specific total RNA was sequenced from the laboratory strain BY4741; a descendant of S288C in Saccharomyces cerevisiae and Saccahromyces paradoxus strain a-CC154; a derivative of CBS432. (REF: Curtsey Dr Wen-Hsuing Li)
We used the criteria that for any position to be considered in this analysis, it should have a read depth greater than or equal to five. (ii) We extended the boundary in both directions by one base pair until the mean read depth of the transcript was at least four times higher than the read depth of the neighboring position. (iii) The boundary of this transcript was reassigned to include the reads that contained the position at which the mean read depth satisfied the criteria in step (ii). (iv) The region that was already assigned as a transcript was flagged and excluded from the following cycles
Summary
Recent studies have demonstrated that antisense transcription is pervasive in budding yeasts and is conserved between Saccharomyces cerevisiae and S. paradoxus. 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. The pervasive transcription is comprised of many non-coding RNAs (ncRNAs) Some of these ncRNAs are transcribed from the opposite DNA strand of the protein-coding sequences and overlap in part with the sense RNAs, forming an interspersed transcriptional organization [6,7]. These are known as antisense RNAs (asRNAs or cis-natural antisense transcripts). Other examples include the role of antisense transcription in control of PHO4 [15], the phosphate metabolism gene and GAL10, the galactose metabolism gene [17]
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