title: Binary gene induction and protein expression in individual cells.
abstract: BACKGROUND
  Eukaryotic 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.
  
  
  RESULTS
  In 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 beta-galactosidase, we also demonstrated that graded gene expression is more likely to be observed with GFP, a longer-lived protein with low detection sensitivity.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Division of Computational Biology, CIIT Centers for Health Research, Research Triangle Park, NC 27709, USA. qzhang@ciit.org
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhang
authors.forename: Melvin E
authors.initials: ME
authors.lastname: Andersen
authors.forename: Rory B
authors.initials: RB
authors.lastname: Conolly
mesh_terms: D003198:Computer Simulation; D015870:Gene Expression / Q000502:physiology*; D005786:Gene Expression Regulation; D017930:Genes, Reporter; D049452:Green Fluorescent Proteins / Q000235:genetics; D006207:Half-Life; D008156:Luciferases / Q000235:genetics; D008957:Models, Genetic; D010641:Phenotype; D011401:Promoter Regions, Genetic / Q000502:physiology; D011506:Proteins / Q000378:metabolism; D013269:Stochastic Processes; D013698:Templates, Genetic; D013997:Time Factors; D015534:Trans-Activators / Q000502:physiology*; D014158:Transcription, Genetic; D015533:Transcriptional Activation; D001616:beta-Galactosidase / Q000235:genetics
chemical_list: D011506:Proteins; D015534:Trans-Activators; D049452:Green Fluorescent Proteins; D008156:Luciferases; D001616:beta-Galactosidase