Binary gene induction and protein expression in individual cells

Qiang Zhang,Melvin E Andersen,Rory B Conolly

doi:10.1186/1742-4682-3-18

Abstract

BackgroundEukaryotic gene transcription is believed to occur in either a binary or a graded fashion. With binary induction, a transcription activator (TA) regulates the probability with which a gene template is switched from the inactive to the active state without affecting the rate at which RNA molecules are produced from the template. With graded, also called rheostat-like, induction the gene template has continuously varying levels of transcriptional activity, and the TA regulates the rate of RNA production. Support for each of these two mechanisms arises primarily from experimental studies measuring reporter proteins in individual cells, rather than from direct measurement of induction events at the gene template.Methods and resultsIn this paper, using a computational model of stochastic gene expression, we have studied the biological and experimental conditions under which a binary induction mode operating at the gene template can give rise to differentially expressed "phenotypes" (i.e., binary, hybrid or graded) at the protein level. We have also investigated whether the choice of reporter genes plays a significant role in determining the observed protein expression patterns in individual cells, given the diverse properties of commonly-used reporter genes. Our simulation confirmed early findings that the lifetimes of active/inactive promoters and half-lives of downstream mRNA/protein products are important determinants of various protein expression patterns, but showed that the induction time and the sensitivity with which the expressed genes are detected are also important experimental variables. Using parameter conditions representative of reporter genes including green fluorescence protein (GFP) and β-galactosidase, we also demonstrated that graded gene expression is more likely to be observed with GFP, a longer-lived protein with low detection sensitivity.ConclusionThe choice of reporter genes may determine whether protein expression is binary, graded or hybrid, even though gene induction itself operates in an all-or-none fashion.

Highlights

Eukaryotic gene transcription is believed to occur in either a binary or a graded fashion
The choice of reporter genes may determine whether protein expression is binary, graded or hybrid, even though gene induction itself operates in an all-or-none fashion
Expression data are routinely presented as distribution histograms, in which the x-axis denotes the levels of protein expression and the y-axis represents the number or percentage of cells expressing the reporter protein at different levels (Fig. 1)

Summary

Introduction

Eukaryotic gene transcription is believed to occur in either a binary or a graded fashion. Once in the active state, gene transcription proceeds at a relatively constant rate; whereas in the inactive state, no transcription occurs With this binary mode of action, transcription activators, repressors and cis-acting elements would induce/repress gene expression by affecting, essentially, the probability with which a promoter is switched on/off. In contrast to this all-or-none mode of operation, the graded induction model argues (page number not for citation purposes). That a promoter can have continuously varying levels of transcriptional activity, and transcription factors regulate gene expression by affecting the rate at which RNA is produced from the gene template. Simulations started with 1 copy of inactive promoter, 0 ~

Methods

Results

Conclusion