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10.1371/journal.pcbi.1005337 http://scihub22266oqcxt.onion/10.1371/journal.pcbi.1005337 C5279812!5279812 !28085884     free     free     free Warning: imagejpeg(C:\Inetpub\vhosts\kidney.de\httpdocs\phplern\28085884 .jpg): Failed to open stream: No such file or directory in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 117       PLoS+Comput+Biol 2017 ; 13 (1 ): e1005337 Nephropedia Template TP {{tp|p=28085884 |t=2017. A Looping-Based Model for Quenching Repression |pdf=|usr=}}{{28085884 }} gab.com Text A Looping-Based Model for Quenching Repression JO: PLoS Comput Biol http://www.kidney.de/pget.php?&tw=1&pmid=28085884 #FOAvip 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. Twit Text FOAVip A Looping-Based Model for Quenching Repression ????PLoS Comput Biol http://www.kidney.de/pget.php?&tw=1&pmid=28085884 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=28085884 #FOAvip English Wikipedia <ref>{{Cite pmid|28085884 }}</ref> 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. |*DNA/chemistry/metabolism [MESH] |*Models, Genetic [MESH] |*Monte Carlo Method [MESH] |Animals [MESH] |Computational Biology [MESH] |Drosophila melanogaster/genetics [MESH] |Enhancer Elements, Genetic/*genetics [MESH]A Looping-Based Model for Quenching Repression (epmc).pdf DeepDyve Pubget Overpricing