Fig. 1

TF binding is tightly linked to endogenous G4 structures in the human genome. a Enrichment of 524 ENCODE proteins at G4 ChIP-seq sites in K562 for randomization in open chromatin (DHS). Top 20 and bottom 20 candidates are highlighted. Green shading indicates proteins with reported G4-association. b Genomic association with endogenous G4s is consistent in K562 and HepG2 cells. Spearman correlation test (r_s, ****P < 0.0001) is based on the maximum enrichment observed for TFs that have been mapped in both K562 (x-axis) and HepG2 (y-axis) cells. Green shading indicates proteins with reported G4-association. c Genomic association of TFs obtained from ENCODE with endogenous G4s (x-axis) and potential G4 control sites at promoters (y-axis). Proteins for which binding is independent of secondary structure formation should show similar enrichment for both data sets (white dashed line). Green shading indicates proteins with reported G4 association. d Occupancy profiles of enriched candidates SP2, E2F4, FUS, and NRF1 and a non-enriched TF, CBX8, around endogenous G4 sites (green) and control sequences (gray). The strandedness of endogenous G4s was derived from stranded data of sequences with G4 forming potential [26] (see “Materials and methods”)