Dynamic Estrogen Receptor Interactomes Control Estrogen-Responsive Trefoil Factor (TFF) Locus Cell-Specific Activities

Abstract

Estradiol signaling is ideally suited for analyzing the molecular and functional linkages between the different layers of information directing transcriptional regulations: the DNA sequence, chromatin modifications, and the spatial organization of the genome. Hence, the estrogen receptor (ER) can bind at a distance from its target genes and engages timely and spatially coordinated processes to regulate their expression. In the context of the coordinated regulation of colinear genes, identifying which ER binding sites (ERBSs) regulate a given gene still remains a challenge. Here, we investigated the coordination of such regulatory events at a 2-Mb genomic locus containing the estrogen-sensitive trefoil factor (TFF) cluster of genes in breast cancer cells. We demonstrate that this locus exhibits a hormone- and cohesin-dependent reduction in the plasticity of its three-dimensional organization that allows multiple ERBSs to be dynamically brought to the vicinity of estrogen-sensitive genes. Additionally, by using triplex-forming oligonucleotides, we could precisely document the functional links between ER engagement at given ERBSs and the regulation of particular genes. Hence, our data provide evidence of a formerly suggested cooperation of enhancers toward gene regulation and also show that redundancy between ERBSs can occur.

SUPPLEMENTAL MATERIAL

Supplemental material for this article may be found at http://dx.doi.org/10.1128/MCB.00918-13.

ACKNOWLEDGMENTS

This work was supported by the CNRS and the University of Rennes I and benefited from grants from the ARC, the Ligue contre le Cancer (Equipe Labelisée Ligue 2009), the Région Bretagne (CREATE 4793), and the Agence Nationale pour la Recherche (ANR-09-BLAN-0268-01). S.H. was supported by funds from the Agence Nationale de la Recherche (JCJC-SVSE2-2011, ChromaTranscript project) and the European Union (FP7-PEOPLE-2011-CIG, ChromaTranscript project). J.Q. was the recipient of a joint fellowship from the CNRS and the Region Bretagne. A.A.S. was supported by a fellowship from the French Ministère de l'Enseignement Supérieur et de la Recherche, and S.C. was funded by a CNRS postdoctoral fellowship.

We greatly acknowledge Denis Habauzit for all his advice and help on the design and analysis of TFOs. We also thank Stephanie Dutertre and the other members of the Microscopy Rennes Imaging Center from the IFR biosit for technical assistance with the microscopes.