Biology

A primer on thermodynamic-based models for deciphering transcriptional regulatory logic

Document Type

Article

Abstract

A rigorous analysis of transcriptional regulation at the DNA level is crucial to the understanding of many biological systems. Mathematical modeling has offered researchers a new approach to understanding this central process. In particular, thermodynamic-based modeling represents the most biophysically informed approach aimed at connecting DNA level regulatory sequences to the expression of specific genes. The goal of this review is to give biologists a thorough description of the steps involved in building, analyzing, and implementing a thermodynamic-based model of transcriptional regulation. The data requirements for this modeling approach are described, the derivation for a specific regulatory region is shown, and the challenges and future directions for the quantitative modeling of gene regulation are discussed.© 2013 Elsevier B.V.

Publication Title

Biochimica et Biophysica Acta - Gene Regulatory Mechanisms

Publication Date

9-1-2013

Volume

1829

Issue

9

First Page

946

Last Page

953

ISSN

1874-9399

DOI

10.1016/j.bbagrm.2013.04.011

Keywords

enhancer, parameter estimation, sensitivity analysis, Thermodynamic modeling, transcriptional regulation

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