Supplementary Figure 6: Absolute Quantification of Architecture (AQuA-HiChIP) at core regulatory gene loci.
From: Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma
a, Regular HiChIP (contacts per million), H3K27ac ChIP target, in RH4 cells treated with either DMSO or Entinostat (top), compared with AQuA-HiChIP using exogenous reference chromatin spike-in (bottom), at the MYOD1 super enhancer containing locus. b, SE-to-SE contact loss, amidst aberrant SE-contact spreading at SOX8 cis-regulatory elements. Top, AQuA-HiChIP contact heatmaps (DMSO, Entinostat 6 hours, in RH4 cells); bottom, virtual 4C analysis (change in AQuA-HiChIP contact frequency, with increases colored dark pink and decreases in blue) anchored at SE1 upstream or SE3 downstream of SOX8. c, Hyper-acetylation causes expansive gains of aberrant SE contacts, shown by AQuA-HiChIP of H3K27ac in RH4 cells, treated for 6 hours with DMSO (top row) or Entinostat (bottom row), visualized at 7 core regulatory domains. Super enhancers are indicated by red bars above the contact frequency heatmaps. CR TF genes are shown in dark blue.
