DNA G-Quadruplexes Contribute to CTCF Recruitment

Abstract

G-quadruplex (G4) sites in the human genome frequently colocalize with CCCTC-binding factor (CTCF)-bound sites in CpG islands (CGIs). We aimed to clarify the role of G4s in CTCF positioning. Molecular modeling data suggested direct interactions, so we performed in vitro binding assays with quadruplex-forming sequences from CGIs in the human genome. G4s bound CTCF with Kd values similar to that of the control duplex, while respective i-motifs exhibited no affinity for CTCF. Using ChIP-qPCR assays, we showed that G4-stabilizing ligands enhance CTCF occupancy at a G4-prone site in STAT3 gene. In view of the reportedly increased CTCF affinity for hypomethylated DNA, we next questioned whether G4s also facilitate CTCF recruitment to CGIs via protecting CpG sites from methylation. Bioinformatics analysis of previously published data argued against such a possibility. Finally, we questioned whether G4s facilitate CTCF recruitment by affecting chromatin structure. We showed that three architectural chromatin proteins of the high mobility group colocalize with G4s in the genome and recognize parallel-stranded or mixed-topology G4s in vitro. One of such proteins, HMGN3, contributes to the association between G4s and CTCF according to our bioinformatics analysis. These findings support both direct and indirect roles of G4s in CTCF recruitment.

G-Quadruplex Matters in Tissue-Specific Tumorigenesis by BRCA1 Deficiency

“…Then in turn, this suggests considering how the generated CNVs change G4 structures and gene expression via a G4/BER-mediated mechanism. Given the crucial role of G4s in 3D genome organization through interactions with key architectural proteins [ 67 , 68 , 69 ], this is in line with recent views of analyzing CNVs in terms of rearrangement in which distant regions of the genome are brought together [ 189 ]. In recent years, many similar studies have been conducted with keywords such as enhancer-hijacking, TAD disruption, 3D genome rewiring, and insulator dysfunction [ 189 , 190 , 191 , 192 ].…”

“…G4s influence the regional variations of mutation rates associated with CTCF, in that CTCF are preferentially located surrounding G4 which can strengthen the insulation ability of CTCF binding sites [ 67 ]. An in vitro assay demonstrated that G4s contribute to CTCF recruitment [ 68 ]. Another structural regulator of enhancer-promoter loops, YY1 [ 54 ], is also a DNA G4-binding protein, and YY1-mediated long-range DNA looping occurs through its recognition of the G4 structure [ 69 ].…”

G-quadruplexes are promoter elements controlling nucleosome exclusion and RNA polymerase II pausing

“…In any of these scenarios, the barrier constituted by the G4s would dock the surrounding nucleosomes. It will thus be interesting in future studies to investigate the precise interplay between G4 and CTCF since recent work suggest they could be locally associated (Tikhonova et al, 2021).…”

Phase Separation Modulates the Formation and Stabilities of DNA Guanine Quadruplex

“…, ATRX and REV1), , long-range DNA interactions ( e.g. , YY1 and CTCF), , and genetic diseases ( e.g. , WRN and BLM). , Moreover, G4 structures are known to be dynamic during cell cycle progression, where higher levels of G4 structures were observed in S-phase cells .…”

“…2−4 These studies also unveiled the enrichment of G4 structures at replication origins, oncogene promoters, and telomeres, suggesting the important functions of G4 structures in regulating DNA replication, transcription, telomere maintenance, and other biological processes. 5 G4 structures are highly dynamic in cells, 6,7 and effective regulations of G4s are crucial for maintaining genomic and epigenetic stability, as manifested by the functions of known G4-binding proteins in chromatin remodeling (e.g., ATRX and REV1), 8,9 long-range DNA interactions (e.g., YY1 and CTCF), 10,11 and genetic diseases (e.g., WRN and BLM). 12,13 Moreover, G4 structures are known to be dynamic during cell cycle progression, where higher levels of G4 structures were observed in S-phase cells.…”