Transcriptional Regulation by the Numbers 2: Applications

By Lacramioara Bintu, Nicolas E. Buchler, Hernan G. Garcia, U. Gerland, Terence Hwa, J. Kondev, T. Kuhlman, Rob Phillips. 2004

271 citations recorded by the source corpus.

With the increasing amount of experimental data on gene expression and regulation, there is a growing need for quantitative models to describe the data and relate them to the different contexts. The thermodynamic models reviewed in the preceding paper provide a useful framework for the quantitative analysis of bacterial transcription regulation. We review a number of well-characterized bacterial promoters that are regulated by one or two species of transcription factors, and apply the thermodynamic framework to these promoters. We show that the framework allows one to quantify vastly different forms of gene expression using a few parameters. As such, it provides a compact description useful for higher-level studies, e.g., of genetic networks, without the need to invoke the biochemical details of every component. Moreover, it can be used to generate hypotheses on the likely mechanisms of transcriptional control.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1cd406a4866854b410c0a13cd7b42cbc64e0bf48

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In Genetics

1. Debashish Chowdhury
2. Howard M. Salis
3. Zachary Booth Simpson
4. Christopher A. Voigt
5. James C. Liao

In Molecular Biology

1. Debashish Chowdhury
2. Edward M. Marcotte
3. Howard M. Salis
4. Zachary Booth Simpson
5. Christopher A. Voigt
6. Yaakov Benenson
7. James J. Collins
8. Ahmad S. Khalil

Citations in the corpus

• A Synthetic Genetic Edge Detection Program (2009, methodology): “The transfer function, which characterizes how the output of a circuit varies with input at steady-state, has been shown to be a useful tool for connecting genetic circuits (Anderson et al., 2007; Bintu et al., 2005a; Voigt, 2006; Weiss et al., 1999; Yoko- bayashi et al., 2002).”
• Transcriptional Regulation by the Numbers 1: Models (2004, unknown): “In a companion paper [1], these ideas are applied to several case studies which illustrate the use of the general formalism.”
• Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist’s perspective (2012, methodology): “RNAP binding has been treated within the framework of equilibrium statistical mechanics [1492, 1493].”