title: Physical Modeling of Dynamic Coupling between Chromosomal Loci.
abstract: The motion of chromosomal DNA is essential to many biological processes, including segregation, transcriptional regulation, recombination, and packaging. Physical understanding of these processes would be dramatically enhanced through predictive, quantitative modeling of chromosome dynamics of multiple loci. Using a polymer dynamics framework, we develop a prediction for the correlation in the velocities of two loci on a single chromosome or otherwise connected by chromatin. These predictions reveal that the signature of correlated motion between two loci can be identified by varying the lag time between locus position measurements. In general, this theory predicts that as the lag time interval increases, the dual-loci dynamic behavior transitions from being completely uncorrelated to behaving as an effective single locus. This transition corresponds to the timescale of the stress communication between loci through the intervening segment. This relatively simple framework makes quantitative predictions based on a single timescale fit parameter that can be directly compared to the in vivo motion of fluorescently labeled chromosome loci. Furthermore, this theoretical framework enables the detection of dynamically coupled chromosome regions from the signature of their correlated motion.
authors.affiliation: Chemical Engineering, Stanford University, Stanford, California.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Lampo
authors.affiliation: Biophysics Program, Stanford University, Stanford, California.
authors.forename: Andrew S
authors.initials: AS
authors.lastname: Kennard
authors.affiliation: Chemical Engineering, Stanford University, Stanford, California; Biophysics Program, Stanford University, Stanford, California; Department of Materials Science and Engineering, Stanford University, Stanford, California; Department of Applied Physics, Stanford University, Stanford, California. Electronic address: ajspakow@stanford.edu.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Spakowitz
mesh_terms: D002875:Chromosomes / Q000737:chemistry* / Q000235:genetics; D004247:DNA / Q000737:chemistry*; D056426:Genetic Loci; D056004:Molecular Dynamics Simulation; D009038:Motion
chemical_list: D004247:DNA