G-quadruplexes associated with R-loops promote CTCF binding. Wulfridge et al.
Description
CTCF is a critical regulator of genome architecture and gene expression that binds to thousands of sites on chromatin. CTCF genomic localization is controlled by its interaction to a DNA sequence motif and regulated by DNA modifications. However, CTCF does not bind to all its potential sites in all cell types, raising the question of whether the underlying chromatin structure can regulate CTCF binding. Here we report that R-loops, three-stranded chromatin structures that contain DNA:RNA hybrids, facilitate CTCF binding through formation of the associated G-quadruplex (G4) secondary DNA structure. R-loops and G4 structures are co-localized with CTCF at many genomic regions in vivo and promote CTCF binding to its cognate DNA motif in vitro. Removal of R-loops and local deletion of a G4 forming motif reduce CTCF binding, which in turn can alter gene expression. Conversely, chemical stabilization of G4s in undifferentiated stem cells results in CTCF gains and accompanying alterations in chromatin organization. Finally, G4 induction upon neurodifferentiation is associated with CTCF increase at bivalent genes. Our results suggest that formation of G4 structures by R-loops plays a pivotal role in reinforcing long range chromatin interactions through CTCF.