Fig. 2: G4s are found in stem cell regulatory elements.
From: G-quadruplex DNA structures in human stem cells and differentiation
a Fold enrichment over random (n = 1000 permutations) for G4s at genomic features from the reference human annotation GENECODE v.28 or at enhancers, defined as promoter distal H3K27ac. UTR untranslated region; Promoter defined as ±1 kb around transcription start site. b Genome browser view of G4 signal across hESC-specific proximal and distal enhancer of POU5F1 (as defined in Yang et al.89). CR conserved region. The yellow box highlights regions where G4s overlaps open chromatin (ATAC) and genome sites which have the ability to fold into G4 structures in vitro (OQs13). c–f Fold-enrichments over random (n = 1000 permutations) and proportion of G4s per stem cell type at c the binding sites of cell-specific transcription factors (TF); d super-enhancer elements as defined in Hnisz et al.34 and Wilderman et al.90; e promoter (bait) and promoter-interacting regions (PIRs) from promoter-capture HiC experiments (as defined in Freire-Pritchett et al.40. Centre and left panel: hESCs active promoters (H3K4me3 and/or H3K27ac), poised promoters (H3K4me3 and H3K27me3), repressed promoters (H3K27me3) and background (none). Right-most panel: NSC promoter-promoter PIRs and promoter-non-promoter PIR interactions of developmentally analogous H1-hESC-derived neural progenitor cells from Jung et al.41; f binding sites of chromatin architecture proteins involved in promoter-enhancer looping.
