Posttranscriptional processing of mRNA is an integral component of the gene expression program. By using DNA microarrays, we precisely measured the decay of each yeast mRNA, after thermal inactivation of a temperature-sensitive RNA polymerase II. The half-lives varied widely, ranging from ϳ3 min to more than 90 min. We found no simple correlation between mRNA half-lives and ORF size, codon bias, ribosome density, or abundance. However, the decay rates of mRNAs encoding groups of proteins that act together in stoichiometric complexes were generally closely matched, and other evidence pointed to a more general relationship between physiological function and mRNA turnover rates. The results provide strong evidence that precise control of the decay of each mRNA is a fundamental feature of the gene expression program in yeast.A though initiation of transcription is well studied and its importance in regulation is clear, we know much less about the specificity, precision and regulatory role of mRNA decay. The abundance of each mRNA in the cell is determined not only by the rate at which it is produced, but also by its rate of degradation. mRNA decay rates determine how quickly each message can adapt to a new steady-state level after a change in transcription rate, and dynamic control of the decay of specific transcripts can have an important role in their regulation (1). The decay rates of specific mRNAs can vary by 100-fold or more (2, 3) and are affected by a wide variety of stimuli and cellular signals, including specific hormones (2, 4), iron (5, 6), cell cycle progression (7,8), cell differentiation (9, 10), and viral infection (11). Characterizing this stage in the natural history of each mRNA is an important step toward understanding the logic and molecular mechanisms underlying the regulation of the gene expression program of a genome.With its ease of biochemical and genetic manipulation, yeast makes an excellent model for studying eukaryotic mRNA turnover. Simple and reliable procedures have been developed to measure the decay rates of individual mRNAs in yeast, including global or specific transcriptional shut-off assays (12)(13)(14) and in vivo kinetic labeling (15). However, the global profile of yeast mRNA turnover has not been systematically and quantitatively determined. In this report, we present the results of a genomewide determination of mRNA decay rates, coupling the global transcriptional shut-off assay with DNA microarray analysis. ura3-52 his4-939am rpb1-1), carrying a temperature-sensitive mutation in RNA polymerase II (13), was used in this study. Y262 was grown in 500 ml of yeast extract͞peptone͞dextrose (YPD) medium at 24°C to OD 600 ϳ0.5. The temperature of the culture was abruptly shifted to 37°C by adding an equal volume of YPD medium that had been prewarmed to 49°C. Aliquots of the culture (100 ml) were removed at 0,5,10,15,20,30,40, 50, and 60 min after the temperature shift. Cells were rapidly harvested on a nitrocellulose filter (Whatman no. 141109) followed by immediate freezing in l...