PT  - JOURNAL ARTICLE
AU  - Y. Pollak
AU  - S. Goldberg
AU  - R. Amit
TI  - A looping-based model for quenching repression
AID  - 10.1101/085217
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 085217
4099  - http://biorxiv.org/content/early/2016/11/06/085217.short
4100  - http://biorxiv.org/content/early/2016/11/06/085217.full
AB  - 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 simu-late 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 eve 3/7 enhancer, and show that it provides a possible explanation for the experimentally-observed eve stripe 3 and 7 expression patterns.The authors declare no conflict of interests