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Nucleic Acids Res. 2014;42(16):10425-32. doi: 10.1093/nar/gku759. Epub 2014 Aug 14.

Effects of supercoiling on enhancer-promoter contacts.

Author information

1
Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015-Lausanne, Switzerland.
2
Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015-Lausanne, Switzerland andrzej.stasiak@unil.ch.

Abstract

Using Brownian dynamics simulations, we investigate here one of possible roles of supercoiling within topological domains constituting interphase chromosomes of higher eukaryotes. We analysed how supercoiling affects the interaction between enhancers and promoters that are located in the same or in neighbouring topological domains. We show here that enhancer-promoter affinity and supercoiling act synergistically in increasing the fraction of time during which enhancer and promoter stay in contact. This stabilizing effect of supercoiling only acts on enhancers and promoters located in the same topological domain. We propose that the primary role of recently observed supercoiling of topological domains in interphase chromosomes of higher eukaryotes is to assure that enhancers contact almost exclusively their cognate promoters located in the same topological domain and avoid contacts with very similar promoters but located in neighbouring topological domains.

PMID:
25123662
PMCID:
PMC4176356
DOI:
10.1093/nar/gku759
[Indexed for MEDLINE]
Free PMC Article

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