Fig. 3
From: Promoter G-quadruplex folding precedes transcription and is controlled by chromatin
G4 stabilisation in compacted chromatin retains promoter Pol II occupancy. a Graphical representation of experimental design examining the consequences of G4 stabilisation by pyPDS on chromatin compaction and Pol II occupancy. b Chromatin accessibility differences for promoters of active genes with a G4 (Pol II+ G4+) under hypoxia for cells treated with DMSO or pyPDS. Top panel, metagene plot of ATAC signal centred at the TSS showing the signal difference between DMSO- and pyPDS-treated hypoxic cells. Bottom panel, data plotted for individual loci and represented by a heatmap plot. c Venn diagram showing sites that have lost Pol II occupancy between normoxic and hypoxic cells treated with DMSO and its overlap with Pol II sites lost on treatment with pyPDS in hypoxic conditions compared to DMSO treatment in normoxic conditions. This shows that the majority of Pol II sites seen reduced in hypoxia are retained by pyPDS. d Similar to panel b but for signal differences in Pol II occupancy. e Genome browser view displaying examples of genes involved in chromatin biology (e.g. BRD4 and CBX1) that show changes in chromatin accessibility (ATAC-seq, green) and Pol II occupancy (Pol II ChIP-seq, black) for cells under normoxic (top), hypoxic (middle) or hypoxic conditions treated with pyPDS (bottom). Genomic coordinates are indicated above and signal quantified as counts per million (CPM)