title: A Looping-Based Model for Quenching Repression.
abstract: We model the regulatory role of proteins bound to looped DNA using a simulation in which dsDNA is represented as a self-avoiding chain, and proteins as spherical protrusions. We simulate long self-avoiding chains using a sequential importance sampling Monte-Carlo algorithm, and compute the probabilities for chain looping with and without a protrusion. We find that a protrusion near one of the chain's termini reduces the probability of looping, even for chains much longer than the protrusion-chain-terminus distance. This effect increases with protrusion size, and decreases with protrusion-terminus distance. The reduced probability of looping can be explained via an eclipse-like model, which provides a novel inhibitory mechanism. We test the eclipse model on two possible transcription-factor occupancy states of the D. melanogaster eve 3/7 enhancer, and show that it provides a possible explanation for the experimentally-observed eve stripe 3 and 7 expression patterns.
authors.affiliation: Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel.|Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa, Israel.
authors.forename: Yaroslav
authors.initials: Y
authors.lastname: Pollak
authors.affiliation: Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel.
authors.forename: Sarah
authors.initials: S
authors.lastname: Goldberg
authors.affiliation: Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel.|Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa, Israel.
authors.forename: Roee
authors.initials: R
authors.lastname: Amit
mesh_terms: D000818:Animals; D019295:Computational Biology; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004331:Drosophila melanogaster / Q000235:genetics; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D008957:Models, Genetic; D009010:Monte Carlo Method; D014157:Transcription Factors / Q000235:genetics
chemical_list: D014157:Transcription Factors; D004247:DNA