Half lives of mRNAs and of Poly(A) of mRNAs of 4687 genes

Range Excel Table - link
Organism Budding yeast Saccharomyces cerevisiae
Reference 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) supporting site, please see primary sourcePubMed ID11972065
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Method By using DNA microarrays, researchers precisely measured the decay of each yeast mRNA, after thermal inactivation of a temperature-sensitive RNA polymerase II: Yeast was grown on YPD at 24 degrees celsius, transferred to a similar medium at 49 degrees and 0, 5, 10, 15, 20, 30, 40, 50, and 60 min after the temperature shift harvested on a nitrocellulose filter followed by liquid nitrogen freezing and total RNA extraction by hot phenol extraction. 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 in article), 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 in article). To examine the global relationship between poly(A) shortening and mRNA turnover, researchers made a separate series of measurements of the fate of each mRNA, using an anchored oligo(dT) primer (5'-T20VN-3'), rather than random primers, in the cDNA probe synthesis. This approach allowed them to track specifically the mRNAs that retained poly(A) tails of sufficient length to allow priming. The poly(A)+ mRNA decay half-lives, as defined in their assay, were distributed within a narrower range and were significantly shorter (peak at 10–15 min) than the overall mRNA decay half-lives (Fig. 2A).
Comments Look at 'Data' sheet in Excel file. Note, in 'Data' sheet column BF has half lives with greater values than column DM and thus BF would seem to be overall mRNA half life and DM the Poly(A) half life. However, the designation in the table (DE and BE) says the opposite, which seems to be in error. Column B gives gene name and protein function.
Entered by Uri M
ID 105512