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A Looping-Based Model for Quenching Repression.
- Source :
- PLoS Computational Biology; 1/13/2017, Vol. 13 Issue 1, p1-21, 21p, 1 Color Photograph, 1 Black and White Photograph, 1 Chart, 5 Graphs
- Publication Year :
- 2017
-
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. [ABSTRACT FROM AUTHOR]
- Subjects :
- PROTEINS
DNA
TRANSCRIPTION factors
GENE expression
MONTE Carlo method
Subjects
Details
- Language :
- English
- ISSN :
- 1553734X
- Volume :
- 13
- Issue :
- 1
- Database :
- Complementary Index
- Journal :
- PLoS Computational Biology
- Publication Type :
- Academic Journal
- Accession number :
- 120746435
- Full Text :
- https://doi.org/10.1371/journal.pcbi.1005337