1. Large-Scale Measurement of mRNA Degradation in Escherichia coli: To Delay or Not to Delay.
- Author
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Laguerre S, González I, Nouaille S, Moisan A, Villa-Vialaneix N, Gaspin C, Bouvier M, Carpousis AJ, Cocaign-Bousquet M, and Girbal L
- Subjects
- RNA Stability genetics, Transcription, Genetic genetics, Escherichia coli genetics, RNA Stability physiology, RNA, Bacterial metabolism, RNA, Messenger metabolism
- Abstract
In this study, we compared different computational methods used for genome-wide determination of mRNA half-lives in Escherichia coli with a special focus on the impact on considering a delay before the onset of mRNA decay after transcription arrest. A wide variety of datasets were analyzed coming from different technical methods for mRNA quantification (microarrays, RNA-seq, and RT-qPCR) and different bacterial growth conditions. The exponential decay of mRNA levels was fitted using both linear and exponential models and with or without a delay. We showed that for all the models, independently of mRNA quantification methods and growth conditions, ignoring the delay resulted in only a modest overestimation of the half-life. For approximately 80% of the mRNAs, differences in mRNA half-life values were less than 34s. The correlation between half-lives estimated with and without a delay was extremely high. However, the slope of the linear regression between the half-lives with and without a delay tended to decrease with the delay. For the few mRNAs for which taking into account the delay influenced the estimated half-life, the impact was dependent on the model and the growth condition. The smallest impact was obtained for the linear model., (© 2018 Elsevier Inc. All rights reserved.)
- Published
- 2018
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