title: Single-site transcription rates through fitting of ensemble-averaged data from fluorescence recovery after photobleaching: a fat-tailed distribution.
abstract: The stochastic process of gene expression is commonly controlled at the level of RNA transcription. The synthesis of messenger RNA (mRNA) is a multistep process, performed by RNA polymerase II and controlled by many transcription factors. Although mRNA transcription is intensively studied, real-time in vivo dynamic rates of a single transcribing polymerase are still not available. A popular method for examining transcription kinetics is the fluorescence recovery after photobleaching (FRAP) approach followed by kinetic modeling. Such analysis has yielded a surprisingly broad range of transcription rates. As transcription depends on many variables such as the chromatin state, binding and unbinding of transcription factors, and cell phase, transcription rates are stochastic variables. Thus, the distribution of rates is expected to follow Poissonian statistics, which does not coincide with the wide range of transcription rate results. Here we present an approach for analyzing FRAP data for single-gene transcription. We find that the transcription dynamics of a single gene can be described with a constant rate for all transcribing polymerases, while cell population transcription rates follow a fat-tailed distribution. This distribution suggests a larger probability for extreme rates than would be implied by normal distribution. Our analysis supports experimental results of transcription from two different promoters, and it explains the puzzling observation of extreme average rate values of transcription.
authors.affiliation: The Department of Physics and Institute of Nanotechnology, Bar Ilan University, Ramat Gan 52900, Israel.
authors.forename: Liat
authors.initials: L
authors.lastname: Rosenfeld
authors.affiliation: The Department of Physics and Institute of Nanotechnology, Bar Ilan University, Ramat Gan 52900, Israel.
authors.forename: Eldad
authors.initials: E
authors.lastname: Kepten
authors.affiliation: The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar Ilan University, Ramat Gan 52900, Israel.
authors.forename: Sharon
authors.initials: S
authors.lastname: Yunger
authors.affiliation: The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar Ilan University, Ramat Gan 52900, Israel.
authors.forename: Yaron
authors.initials: Y
authors.lastname: Shav-Tal
authors.affiliation: The Department of Physics and Institute of Nanotechnology, Bar Ilan University, Ramat Gan 52900, Israel.
authors.forename: Yuval
authors.initials: Y
authors.lastname: Garini
mesh_terms: D003198:Computer Simulation; D019938:Cyclin D1 / Q000235:genetics / Q000378:metabolism; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism; D036681:Fluorescence Recovery After Photobleaching / Q000379:methods; D049452:Green Fluorescent Proteins / Q000235:genetics / Q000378:metabolism; D057809:HEK293 Cells; D006801:Humans; D007700:Kinetics; D018613:Microscopy, Confocal; D008957:Models, Genetic; D016012:Poisson Distribution; D012333:RNA, Messenger / Q000378:metabolism; D013269:Stochastic Processes; D014158:Transcription, Genetic; D014162:Transfection
chemical_list: C530104:CCND1 protein, human; D012333:RNA, Messenger; D019938:Cyclin D1; D049452:Green Fluorescent Proteins; D004259:DNA-Directed DNA Polymerase