title: Collective Properties of a Transcription Initiation Model Under Varying Environment.
abstract: The dynamics of gene transcription is tightly regulated in eukaryotes. Recent experiments have revealed various kinds of transcriptional dynamics, such as RNA polymerase II pausing, that involves regulation at the transcription initiation stage, and the choice of different regulation pattern is closely related to the physiological functions of the target gene. Here we consider a simplified model of transcription initiation, a process including the assembly of transcription complex and the pausing and releasing of the RNA polymerase II. Focusing on the collective behaviors of a population level, we explore the potential regulatory functions this model can offer. These functions include fast and synchronized response to environmental change, or long-term memory about the transcriptional status. As a proof of concept we also show that, by selecting different control mechanisms cells can adapt to different environments. These findings may help us better understand the design principles of transcriptional regulation.
authors.affiliation: 1 Zhou Pei-yuan Center for Applied Mathematics, Tsinghua University , Beijing, China .
authors.forename: Yucheng
authors.initials: Y
authors.lastname: Hu
authors.affiliation: 2 Department of Mathematics, University of California-Irvine , Irvine, California.|3 Center for Complex Biological Systems, University of California-Irvine , Irvine, California.|4 Department of Biomedical Engineering, University of California-Irvine , Irvine, California.|5 Chao Comprehensive Cancer Center, University of California-Irvine , Irvine, California.
authors.forename: John S
authors.initials: JS
authors.lastname: Lowengrub
mesh_terms: D000818:Animals; D006801:Humans; D008957:Models, Genetic; D012313:RNA / Q000235:genetics* / Q000378:metabolism; D012319:RNA Polymerase II / Q000378:metabolism; D014158:Transcription, Genetic; D015533:Transcriptional Activation
chemical_list: D012313:RNA; D012319:RNA Polymerase II
keywords: RNA polymerase pausing; epigenetic memory; synchronized transcription; transcriptional regulation