title: Path-preference cellular-automaton model for traffic flow through transit points and its application to the transcription process in human cells.
abstract: We all use path routing everyday as we take shortcuts to avoid traffic jams, or by using faster traffic means. Previous models of traffic flow of RNA polymerase II (RNAPII) during transcription, however, were restricted to one dimension along the DNA template. Here we report the modeling and application of traffic flow in transcription that allows preferential paths of different dimensions only restricted to visit some transit points, as previously introduced between the 5' and 3' end of the gene. According to its position, an RNAPII protein molecule prefers paths obeying two types of time-evolution rules. One is an asymmetric simple exclusion process (ASEP) along DNA, and the other is a three-dimensional jump between transit points in DNA where RNAPIIs are staying. Simulations based on our model, and comparison experimental results, reveal how RNAPII molecules are distributed at the DNA-loop-formation-related protein binding sites as well as CTCF insulator proteins (or exons). As time passes after the stimulation, the RNAPII density at these sites becomes higher. Apparent far-distance jumps in one dimension are realized by short-range three-dimensional jumps between DNA loops. We confirm the above conjecture by applying our model calculation to the SAMD4A gene by comparing the experimental results. Our probabilistic model provides possible scenarios for assembling RNAPII molecules into transcription factories, where RNAPII and related proteins cooperatively transcribe DNA.
authors.affiliation: Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Ohta
authors.forename: Akinobu
authors.initials: A
authors.lastname: Nishiyama
authors.forename: Yoichiro
authors.initials: Y
authors.lastname: Wada
authors.forename: Yijun
authors.initials: Y
authors.lastname: Ruan
authors.forename: Tatsuhiko
authors.initials: T
authors.lastname: Kodama
authors.forename: Takashi
authors.initials: T
authors.lastname: Tsuboi
authors.forename: Tetsuji
authors.initials: T
authors.lastname: Tokihiro
authors.forename: Sigeo
authors.initials: S
authors.lastname: Ihara
mesh_terms: D061307:Human Umbilical Vein Endothelial Cells / Q000378:metabolism; D006801:Humans; D008954:Models, Biological; D008957:Models, Genetic; D012319:RNA Polymerase II / Q000378:metabolism; D012097:Repressor Proteins / Q000235:genetics; D013997:Time Factors; D014158:Transcription, Genetic
chemical_list: D012097:Repressor Proteins; C507993:SAMD4A protein, human; D012319:RNA Polymerase II