Global Analysis of Eukaryotic mRNA Degradation Reveals Xrn1-Dependent Buffering of Transcript Levels

The rates of mRNA synthesis and degradation determine cellular mRNA levels and can be monitored by comparative dynamic transcriptome analysis (cDTA) that uses nonperturbing metabolic RNA labeling. Here we present cDTA data for 46 yeast strains lacking genes involved in mRNA degradation and metabolis...

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Bibliographic Details
Published in:Molecular cell 2013-10, Vol.52 (1), p.52-62
Main Authors: Sun, Mai, Schwalb, Björn, Pirkl, Nicole, Maier, Kerstin C., Schenk, Arne, Failmezger, Henrik, Tresch, Achim, Cramer, Patrick
Format: Article
Language:English
Subjects:
Adaptor Proteins, Signal Transducing - metabolism
Cluster Analysis
data analysis
Exoribonucleases - genetics
Exoribonucleases - metabolism
Gene Expression Regulation, Fungal
genes
Kinetics
messenger RNA
metabolism
Models, Genetic
monitoring
Mutation
N-Glycosyl Hydrolases - metabolism
Repressor Proteins - metabolism
RNA Stability
RNA, Fungal - biosynthesis
RNA, Fungal - metabolism
RNA, Messenger - biosynthesis
RNA, Messenger - metabolism
Saccharomyces cerevisiae - enzymology
Saccharomyces cerevisiae - genetics
Saccharomyces cerevisiae Proteins - genetics
Saccharomyces cerevisiae Proteins - metabolism
Substrate Specificity
transcriptomics
yeasts
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Summary:The rates of mRNA synthesis and degradation determine cellular mRNA levels and can be monitored by comparative dynamic transcriptome analysis (cDTA) that uses nonperturbing metabolic RNA labeling. Here we present cDTA data for 46 yeast strains lacking genes involved in mRNA degradation and metabolism. In these strains, changes in mRNA degradation rates are generally compensated by changes in mRNA synthesis rates, resulting in a buffering of mRNA levels. We show that buffering of mRNA levels requires the RNA exonuclease Xrn1. The buffering is rapidly established when mRNA synthesis is impaired, but is delayed when mRNA degradation is impaired, apparently due to Xrn1-dependent transcription repressor induction. Cluster analysis of the data defines the general mRNA degradation machinery, reveals different substrate preferences for the two mRNA deadenylase complexes Ccr4-Not and Pan2-Pan3, and unveils an interwoven cellular mRNA surveillance network. •We report mRNA synthesis and degradation rates in 46 yeast gene deletion strains•Eukaryotic cells buffer mRNA levels, and this requires the exonuclease Xrn1•The data reveal interaction networks among mRNA degradation factors
ISSN:1097-2765
1097-4164
DOI:10.1016/j.molcel.2013.09.010