ArticleeLife2021
Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast.
Article in eLife, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 39 citations in OpenAlex.
- 3D confinement physically regulates cell cycle progression in budding yeast.Nature communications · 2026Article
- Metab8D: a metabolic regulome network from multiomics and machine learning.Communications biology · 2026Article
- EnzymeTuning improves enzyme-constrained metabolic modeling and proteome abundance prediction through deep learning.Nature communications · 2026Article
- Accurate prediction of flux distributions compatible with metabolite concentration effects in genome-scale metabolic networks.PLoS computational biology · 2026Article
- Improved flux profiling in genome-scale modeling of human cell metabolism.Cell reports methods · 2026Article
- Global constraint principle for microbial growth laws.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Interaction of genetic variants activates latent metabolic pathways in yeast.Nature communications · 2025Article
- Coarse-Grained Modeling Elucidates Differential Metabolism ofACS synthetic biology · 2025Article
- Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community.Molecular systems biology · 2024Article
- Machine learning of metabolite-protein interactions from model-derived metabolic phenotypes.NAR genomics and bioinformatics · 2024Article
- siqRNA-seq is a spike-in-independent technique for quantitative mapping of mRNA landscape.BMC genomics · 2024Article
- Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress.Nucleic acids research · 2024Article
- PARROT: Prediction of enzyme abundances using protein-constrained metabolic models.PLoS computational biology · 2023Article
- A coarse-grained resource allocation model of carbon and nitrogen metabolism in unicellular microbes.Journal of the Royal Society, Interface · 2023Article
- Growth-dependent Gene Expression Variation Influences the Strength of Codon Usage Biases.Molecular biology and evolution · 2023Article
- Growth-dependent gene expression variation influences the strength of codon usage biases.bioRxiv : the preprint server for biology · 2023Article
- Article
- Data integration across conditions improves turnover number estimates and metabolic predictions.Nature communications · 2023Article
- Enhanced glycerol assimilation and lipid production in Rhodotorula toruloides CBS14 upon addition of hemicellulose primarily correlates with early transcription of energy-metabolism-related genes.Biotechnology for biofuels and bioproducts · 2023Article
- Validated Growth Rate-Dependent Regulation of Lipid Metabolism inInternational journal of molecular sciences · 2022Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
In addition to controlled expression of genes by specific regulatory circuits, the abundance of proteins and transcripts can also be influenced by physiological states of the cell such as growth rate and metabolism. Here we examine the control of gene expression by growth rate and metabolism, by analyzing a multi-omics dataset consisting of absolute-quantitative abundances of the transcriptome, proteome, and amino acids in 22 steady-state yeast cultures. We find that transcription and translation are coordinately controlled by the cell growth rate via RNA polymerase II and ribosome abundance, but they are independently controlled by nitrogen metabolism via amino acid and nucleotide availabilities. Genes in central carbon metabolism, however, are distinctly regulated and do not respond to the cell growth rate or nitrogen metabolism as all other genes. Understanding these effects allows the confounding factors of growth rate and metabolism to be accounted for in gene expression profiling studies.
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