Anna Nordin1,2,3, Chaitali Chakraborty4,5, Mattias Jonasson1,2, Orgena Dano1,2, Gianluca Zambanini1,2,6, Pierfrancesco Pagella1,2,7, Silvia Remeseiro4,5 and Claudio Cantù1,2,3 1Wallenberg Centre for Molecular Medicine, Linköping University, SE-581 83 Linköping, Sweden; 2Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, SE-581 83 Linköping, Sweden; 3Science for Life Laboratory, Linköping University, SE-581 83 Linköping, Sweden; 4Wallenberg Centre for Molecular Medicine, Umeå University, 901 87 Umeå, Sweden; 5Department of Medical and Translational Biology, Division of Molecular Medicine, Umeå University, 901 87 Umeå, Sweden

↵Present addresses: 6Max-Planck-Institut für molekulare Genetik, 14195 Berlin, Germany; 7Department of Physics, Chemistry, and Biology, Division of Biophysics and Bioengineering, Faculty of Science and Engineering, Linköping University, SE-581 83 Linköping, Sweden

Corresponding authors: claudio.cantuliu.se, anna.nordinliu.se, silvia.remeseiroumu.se Abstract

Wnt signaling plays a pivotal role during development and homeostasis. Upon pathway activation, CTNNB1 (also known as beta-catenin) drives the expression of target genes from regulatory regions bound by TCF/LEF transcription factors. Gene regulation, however, entails the interplay between sequence information and 3D genome structure, yet the impact of Wnt signaling on genome structure has been poorly explored. Here, we investigate how Wnt signaling influences CTCF and cohesin, key regulators of 3D genome organization. We identify a series of novel CTCF binding sites that emerge upon Wnt stimulation: CTCF Redistributions Under Wnt (RUW). RUW sites are characterized by CTCF, cohesin, and TCF/LEF occupancy, and are dependent on beta-catenin. Beta-catenin and CTCF colocalize upon pathway activation, and disruption of selected binding sites perturbs target gene regulation. Moreover, Wnt signaling reorganizes the 3D genome as evidenced by genome-wide alterations in CTCF-bound loops. This work reveals a previously unexplored role for CTCF in the regulation of Wnt signaling.

Footnotes

[Supplemental material is available for this article.]

Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.279684.124.

Freely available online through the Genome Research Open Access option.

Received June 14, 2024. Accepted June 17, 2025.