title: Quantifying extrinsic noise in gene expression using the maximum entropy framework.
abstract: We present a maximum entropy framework to separate intrinsic and extrinsic contributions to noisy gene expression solely from the profile of expression. We express the experimentally accessible probability distribution of the copy number of the gene product (mRNA or protein) by accounting for possible variations in extrinsic factors. The distribution of extrinsic factors is estimated using the maximum entropy principle. Our results show that extrinsic factors qualitatively and quantitatively affect the probability distribution of the gene product. We work out, in detail, the transcription of mRNA from a constitutively expressed promoter in Escherichia coli. We suggest that the variation in extrinsic factors may account for the observed wider-than-Poisson distribution of mRNA copy numbers. We successfully test our framework on a numerical simulation of a simple gene expression scheme that accounts for the variation in extrinsic factors. We also make falsifiable predictions, some of which are tested on previous experiments in E. coli whereas others need verification. Application of the presented framework to more complex situations is also discussed.
authors.affiliation: Biosciences Department, Brookhaven National Laboratory, Upton, New York, USA. pdixit@bnl.gov
authors.forename: Purushottam D
authors.initials: PD
authors.lastname: Dixit
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D019277:Entropy; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D008954:Models, Biological; D011401:Promoter Regions, Genetic; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D012333:RNA, Messenger