title: Distribution and regulation of stochasticity and plasticity in Saccharomyces cerevisiae.
abstract: Stochasticity is an inherent feature of complex systems with nanoscale structure. In such systems information is represented by small collections of elements (e.g., a few electrons on a quantum dot), and small variations in the populations of these elements may lead to big uncertainties in the information. Unfortunately, little is known about how to work within this inherently noisy environment to design robust functionality into complex nanoscale systems. Here, we look to the biological cell as an intriguing model system where evolution has mediated the trade-offs between fluctuations and function, and in particular we look at the relationships and trade-offs between stochastic and deterministic responses in the gene expression of budding yeast (Saccharomyces cerevisiae). We find gene regulatory arrangements that control the stochastic and deterministic components of expression, and show that genes that have evolved to respond to stimuli (stress) in the most strongly deterministic way exhibit the most noise in the absence of the stimuli. We show that this relationship is consistent with a bursty two-state model of gene expression, and demonstrate that this regulatory motif generates the most uncertainty in gene expression when there is the greatest uncertainty in the optimal level of gene expression.
authors.affiliation: Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Bethel Valley Road, Oak Ridge, Tennessee 37831, USA.
authors.forename: R D
authors.initials: RD
authors.lastname: Dar
authors.forename: D K
authors.initials: DK
authors.lastname: Karig
authors.forename: J F
authors.initials: JF
authors.lastname: Cooke
authors.forename: C D
authors.initials: CD
authors.lastname: Cox
authors.forename: M L
authors.initials: ML
authors.lastname: Simpson
mesh_terms: D003198:Computer Simulation; D053263:Gene Regulatory Networks / Q000235:genetics; D005800:Genes, Fungal / Q000235:genetics; D008957:Models, Genetic; D009707:Nucleosomes / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D013269:Stochastic Processes; D014158:Transcription, Genetic
chemical_list: D009707:Nucleosomes