The general objective of this proposal is to develop a general protocol to dissect complex gene regulatory networks into elementary modules by integrating stochastic mathematical models with quantitative gene expression experiments in single cells. Gene regulatory networks, especially containing regulatory feedback, exhibit multistability. As genetic regulatory reactions involve small number of molecules, gene expression is stochastic and genetic noise leads to random transitions between the stable states. Therefore, a successful protocol for dissecting complex gene regulatory networks into elementary modules must include both stochastic mathematical methods and gene expression experiments performed on single cells. Both aspects are described in this proposal and are concentrated towards the following three specific aims: (1) Develop a stochastic mathematical model that successfully predicts the connectivity of synthetic genetic networks based on the experimentally obtained multistable dynamics. The expression dynamics of a collection of genetic synthetic networks with arbitrary connectivity will be quantified. Each gene will be monitored by a separate fluorescent protein reporter. As these synthetic networks are well isolated from other genetic modules in the cell, they are ideal calibration tools for mathematical models. (2) Identify the functional role of genetic noise on the bistability of the lactose uptake system of E. coll. The genetic regulation of lactose uptake is, in its simplest form, a positive feedback module leading to two stable states. Preliminary experimental data strongly suggest the presence of these two stable states and demonstrate that genetic noise induces stochastic transitions between the states. The functional role of noise in the context of evolution will be addressed by constructing mathematical models and experiments that explore the fitness of a bistable population in a fluctuating environment. (3) Identify multi-stability in the PTS system of E. coil and explore robustness of different stable states against stochastic fluctuations. The genetic architecture of the PTS system may be modeled as multiple positive feedback loops competing for the same phosphate flux. Mathematical methods will be developed that quantify the multistable behavior of this system illustrated by genetic phase diagrams. The predicted phase diagrams, reflecting the genetic wiring, will be validated by single cell gene expression experiments.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Special Emphasis Panel (ZGM1-MBP-1 (01))
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Whitmarsh, John
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Massachusetts Institute of Technology
Schools of Arts and Sciences
United States
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Soh, Y Q Shirleen; Junker, Jan Philipp; Gill, Mark E et al. (2015) A Gene Regulatory Program for Meiotic Prophase in the Fetal Ovary. PLoS Genet 11:e1005531
Slavov, Nikolai; Semrau, Stefan; Airoldi, Edoardo et al. (2015) Differential Stoichiometry among Core Ribosomal Proteins. Cell Rep 13:865-73
Slavov, Nikolai; Budnik, Bogdan A; Schwab, David et al. (2014) Constant growth rate can be supported by decreasing energy flux and increasing aerobic glycolysis. Cell Rep 7:705-14
Junker, Jan Philipp; Peterson, Kevin A; Nishi, Yuichi et al. (2014) A predictive model of bifunctional transcription factor signaling during embryonic tissue patterning. Dev Cell 31:448-60
Fang, Miaoqing; Xie, Huangming; Dougan, Stephanie K et al. (2013) Stochastic cytokine expression induces mixed T helper cell States. PLoS Biol 11:e1001618
Tan, Rui Zhen; Ji, Ni; Mentink, Remco A et al. (2013) Deconvolving the roles of Wnt ligands and receptors in sensing and amplification. Mol Syst Biol 9:631
Kim, Dong hyun; GrĂ¼n, Dominic; van Oudenaarden, Alexander (2013) Dampening of expression oscillations by synchronous regulation of a microRNA and its target. Nat Genet 45:1337-44
Teytelman, Leonid; Thurtle, Deborah M; Rine, Jasper et al. (2013) Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins. Proc Natl Acad Sci U S A 110:18602-7
Tan, Rui Zhen; van Oudenaarden, Alexander (2010) Transcript counting in single cells reveals dynamics of rDNA transcription. Mol Syst Biol 6:358
Dong, Guogang; Yang, Qiong; Wang, Qiang et al. (2010) Elevated ATPase activity of KaiC applies a circadian checkpoint on cell division in Synechococcus elongatus. Cell 140:529-39

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