Inferringgeneexpressiondynamicsfromreporterprotein.docVIP

Inferring Gene Expression Dynamics from Reporter Protein Levels Authors: David Brown, Dept. of Mathematics and Computer Science, Colorado College C. Phoebe Lostroh, Dept. of Biology, Colorado College Keywords: promoter activity; beta-galactosidase; reporter proteins; mathematical model; gene expresssion Contact: Dr. David Brown Dept. of Mathematics and Computer Science 14 E. Cache la Poudre St. Colorado Springs, CO 80903 dbrown@ List of Abbreviations: CAT (chloramphenicol acetyl transferase), GFP (green fluorescent protein) Abstract We present a mathematical method for inferring the dynamics of gene expression from time series of reporter protein assays and cell populations. We show that estimating temporal expression dynamics from direct visual inspection of reporter protein data is unreliable when the half-life of the protein is comparable to the time scale of the expression dynamics. Our method is simple and general because it is designed only to reconstruct the pattern of protein synthesis, without assuming any specific regulatory mechanisms. It can be applied to a wide range of cell types, patterns of expression, and reporter systems, and is implemented in publicly available spreadsheets. We show that our method is robust to a several possible types of error, and argue that uncertainty about the decay kinetics of reporter proteins is the limiting factor in reconstructing the temporal pattern of gene expression dynamics from reporter protein assays. With improved estimates of reporter protein decay rates, our approach could allow for detailed reconstruction of gene expression dynamics from commonly used reporter protein systems. Introduction Assays of reporter proteins such as (-galactosidase, luciferase, chloramphenicol acetyl transferase (CAT), and green fluorescent protein (GFP) are among the most widely used methods for investigating the dynamics of gene expression and protein synthesis [1]. In