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Purpose: There are over 700,000 DNA sequences in every one of our cells that can form a different structure to the canonical DNA double helix. This structure is the G-quadruplex (G4). However, only a small subset of these motifs are found to form a structure in cells. These G4 structure landscapes are cell type-specific, and are enriched in enhancers, particularly ones specific to a given cell state. This could suggest that G-quadruplexes could play a role in determining cell state through regulating gene expression programmes via enhancers. I will present our work on studying the role of G-quadruplexes in these cis-regulatory elements, using the alpha and beta globin locus control regions as examples (Doyle et al, 2025). These two loci control expression of haemoglobin and are paradigmatic for studying enhancer function and mechanism.
Conclusions: Several models have been proposed for how enhancers regulate gene expression at a linear distance; one prominent model involves interactions in 3D space between the enhancer and gene. We have dissected the role of G4s in such interactions, as well as characterising the effect of abolishing the structure on enhancer function more broadly, as defined by changes in the transcriptome, epigenome, and interactome. Notably, structure abrogation through a seven-base sequence mutation leads to phenotypic changes comparable to those observed upon deletion of the dominant enhancer (a c. 350 base pair deletion) at the alpha-globin locus. Wild-type expression, and epigenetic landscape, is restored upon insertion of a G4-forming sequence from a different genomic site in the mutant background.