ArticleBMC genomics2007
Exploiting combinatorial cultivation conditions to infer transcriptional regulation.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 51 citations in OpenAlex.
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- Suboptimal Global Transcriptional Response Increases the Harmful Effects of Loss-of-Function Mutations.Molecular biology and evolution · 2021Article
- Vitamin requirements and biosynthesis in Saccharomyces cerevisiae.Yeast (Chichester, England) · 2020Review
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- Maintenance-energy requirements and robustness of Saccharomyces cerevisiae at aerobic near-zero specific growth rates.Microbial cell factories · 2016Article
- Oxygen availability strongly affects chronological lifespan and thermotolerance in batch cultures ofMicrobial cell (Graz, Austria) · 2015Article
- Reporter pathway analysis from transcriptome data: Metabolite-centric versus Reaction-centric approach.Scientific reports · 2015Article
- Growth-rate dependency of de novo resveratrol production in chemostat cultures of an engineered Saccharomyces cerevisiae strain.Microbial cell factories · 2015Article
- Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions.BMC systems biology · 2015Article
- Environmental Interactions and Epistasis Are Revealed in the Proteomic Responses to Complex Stimuli.PloS one · 2015Article
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- Physiological and transcriptional responses of anaerobic chemostat cultures of Saccharomyces cerevisiae subjected to diurnal temperature cycles.Applied and environmental microbiology · 2014Article
- Transcriptome-based characterization of interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus in lactose-grown chemostat cocultures.Applied and environmental microbiology · 2013Article
- Genome-scale analyses of butanol tolerance in Saccharomyces cerevisiae reveal an essential role of protein degradation.Biotechnology for biofuels · 2013Article
- Cellular responses of Saccharomyces cerevisiae at near-zero growth rates: transcriptome analysis of anaerobic retentostat cultures.FEMS yeast research · 2011Article
- The renaissance of continuous culture in the post-genomics age.Journal of industrial microbiology & biotechnology · 2010Article
- Identity of the growth-limiting nutrient strongly affects storage carbohydrate accumulation in anaerobic chemostat cultures of Saccharomyces cerevisiae.Applied and environmental microbiology · 2009Article
- Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data.Nucleic acids research · 2009Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRegulatory networks often employ the model that attributes changes in gene expression levels, as observed across different cellular conditions, to changes in the activity of transcription factors (TFs). Although the actual conditions that trigger a change in TF activity should form an integral part of the generated regulatory network, they are usually lacking. This is due to the fact that the large heterogeneity in the employed conditions and the continuous changes in environmental parameters in the often used shake-flask cultures, prevent the unambiguous modeling of the cultivation conditions within the computational framework.
resultsWe designed an experimental setup that allows us to explicitly model the cultivation conditions and use these to infer the activity of TFs. The yeast Saccharomyces cerevisiae was cultivated under four different nutrient limitations in both aerobic and anaerobic chemostat cultures. In the chemostats, environmental and growth parameters are accurately controlled. Consequently, the measured transcriptional response can be directly correlated with changes in the limited nutrient or oxygen concentration. We devised a tailor-made computational approach that exploits the systematic setup of the cultivation conditions in order to identify the individual and combined effects of nutrient limitations and oxygen availability on expression behavior and TF activity.
conclusionIncorporating the actual growth conditions when inferring regulatory relationships provides detailed insight in the functionality of the TFs that are triggered by changes in the employed cultivation conditions. For example, our results confirm the established role of TF Hap4 in both aerobic regulation and glucose derepression. Among the numerous inferred condition-specific regulatory associations between gene sets and TFs, also many novel putative regulatory mechanisms, such as the possible role of Tye7 in sulfur metabolism, were identified.
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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.