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Updated: May 21, 2025

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
Published on: March 31, 2019
Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene
Catherine Do1, Guimei Jiang1, Giulia Cova1
1Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA; Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA.
Abstract:
Here we used a series of CTCF mutations to explore CTCF's relationship with chromatin and its contribution to gene regulation. CTCF's impact depends on the genomic context of bound sites and the unique binding properties of WT and mutant CTCF proteins. Specifically, CTCF's signal strength is linked to changes in accessibility, and the ability to block cohesin is linked to its binding stability. Multivariate modeling reveals that both CTCF and accessibility contribute independently to cohesin binding and insulation, but CTCF signal strength has a stronger effect. CTCF and chromatin have a bidirectional relationship such that at CTCF sites, accessibility is reduced in a cohesin-dependent, mutant-specific fashion. In addition, each mutant alters TF binding and accessibility in an indirect manner, changes which impart the most influence on rewiring transcriptional networks and the cell's ability to differentiate. Collectively, the mutant perturbations provide a rich resource for determining CTCF's site-specific effects.
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