Honors Students' Abstracts
Mathematical Analysis of Gene Regulation in Saccharomyces cerevisiae in Response to Cold Shock
Katrina Sherbina, Nick Rohacz
DNA microarray technology was used to measure the effect of cold shock on gene expression within Saccharomyces cerevisiae, budding yeast. To determine which transcription factors control the response to cold shock, total RNA was purified from the wildtype strain and strains deleted for the CIN5, GLN3, HMO1, and ZAP1 transcription factors during growth at 30ºC (t0); at 15, 30, and 60 minutes into cold shock at 13ºC; and at 90 and 120 minutes during recovery at 30ºC. Four to five replicates were performed for each strain and timepoint. A total of 103 DNA microarrays were competitively hybridized with RNA from the t0 timepoint, labeled with the Cy3 dye, mixed with RNA from each of the other time points labeled with Cy5 dye. Spatial and intensity biases present in the microarray data because the two dyes have different properties were corrected using Loess normalization and median absolute deviation scaling performed with R Statistical Software. We then tested for significant changes in gene expression using a modified ANOVA test. Because we performed hypothesis tests for thousands of genes, we used the Bonferroni and Benjamini and Hochberg corrections to minimize the false positive rate. We found that 1686 genes showed differential expression for at least one timepoint in the wild type strain at a corrected p < 0.05. However the strain deleted for HMO1 had only 39 genes that showed significant differences in expression, suggesting that the absence of HMO1 seriously disrupted the cell’s ability to respond to cold shock.