Fig. 6: H3.3 deposition is altered at G4 sequences in ATRX-mutant neuroblastomas.

a Stack bar plot of H3.3 peaks in the ATRX-deficient (CHLA90, SKNMM), MYCN amplified (SKNBE2, IMR32), and ATRX wild type, MYCN non-amplified (LAN6, SKNFI) cell lines. The H3.3 peaks that overlap with G4 sequences are shown in gray. b Stack bar plot of H3.3 peaks that are constitutive (C) across all three groups (ATRX, MYCN, WT), enriched (E) in ATRX mutant, depleted (D) in ATRX mutant, or overlap (O) between ATRX mutant and MYCN or WT. The H3.3 peaks that overlap with G4 sequences are shown in gray and the number of peaks for the D group are shown. c Piechart of the location of D group H3.3 peaks that have a correlation between the presence or absence of an H3.3 peak and ChromHMM state. Separate pie charts are shown for those that overlap with G4 sequences and those that lack G4 sequences. d Heatmap of the ChromHMM states used in this study with color coding. e Stack bar plot of the distribution of ChromHMM states for each cell line in the non-genic regions that have D group H3.3 peaks that correlate with ChromHMM state and overlap with G4 sequences or lack f G4 sequences. g ChromHMM, WGBS, and ChIP-seq tracks for the DUSP26 gene in SKNMM (ATRX mutant) and SKNBE2 (MYCN amplified) cells. Gene expression is indicated (FPKM) and G4 motif sequences are shown below the ChromHMM tracks. h ChromHMM, WGBS, and ChIP-seq tracks for the SLC3A2 gene in SKNMM^MYCN cells with and without doxycycline. Gene expression is indicated (FPKM) and G4 motif sequences are shown below the ChromHMM tracks. DOX doxycycline, ChromHMM chromatin hidden markov modeling, G4 guanine quadruplex structure.