yeastgenomicexpressionstudiesusingdnamicroarrays.docVIP

Yeast Genomic Expression Studies Using DNA Microarrays Audrey P. Gasch, PhD Laboratory of Genetics and Genome Center of Wisconsin University of Wisconsin-Madison Table Of Contents Introduction Microarray Construction Planning the Experiment Conducting the Experiment RNA Isolation and Probe Generation Microarray Hybridization and Data Acquisition Troubleshooting Microarrays SummaryIntroduction The technological developments in the area of genome science have revolutionized the methods of biological exploration, allowing organisms to be studied on a genomic scale. Characterizing whole-genome expression using DNA microarrays provides a snapshot of an organism’s genome in action by revealing the relative transcript levels of thousands of genes at a time. Exploration of the dynamic nature of genomic expression programs throughout the natural life cycle of cells presents a variety of biological insights, hinting at the underlying cellular processes that mediate or respond to changes in gene expression. In a seminal study by DeRisi et al., DNA microarrays were used to follow the global changes in gene expression during the natural transition of yeast cells from fermentative metabolism to respiration, known as the diauxic shift1. Despite decades of study on the metabolic pathways involved, the work demonstrated the potential of genomic expression profiling by revealing many previously unrecognized features of the metabolic transition. Nearly 30% of the yeast genome (approximately 1,700 genes) was significantly altered in expression as the available glucose in the medium was depleted, and subsets of genes displayed distinct temporal patterns of transcript variation. DeRisi et al. demonstrated that genes displaying similar expression patterns were functionally related and regulated by upstream sequence motifs common to the genes’ promoters. This result established the enormous potential of genomic expression characterization in implicating hypothetical fu