Control of Transcriptional Variability by Overlapping Feed-Forward Regulatory Motifs.

@article{citeulike:3023082, abstract = {In yeast, beta-oxidation of fatty acids 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 fatty acids such as oleate. The core fatty acid-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 fatty acid-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 that are indicative of peroxisome induction (CTA1 and POT1). Simulations of the model suggest that (i) the intrinsic Adr1p-driven feed-forward loop reduces the steady-state expression variability of target genes; (ii) the parallel Oaf3p-driven inhibitory feed-forward loop modulates the dynamic response of target genes to a transiently varying oleate concentration; and (iii) 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.}, address = {Institute for Systems Biology, Seattle, Washington 98103 USA.}, author = {Ratushny, Alexander V V. and Ramsey, Stephen A A. and Roda, Oriol and Wan, Yakun and Smith, Jennifer J J. and Aitchison, John D D. }, citeulike-article-id = {3023082}, doi = {10.1529/biophysj.108.134064}, issn = {1542-0086}, journal = {Biophysical journal}, keywords = {fluctuations, modeling}, month = {July}, posted-at = {2008-07-20 18:59:00}, priority = {2}, title = {Control of Transcriptional Variability by Overlapping Feed-Forward Regulatory Motifs.}, url = {http://dx.doi.org/10.1529/biophysj.108.134064}, year = {2008} }

TY - JOUR ID - citeulike:3023082 L3 - citeulike-article-id:3023082 TI - Control of Transcriptional Variability by Overlapping Feed-Forward Regulatory Motifs. JF - Biophysical journal AD - Institute for Systems Biology, Seattle, Washington 98103 USA. SN - 1542-0086 N2 - In yeast, beta-oxidation of fatty acids 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 fatty acids such as oleate. The core fatty acid-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 fatty acid-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 that are indicative of peroxisome induction (CTA1 and POT1). Simulations of the model suggest that (i) the intrinsic Adr1p-driven feed-forward loop reduces the steady-state expression variability of target genes; (ii) the parallel Oaf3p-driven inhibitory feed-forward loop modulates the dynamic response of target genes to a transiently varying oleate concentration; and (iii) 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. KW - fluctuations KW - modeling AU - Ratushny, Alexander V AU - Ramsey, Stephen A AU - Roda, Oriol AU - Wan, Yakun AU - Smith, Jennifer J AU - Aitchison, John D PY - 2008/07/11/ UR - http://dx.doi.org/10.1529/biophysj.108.134064 ER -