CoChat
Sign Up
PreprintCited by 35Fungal and yeast genetics researchGene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast

Open access
Yu, Rosemary, Vorontsov, Egor, Sihlbom, Carina, Nielsen, Jens·2020·eLife
DOI 10.1101/2020.12.22.423946PMC PMC8016476

Preprint — published as 10.7554/elife.65722 · Paper page

Open this paper in CoChat — free account

Abstract

In addition to specific regulatory circuits, gene expression is also regulated by global physiological cues such as the cell growth rate and metabolic parameters. Here we examine these global control mechanisms by analyzing an orthogonal multi-omics dataset consisting of absolute-quantitative abundances of the transcriptome, proteome, and intracellular amino acids in 22 steady-state yeast cultures. Our model indicates that transcript and protein abundance are coordinately controlled by the cell growth rate via RNA polymerase II and ribosome abundance, but are independently controlled by metabolic parameters relating to amino acid and nucleotide availability. Genes in central carbon metabolism, however, are regulated independently of these global physiological cues. Our findings can be used to augment gene expression profiling analyses in the distantly related yeast Schizosaccharomyces pombe and a human cancer cell model. Our results provide a framework to analyze gene expression profiles to gain novel biological insights, a key goal of systems biology.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/2020.12.22.423946

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 46

  1. 10.1038/msb.2013.14 · DOI
  2. 10.1016/j.copbio.2014.01.001 · DOI
  3. 10.1186/1754-1611-7-22 · DOI
  4. 10.1016/j.cell.2009.12.001 · DOI · Paper page
  5. 2016, The metabolic background is a global player in Saccharomyces gene expression epistasis, Nat Microbiol, 1, 15030, 10.1038/nmicrobiol.2015.30 · DOI
  6. S. R. Hackett et al., Systems-level analysis of mechanisms regulating yeast metabolic flux. Science 354, (2016). · DOI
  7. 10.1186/gb-2006-7-11-r107 · DOI
  8. 10.1038/s41467-020-15749-0 · DOI
  9. 10.1016/j.mib.2015.05.012 · DOI
  10. 10.1073/pnas.1116998108 · DOI
  11. 10.1091/mbc.E07-08-0779 · DOI · Paper page
  12. 10.1091/mbc.E09-07-0597 · DOI
  13. 10.1091/mbc.E11-02-0132 · DOI
  14. 10.1128/MCB.01084-06 · DOI
  15. 10.1007/BF00430373 · DOI
  16. 10.1128/jb.175.15.4809-4816.1993 · DOI
  17. 2017, Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast, Cell Syst, 4, 495, 10.1016/j.cels.2017.03.003 · DOI · Paper page
  18. 10.1016/j.cell.2012.09.019 · DOI · Paper page
  19. 2018, Production of Protein-Complex Components Is Stoichiometric and Lacks General Feedback Regulation in Eukaryotes, Cell Syst, 7, 580, 10.1016/j.cels.2018.11.003 · DOI
  20. 10.1073/pnas.1921890117 · DOI
  21. 2014, NbClust: An R Package for Determining the Relevant Number of Clusters in a Data Set, 2014, 61, 36
  22. 10.1093/nar/gkr1029 · DOI
  23. C. Carlberg , F. Molnár , in Mechanisms of Gene Regulation. (Springer Netherlands, Dordrecht, 2014), pp. 37–54. · DOI
  24. 10.1073/pnas.0804953105 · DOI
  25. 10.1371/journal.pcbi.1006548 · DOI
  26. R. Yu , J. Nielsen , Big data in yeast systems biology. FEMS Yeast Res 19, (2019). · DOI
  27. 10.1038/nature04785 · DOI · Paper page
  28. 10.1371/journal.pgen.1005206 · DOI · Paper page
  29. E. Metzl-Raz et al., Principles of cellular resource allocation revealed by condition-dependent proteome profiling. Elife 6, (2017). · DOI
  30. 10.1126/science.1168978 · DOI · Paper page
  31. 10.1016/j.celrep.2016.01.043 · DOI · Paper page
  32. 2019, PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information, Nucleic Acids Res, 47, D821, 10.1093/nar/gky961 · DOI
  33. 10.1016/j.cell.2012.08.026 · DOI
  34. 10.1038/s41467-018-03803-x · DOI
  35. 10.1016/S0960-9822(99)80507-7 · DOI
  36. 10.1093/bioinformatics/btn615 · DOI
  37. 10.1038/s41467-017-01242-8 · DOI
  38. 10.1039/c4mb00721b · DOI · Paper page
  39. 10.1039/c3mb70119k · DOI · Paper page
  40. 10.1016/j.cell.2019.12.023 · DOI · Paper page
  41. 2019, Emergent Gene Expression Responses to Drug Combinations Predict Higher-Order Drug Interactions, Cell Syst, 9, 423, 10.1016/j.cels.2019.10.004 · DOI
  42. 10.1038/nm.3060 · DOI
  43. 10.1016/j.celrep.2014.10.065 · DOI · Paper page
  44. 10.1074/mcp.M111.011072 · DOI
  45. 10.1093/nar/gky1106 · DOI
  46. 10.1093/nar/gky1055 · DOI · Paper page

Metadata

Authors
Yu, R., Vorontsov, E., Sihlbom, C., & Nielsen, J.
Affiliations
  • Chalmers University of Technology (SE)
  • University of Gothenburg (SE)
  • Novo Nordisk Foundation (DK)
Corresponding author
Nielsen, Jens
ORCID
Venue
eLife
Publisher
openRxiv
Published
2020-12-22
Volume
10
ISSN
2050-084X (ISSN-L)
DOI
10.1101/2020.12.22.423946
PMC
PMC8016476
OpenAlex
W3136840376
Cited by
35
References
1
Citations by year
2026: 4 · 2025: 5 · 2024: 7 · 2023: 10 · 2022: 4 · 2021: 5
FWCI
2.04
Type
journal article
Language
en
Open access
Licence
Locations
  • eLife (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion, other-oa)
  • Chalmers Research (Chalmers University of Technology) (submittedVersion)
Funders
  • Knut och Alice Wallenbergs Stiftelse (NNF10CC1016517)
  • Novo Nordisk (NNF10CC1016517)
  • Danmarks Tekniske Universitet (NNF10CC1016517)
  • Göteborgs Universitet
  • Novo Nordisk Fonden (NNF17SA0032514, NNF10CC1016517)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
Keywords
gene expression regulation, central carbon metabolism, Saccharomyces cerevisiae, growth rate, nitrogen metabolism, amino acid availability, RNA polymerase II, ribosome abundance, transcription, translation (biology), transcriptome, proteome, multi-omics
MeSH terms
Carbon, Genes, Fungal, Nitrogen, Saccharomyces cerevisiae, Transcriptome

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review