Swamy Krishna B S, Lin Chih-Hsu, Yen Ming-Ren, Wang Chuen-Yi, Wang Daryi
Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan.
BMC Genomics. 2014 Jun 25;15(1):521. doi: 10.1186/1471-2164-15-521.
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.
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.
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.
最近的研究表明，反义转录在芽殖酵母中普遍存在，并且在酿酒酵母和奇异酵母之间保守。虽然已有研究检测了酿酒酵母在稳定期和应激条件下反义转录本的反向表达，但缺乏对酵母间反义转录的条件特异性进化特征的全面分析。在此，我们试图解析酿酒酵母和奇异酵母在对数中期、稳定期早期和热休克条件下培养时反义转录的进化关系。
对从处于对数中期、稳定期和热休克条件下的酿酒酵母和奇异酵母细胞中分离的RNA进行了序列链特异性cDNA文库的大规模平行测序。我们使用一组严格的有义开放阅读框转录本和非编码反义转录本进行了此分析，这些转录本在所有三种条件下以及两个物种中均有表达。我们发现条件特异性反义转录水平的差异高于条件特异性有义转录水平的差异，这表明反义转录在适应不同条件中发挥了潜在作用。此外，43%的有义-反义转录本对在稳定期或热休克条件下相对于对数中期条件表现出反向表达。此外，很大一部分表现出反向表达的有义-反义转录本对（67%）在两个物种之间高度保守。我们的结果也与先前研究中的已知功能分析以及单个基因作用的机制实验证据一致。
通过进行全基因组规模的计算分析，我们试图评估反义转录在介导两个相关酵母物种在不同环境条件下的有义转录中的作用。我们的研究结果表明，反义调控可以在一系列不同情况下通过反向表达来控制相应有义转录本的表达。
