G-Quadruplex-Protein Interactome at Human Gene Promoters

DNA-protein interactions at gene promoters play a critical role in gene expression. The promoters of human cells are highly enriched in guanine-rich sequences, which can form four-stranded G-quadruplex (G4) structures. G4s are emerging as a distinct class of structure-based regulatory elements in gene regulation, and their interaction with proteins is essential for the role G4s play. Currently, our understanding of G4-protein interaction is mainly on a case-by-case basis, without systematic information. In this work, we examined the spatial occupancy of 1,183 human DNA-binding proteins, including transcription factors, histones and their modifying enzymes, around the consensus G4-forming region, G4(+), using data from the ENCODE project. We found that the G4(+), its immediate proximal side, and its distal side serve as three primary protein binding sites. Nearly all proteins are either enriched or depleted at these sites, likely due to competition, or in a spatiotemporal transition between the sites, resulting in different degrees of variation or persistence within or across cell/tissue types. Notably, histones were excluded from the proximal side of G4(+), and their binding to G4(+) was turned on and off by acetylation and methylation, respectively. Furthermore, the distal side is preferentially enriched for H3K23me2 and H3K4me2. Our experiments also revealed corresponding patterns of G4-protein interaction. Taken together, our results suggest a general role for G4s in dynamically defining and coordinating chromatin architecture and DNA-protein interactions at gene promoters for transcriptional regulation, a task that is unlikely to be accomplished by sequence-based DNA recognition.