ArticleGenome biology2007
Common gene expression strategies revealed by genome-wide analysis in yeast.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 35 citations in OpenAlex.
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- The importance of controlling mRNA turnover during cell proliferation.Current genetics · 2016Review
- The Rtr1p CTD phosphatase autoregulates its mRNA through a degradation pathway involving the REX exonucleases.RNA (New York, N.Y.) · 2016Article
- A geometric analysis of fast-slow models for stochastic gene expression.Journal of mathematical biology · 2016Article
- Transcriptomics of cryophilic Saccharomyces kudriavzevii reveals the key role of gene translation efficiency in cold stress adaptations.BMC genomics · 2014Article
- Cytoplasmic 5'-3' exonuclease Xrn1p is also a genome-wide transcription factor in yeast.Frontiers in genetics · 2014Article
- Nonsense-mediated mRNA decay controls the changes in yeast ribosomal protein pre-mRNAs levels upon osmotic stress.PloS one · 2013Article
- Exact and approximate distributions of protein and mRNA levels in the low-copy regime of gene expression.Journal of mathematical biology · 2012Article
- A dynamic model of proteome changes reveals new roles for transcript alteration in yeast.Molecular systems biology · 2011Article
- Heat shock response in yeast involves changes in both transcription rates and mRNA stabilities.PloS one · 2011Article
- Multiple levels of gene regulation mediate differentiation of the intracellular pathogen Leishmania.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2011Article
- Genomic insights into the different layers of gene regulation in yeast.Genetics research international · 2011Article
- Article
- Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line.Molecular systems biology · 2010Article
- A comprehensive, quantitative, and genome-wide model of translation.PLoS computational biology · 2010Article
- Multidimensional gene set analysis of genomic data.PloS one · 2010Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGene expression is a two-step synthesis process that ends with the necessary amount of each protein required to perform its function. Since the protein is the final product, the main focus of gene regulation should be centered on it. However, because mRNA is an intermediate step and the amounts of both mRNA and protein are controlled by their synthesis and degradation rates, the desired amount of protein can be achieved following different strategies.
resultsIn this paper we present the first comprehensive analysis of the relationships among the six variables that characterize gene expression in a living organism: transcription and translation rates, mRNA and protein amounts, and mRNA and protein stabilities. We have used previously published data from exponentially growing Saccharomyces cerevisiae cells. We show that there is a general tendency to harmonize the levels of mRNA and protein by coordinating their synthesis rates and that functionally related genes tend to have similar values for the six variables.
conclusionWe propose that yeast cells use common expression strategies for genes acting in the same physiological pathways. This trend is more evident for genes coding for large and stable protein complexes, such as ribosomes or the proteasome. Hence, each functional group can be defined by a 'six variable profile' that illustrates the common strategy followed by the genes included in it. Genes encoding subunits of protein complexes show a tendency to have relatively unstable mRNAs and a less balanced profile for mRNA than for protein, suggesting a stronger regulation at the transcriptional level.
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