Global transcriptional response of wild type and transcription factor deletion strains of Saccharomyces cerevisiae to the environmental stress of cold shock and subsequent recovery

Previous studies on the global transcriptional response of budding yeast, Saccharomyces cerevisiae, to cold shock have revealed that the response can be divided into a set of early response genes (after 15 minutes to 2 hours of cold temperatures) and late response genes (after 12 to 60 hours of cold temperatures). The late response genes include the ESR genes induced by many environmental stresses and are regulated by the Msn2 and Msn4 transcription factors, as they are during other environmental stresses (Kandror et al. 2004 PMID:15053871; Schade et al. 2004 PMID:15483057). However, the transcription factors responsible for the induction of the early response genes, the overall regulatory mechanism governing this early response, and the transcriptional response to recovery after cold shock remain largely unknown. Thus, we measured the early transcriptional response of S. cerevisiae to cold shock and subsequent recovery using DNA microarrays. To determine which transcription factors were responsible for these changes in expression, the same cold shock and recovery microarray experiments were then performed on six strains individually deleted for the transcription factors Cin5, Gln3, Hap4, Hmo1, Swi4, and Zap1. Yeast cells were grown to early log phase at 30°C, then shifted to 13°C for 60 minutes (cold shock), and then shifted back to 30°C for another 60 minutes (recovery). Samples from independently grown replicate cultures (flasks) were collected before cold shock (t0), after 15 (t15), 30 (t30), and 60 minutes (t60) of cold shock, and after 60 minutes of cold shock followed by 30 (t90) and 60 minutes (t120) of recovery at 30°C. Data was collected for the following strains: wild type (BY4741 or BY4739), BY4741 Δcin5, BY4741 Δgln3, BY4741 Δhap4, BY4741 Δhmo1, BY4741 Δswi4, and BY4741 Δzap1. Generally, 4 independent biological replicates were performed for each strain (independent culture flasks), although for some timepoints and strains there are 3 or 5 replicates instead. Note that the t15 sample was not collected for the BY4741 Δswi4 strain. The sample from each experimental timepoint (t15, t30, t60, t90, and t120) was labeled with Cy5, and the t0 sample (before cold shock control) was labeled with Cy3. Experimental and control samples from the same flask were co-hybridized onto the same microarray slide. The dye orientation was swapped for two of the biological replicates per timepoint per strain (experimental sample labeled with Cy3 and control sample labeled with Cy5), except in one instance when there was only one dye swap performed for a particular strain and timepoint. Technical replicates were not performed. There were a total of 137 microarrays hybridized in this study.