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

被引：5

作者：

Dresch, Jacqueline M. ^{[1
]}

Richards, Megan ^{[2
]}

Ay, Ahmet ^{[3
,4
]}

机构：

[1] Harvey Mudd Coll, Dept Math, Claremont, CA 91711 USA

[2] Colgate Univ, Dept Psychol, Hamilton, NY 13346 USA

[3] Colgate Univ, Dept Biol, Hamilton, NY 13346 USA

[4] Colgate Univ, Dept Math, Hamilton, NY 13346 USA

来源：

BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS | 2013年 / 1829卷 / 09期

基金：

美国国家科学基金会;

关键词：

Transcriptional regulation; Enhancer; Thermodynamic modeling; Parameter estimation; Sensitivity analysis; PROTEIN-DNA INTERACTIONS; FACTOR-BINDING SITES; SENSITIVITY-ANALYSIS-METHODS; QUANTIFYING GENE-EXPRESSION; EARLY DROSOPHILA EMBRYOS; SYSTEMS BIOLOGY; MOTIF DISCOVERY; CHIP-CHIP; GENOME; SEGMENTATION;

D O I：

10.1016/j.bbagrm.2013.04.011

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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. (c) 2013 Elsevier B.V. All rights reserved.

引用

页码：946 / 953

页数：8

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