ArticlePLoS computational biology2012
Stochastic modeling of expression kinetics identifies messenger half-lives and reveals sequential waves of co-ordinated transcription and decay.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- StaRTrEK:in silico estimation of RNA half-lives from genome-wide time-course experiments without transcriptional inhibition.BMC bioinformatics · 2022Article
- Species-specific pace of development is associated with differences in protein stability.Science (New York, N.Y.) · 2020Article
- Methods for the analysis of transcriptome dynamics.Toxicology research · 2019Review
- Sex Bias and Maternal Contribution to Gene Expression Divergence in Drosophila Blastoderm Embryos.PLoS genetics · 2015Article
- XRN1 stalling in the 5' UTR of Hepatitis C virus and Bovine Viral Diarrhea virus is associated with dysregulated host mRNA stability.PLoS pathogens · 2015Article
- Global analysis of mRNA isoform half-lives reveals stabilizing and destabilizing elements in yeast.Cell · 2014Article
- Identification of under-detected periodicity in time-series microarray data by using empirical mode decomposition.PloS one · 2014Article
Corrections and comments
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Authors and funding
5 authors.
Funding
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Abstract
The transcriptome in a cell is finely regulated by a large number of molecular mechanisms able to control the balance between mRNA production and degradation. Recent experimental findings have evidenced that fine and specific regulation of degradation is needed for proper orchestration of a global cell response to environmental conditions. We developed a computational technique based on stochastic modeling, to infer condition-specific individual mRNA half-lives directly from gene expression time-courses. Predictions from our method were validated by experimentally measured mRNA decay rates during the intraerythrocytic developmental cycle of Plasmodium falciparum. We then applied our methodology to publicly available data on the reproductive and metabolic cycle of budding yeast. Strikingly, our analysis revealed, in all cases, the presence of periodic changes in decay rates of sequentially induced genes and co-ordination strategies between transcription and degradation, thus suggesting a general principle for the proper coordination of transcription and degradation machinery in response to internal and/or external stimuli.
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Registered trials
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