Cells adapt to environmental changes through genetic mutations that stabilize novel phenotypes. Often, this adaptation involves regulatory changes which modulate gene expression. In the budding yeast, ribosomal-related gene expression correlates with cell growth rate across different environments. To examine whether the same relationship between gene expression and growth rate is observed also across natural populations, we measured gene expression, growth rate and ethanol production of twenty-f ...[more]
Project description:Total RNA versus genomic DNA hybridization on custom arrays designed for all Saccharomyces paradoxus genes Total RNA was collected in mid-log phase from Saccharomyces paradoxus cells grown in rich medium (abbreviated CM, in house recipe). RNA was then converted to cDNA, Cy3-labeled and hybridized competitively against Cy5 labeled genomic DNA from Saccharomyces paradoxus.
Project description:Total RNA versus genomic DNA hybridization on custom arrays designed for all Saccharomyces paradoxus genes Overall design: Total RNA was collected in mid-log phase from Saccharomyces paradoxus cells grown in rich medium (abbreviated CM, in house recipe). RNA was then converted to cDNA, Cy3-labeled and hybridized competitively against Cy5 labeled genomic DNA from Saccharomyces paradoxus.
Project description:Transcription profile of 12 wt S.paradoxus strains originating from diverse geographical origins and natural habitats. Transcription profiles in two conditioins were compared: growth on glucose and growth on the naturally rare pentose sugar xylulose. Two condition experiment, growth on glucose and on xylulose, 12 wt S.paradoxus strains
Project description: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 transcription 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 transcription 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 transcription, 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: This study provides a comprehensive picture of the role of antisense transcription mediating sense transcription in different conditions across yeast species. We can conclude from our findings that antisense regulation could act like an on-off switch on sense regulation in different conditions. Transcriptomes of two yeast species under mid-log phase, early stationary phase, and after heat shock treatment were generated by Illumina HiSeq 2000 paired-end sequencing
Project description:Transcriptional profiling of four different yeast FZF1 alleles: S. cerevisiae, S. paradoxus and two reciprocal chimeras with the coding and 5' noncoding region from opposite species of S. cerevisiae and S. paradoxus, both before and 15 minutes after sulfite addition. FZF1 is a transcription factor that is known to be turned on in response to sulfite. Here we determine whether the FZF1 allele from two species leads to different transcriptional responses and the effect of the individual noncoding and coding regions on the transcriptional response. Two-color experiment, 4 Strains x 2 Timepoints each compared to a reference pool made up of all samples. 3 Biologic replicates. With dye-swaps