Optimizing information flow in small genetic networks. I

Abstract

In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable randomness of individual molecular events. Here we explore how cells can maximize their control power in the presence of these physical limits; formally, we solve the theoretical problem of maximizing the information transferred from inputs to outputs when the number of available molecules is held fixed. We start with the simplest version of the problem, in which a single transcription factor protein controls the readout of one or more genes by binding to DNA. We further simplify by assuming that this regulatory network operates in steady state, that the noise is small relative to the available dynamic range, and that the target genes do not interact. Even in this simple limit, we find a surprisingly rich set of optimal solutions. Importantly, for each locally optimal regulatory network, all parameters are determined once the physical constraints on the number of available molecules are specified. Although we are solving an over--simplified version of the problem facing real cells, we see parallels between the structure of these optimal solutions and the behavior of actual genetic regulatory networks. Subsequent papers will discuss more complete versions of the problem.

References in corpus (9)

• Information flow and optimization in transcriptional control
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• Mutual information between in- and output trajectories of biochemical networks
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• Information capacity of genetic regulatory elements
• The role of input noise in transcriptional regulation
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• Quantitative transcription factor binding kinetics at the single-molecule level
• Reaction coordinates for the flipping of genetic switches

Cited by in corpus (45)

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• Optimizing information flow in small genetic networks. II: Feed forward interactions
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• Transmission of Information between Complex Networks: 1/f-Resonance
• Noise and information transmission in promoters with multiple internal states
• Optimizing information flow in small genetic networks. III. A self-interacting gene
• Stochastic Thermodynamics of Learning
• Perspectives on theory at the interface of physics and biology
• Thermodynamic limits to information harvesting by sensory systems
• Analytic methods for modeling stochastic regulatory networks
• Reconciling Kinetic and Equilibrium Models of Bacterial Transcription
• Estimating information in time-varying signals
• Trading bits in the readout from a genetic network
• Probing the limits to microRNA-mediated control of gene expression
• Noise expands the response range of the Bacillus subtilis competence circuit
• ceRNA crosstalk stabilizes protein expression and affects the correlation pattern of interacting proteins
• Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information
• Energy consumption and cooperation for optimal sensing
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• Optimal census by quorum sensing
• Redundancy in the information transmission in a two-step cascade
• Only accessible information is useful: insights from gradient-mediated patterning
• Optimal entrainment of circadian clocks in the presence of noise
• The accuracy of telling time via oscillatory signals
• Time-dependent information transmission in a model regulatory circuit
• Extending the dynamic range of transcription factor action by translational regulation
• Trade-offs in delayed information transmission in biochemical networks
• Multiplexing oscillatory biochemical signals
• Pleiotropy enables specific and accurate signaling in the presence of ligand cross talk
• Interplay of synergy and redundancy in diamond motif
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• A statistical method for revealing form-function relations in biological networks
• Information propagation in Gaussian processes on multilayer networks
• Ambitions for theory in the physics of life
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• Weak transcription factor clustering at binding sites can facilitate information transfer from molecular signals
• Optimized two-dimensional Networks with edge crossing cost: frustrated anti-ferromagnetic spin system
• Dissipation in non-steady state regulatory circuits
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• Generalized Inverse Optimal Control and its Application in Biology
• Positional information, positional error, and read-out precision in morphogenesis: a mathematical framework