ArticleMolecular biology of the cell2012
Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway.
Article in Molecular biology of the cell, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 59 citations in OpenAlex.
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- Overexpression of MET4 Leads to the Upregulation of Stress-Related Genes and Enhanced Sulfite Tolerance inCells · 2022Article
- Functional network motifs defined through integration of protein-protein and genetic interactions.PeerJ · 2022Article
- Perturbation-Based Modeling Unveils the Autophagic Modulation of Chemosensitivity and Immunogenicity in Breast Cancer Cells.Metabolites · 2021Article
- Linking the dynamics of chromatin occupancy and transcription with predictive models.Genome research · 2021Article
- A genome-scale yeast library with inducible expression of individual genes.Molecular systems biology · 2021Article
- Acute ethanol stress induces sumoylation of conserved chromatin structural proteins inMolecular biology of the cell · 2021Article
- Learning causal networks using inducible transcription factors and transcriptome-wide time series.Molecular systems biology · 2020Article
- Homotypic cooperativity and collective binding are determinants of bHLH specificity and function.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
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- Design and Implementation of an Automated Illuminating, Culturing, and Sampling System for Microbial Optogenetic Applications.Journal of visualized experiments : JoVE · 2017Article
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- Identifying genetic modulators of the connectivity between transcription factors and their transcriptional targets.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- How to train your microbe: methods for dynamically characterizing gene networks.Current opinion in microbiology · 2015Review
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
In yeast, the pathways of sulfur assimilation are combinatorially controlled by five transcriptional regulators (three DNA-binding proteins [Met31p, Met32p, and Cbf1p], an activator [Met4p], and a cofactor [Met28p]) and a ubiquitin ligase subunit (Met30p). This regulatory system exerts combinatorial control not only over sulfur assimilation and methionine biosynthesis, but also on many other physiological functions in the cell. Recently we characterized a gene induction system that, upon the addition of an inducer, results in near-immediate transcription of a gene of interest under physiological conditions. We used this to perturb levels of single transcription factors during steady-state growth in chemostats, which facilitated distinction of direct from indirect effects of individual factors dynamically through quantification of the subsequent changes in genome-wide patterns of gene expression. We were able to show directly that Cbf1p acts sometimes as a repressor and sometimes as an activator. We also found circumstances in which Met31p/Met32p function as repressors, as well as those in which they function as activators. We elucidated and numerically modeled feedback relationships among the regulators, notably feedforward regulation of Met32p (but not Met31p) by Met4p that generates dynamic differences in abundance that can account for the differences in function of these two proteins despite their identical binding sites.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.