ArticleThe FEBS journal2012
Dynamics of oscillatory phenotypes in Saccharomyces cerevisiae reveal a network of genome-wide transcriptional oscillators.
Article in The FEBS journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Eukaryotic cell biology is temporally coordinated to support the energetic demands of protein homeostasis.Nature communications · 2020Article
- Inference of Large-scale Time-delayed Gene Regulatory Network with Parallel MapReduce Cloud Platform.Scientific reports · 2018Article
- Temporal metabolic partitioning of the yeast and protist cellular networks: the cell is a global scale-invariant (fractal or self-similar) multioscillator.Journal of biomedical optics · 2018Article
- MapReduce Algorithms for Inferring Gene Regulatory Networks from Time-Series Microarray Data Using an Information-Theoretic Approach.BioMed research international · 2017Article
- The molecular basis of metabolic cycles and their relationship to circadian rhythms.Nature structural & molecular biology · 2016Review
- Semi-supervised prediction of gene regulatory networks using machine learning algorithms.Journal of biosciences · 2015Article
- Homeostasis of redox status derived from glucose metabolic pathway could be the key to understanding the Warburg effect.American journal of cancer research · 2015Review
- Homeostasis of redox status derived from glucose metabolic pathway could be the key to understanding the Warburg effect.American journal of cancer research · 2015Review
- Comprehensive analysis of forty yeast microarray datasets reveals a novel subset of genes (APha-RiB) consistently negatively associated with ribosome biogenesis.BMC bioinformatics · 2014Article
- Identifying transcription factor complexes and their roles.Bioinformatics (Oxford, England) · 2014Article
- Free energy rhythms in Saccharomyces cerevisiae: a dynamic perspective with implications for ribosomal biogenesis.Biochemistry · 2013Article
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Authors and funding
4 authors.
Funding
Abstract
Genetic and environmental factors are well-studied influences on phenotype; however, time is a variable that is rarely considered when studying changes in cellular phenotype. Time-resolved microarray data revealed genome-wide transcriptional oscillation in a yeast continuous culture system with ∼ 2 and ∼ 4 h periods. We mapped the global patterns of transcriptional oscillations into a 3D map to represent different cellular phenotypes of redox cycles. This map shows the dynamic nature of gene expression in that transcripts are ordered and coupled to each other through time and concentration space. Although cells differed in oscillation periods, transcripts involved in certain processes were conserved in a deterministic way. When oscillation period lengthened, the peak to trough ratio of transcripts increased and the fraction of cells in the unbudded (G0/G1) phase of the cell division cycle increased. Decreasing the glucose level in the culture medium was one way to increase the redox cycle, possibly from changes in metabolic flux. The period may be responding to lower glucose levels by increasing the fraction of cells in G1 and reducing S-phase gating so that cells can spend more time in catabolic processes. Our results support that gene transcripts are coordinated with metabolic functions and the cell division cycle.
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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.