title: Control of transcriptional variability by overlapping feed-forward regulatory motifs.
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.
authors.affiliation: Institute for Systems Biology, Seattle, Washington, USA.
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Ratushny
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Ramsey
authors.forename: Oriol
authors.initials: O
authors.lastname: Roda
authors.forename: Yakun
authors.initials: Y
authors.lastname: Wan
authors.forename: Jennifer J
authors.initials: JJ
authors.lastname: Smith
authors.forename: John D
authors.initials: JD
authors.lastname: Aitchison
mesh_terms: D019295:Computational Biology; D003198:Computer Simulation; D019281:Dimerization; D017353:Gene Deletion; D015966:Gene Expression Regulation, Fungal / Q000187:drug effects; D053263:Gene Regulatory Networks; D005800:Genes, Fungal; D008957:Models, Genetic; D019301:Oleic Acid / Q000494:pharmacology; D012441:Saccharomyces cerevisiae / Q000187:drug effects / Q000235:genetics*; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic / Q000187:drug effects; D015533:Transcriptional Activation / Q000187:drug effects
chemical_list: D014157:Transcription Factors; D019301:Oleic Acid