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Annu Rev Biophys DOI:10.1146/annurev-biophys-121219-081542

Gene Regulation in and out of Equilibrium.

Publication TypeJournal Article
Year of Publication2020
AuthorsWong, F, Gunawardena, J
JournalAnnu Rev Biophys
Volume49
Pages199-226
Date Published2020 May 06
ISSN1936-1238
Abstract

Determining whether and how a gene is transcribed are two of the central processes of life. The conceptual basis for understanding such gene regulation arose from pioneering biophysical studies in eubacteria. However, eukaryotic genomes exhibit vastly greater complexity, which raises questions not addressed by this bacterial paradigm. First, how is information integrated from many widely separated binding sites to determine how a gene is transcribed? Second, does the presence of multiple energy-expending mechanisms, which are absent from eubacterial genomes, indicate that eukaryotes are capable of improved forms of genetic information processing? An updated biophysical foundation is needed to answer such questions. We describe the linear framework, a graph-based approach to Markov processes, and show that it can accommodate many previous studies in the field. Under the assumption of thermodynamic equilibrium, we introduce a language of higher-order cooperativities and show how it can rigorously quantify gene regulatory properties suggested by experiment. We point out that fundamental limits to information processing arise at thermodynamic equilibrium and can only be bypassed through energy expenditure. Finally, we outline some of the mathematical challenges that must be overcome to construct an improved biophysical understanding of gene regulation.

DOI10.1146/annurev-biophys-121219-081542
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/32375018?dopt=Abstract

Alternate JournalAnnu Rev Biophys
PubMed ID32375018