| Autor: |
Sandrine, Laguerre, Ignacio, González, Sébastien, Nouaille, Annick, Moisan, Nathalie, Villa-Vialaneix, Christine, Gaspin, Marie, Bouvier, Agamemnon J, Carpousis, Muriel, Cocaign-Bousquet, Laurence, Girbal |
| Rok vydání: |
2018 |
| Předmět: |
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| Zdroj: |
Methods in enzymology. 612 |
| ISSN: |
1557-7988 |
| Popis: |
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. |
| Databáze: |
OpenAIRE |
| Externí odkaz: |
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