||Budding yeast Saccharomyces cerevisiae
||Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO. Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A. 2002 Apr 30 99(9):5860-5 free online article p.5862 left column 2nd paragraphPubMed ID11972065
||Abstract: "By using DNA microarrays, researchers precisely measured the decay of each yeast mRNA, after thermal inactivation of a temperature-sensitive RNA polymerase II." P.5860 left column bottom paragraph: "Determination of mRNA Decay by Transcriptional Shut-Off Assay: [Yeast strain] Y262 was grown in 500 ml of yeast extract/peptone/dextrose (YPD) medium at 24°C to OD600 ∼0.5. 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 liquid N2. Total RNA was prepared from cells harvested at each time point by hot phenol extraction (ref 16)." P.5860 right column bottom paragraph: "A nonlinear least squares model was fit to determine the decay rate constant (k) and half-life (t1/2) of each mRNA. The decay rate constant, k, is the value that minimized Si = 1,n[y(ti) - exp(-k×ti)]^2, where y(t) is the mRNA abundance at time t and the summation is taken over all observations for the particular mRNA. The half-life is t1/2 = ln2/k. The goodness of fit of the decay model for each gene was assessed with the F statistic (ref 20), based on the null hypothesis that the data fit a first-order decay model.
A bootstrap method was used to calculate confidence intervals for both t1/2 and k (ref 21)."
||P.5862 left column 2nd paragraph: "The half-lives of the 4,687 mRNAs analyzed varied widely, ranging from ~3 min to more than 90 min, with a mean of 23 min (BNID 105511) and median of 20 min (Fig. 2A). No simple correlation was found between the decay rates of mRNAs and their abundance (Cor. Coeff. = 0.06), the size of the ORF (Cor. Coeff. = −0.01), codon adaptation index (Cor. Coeff. = 0.04), or the density of ribosomes bound to the mRNA (Cor. Coeff. = 0.08) (Y. Arava, D.H., and P.O.B., unpublished data) (http://www-genome.stanford.edu/turnover)."
||Ron Milo - Admin