ArticleBiophysical journal2008
Control of transcriptional variability by overlapping feed-forward regulatory motifs.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 26 citations in OpenAlex.
- Signaling dynamics and peroxisomes.Current opinion in cell biology · 2015Review
- Systems cell biology.The Journal of cell biology · 2014Review
- Molecular mechanisms of system responses to novel stimuli are predictable from public data.Nucleic acids research · 2014Article
- Peroxisomes take shape.Nature reviews. Molecular cell biology · 2013Review
- Biological network motif detection: principles and practice.Briefings in bioinformatics · 2012Article
- A self-propelled biological process: Plk1-dependent, product-activated feedforward mechanism.Cell cycle (Georgetown, Tex.) · 2011Article
- A regression model approach to enable cell morphology correction in high-throughput flow cytometry.Molecular systems biology · 2011Article
- Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues.PLoS computational biology · 2011Article
- Feed-forward mechanism of converting biochemical cooperativity to mitotic processes at the kinetochore plate.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Dark matters in AMD genetics: epigenetics and stochasticity.Investigative ophthalmology & visual science · 2011Review
- Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing.Molecular systems biology · 2011Article
- Mathematical modeling of biomolecular network dynamics.Methods in molecular biology (Clifton, N.J.) · 2011Article
- Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction.Molecular & cellular proteomics : MCP · 2010Article
- Genome-wide analysis of effectors of peroxisome biogenesis.PloS one · 2010Article
- Avoiding unscheduled transcription in shared promoters: Saccharomyces cerevisiae Sum1p represses the divergent gene pair SPS18-SPS19 through a midsporulation element (MSE).FEMS yeast research · 2009Article
- Role of the histone variant H2A.Z/Htz1p in TBP recruitment, chromatin dynamics, and regulated expression of oleate-responsive genes.Molecular and cellular biology · 2009Article
- Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture.Molecular systems biology · 2009Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
In yeast, beta-oxidation of fatty acids (FAs) takes place in the peroxisome, an organelle whose size and number are controlled in response to environmental cues. The expression of genes required for peroxisome assembly and function is controlled by a transcriptional regulatory network that is induced by FAs such as oleate. The core FA-responsive transcriptional network consists of carbon source-sensing transcription factors that regulate key target genes through an overlapping feed-forward network motif (OFFNM). However, a systems-level understanding of the function of this network architecture in regulating dynamic FA-induced gene expression is lacking. The specific role of the OFFNM in regulating the dynamic and cell-population transcriptional response to oleate was investigated using a kinetic model comprised of four core transcription factor genes (ADR1, OAF1, PIP2, and OAF3) and two reporter genes (CTA1 and POT1) that are indicative of peroxisome induction. Simulations of the model suggest that 1), the intrinsic Adr1p-driven feed-forward loop reduces the steady-state expression variability of target genes; 2), the parallel Oaf3p-driven inhibitory feed-forward loop modulates the dynamic response of target genes to a transiently varying oleate concentration; and 3), heterodimerization of Oaf1p and Pip2p does not appear to have a noise-reducing function in the context of oleate-dependent expression of target genes. The OFFNM is highly overrepresented in the yeast regulome, suggesting that the specific functions described for the OFFNM, or other properties of this motif, provide a selective advantage.
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Registered trials
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.