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A Looping-Based Model for Quenching Repression
#MMPMID28085884
Pollak Y
; Goldberg S
; Amit R
PLoS Comput Biol
2017[Jan]; 13
(1
): e1005337
PMID28085884
show ga
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.
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