Fig. 2: SS18::SSX distributes to transcriptional regulatory elements with monoubiquitylated histone H2A bearing nucleosomes.
a Fusion ChIP-seq summed enrichment at enhancer loci (distal anchors ±2 kb of H3K27ac-HiChIP loop to selected promoters, with enrichment multiplied by loop score) versus promoter enrichment (transcription start site, TSS ± 2 kb) for genes discretely associated with sarcomagenesis activated transcription (SAT) and maintained active transcription (MAT). b Fusion ChIP-seq peak width versus enrichment for all peaks that are within 2 kb of any TSS, with those near MAT or strong SAT gene promoters indicated. c Heatmaps for ChIP-seq enrichment centered at the TSS of each strong SAT gene promoter. d ChIP-seq enrichment plots for histone marks at strong SAT gene promoters. e Distal fusion ChIP-seq peak width and distance from its looped SAT gene TSS versus enrichment. f ChIP-seq enrichment plots at distal fusion peaks looped to SAT gene promoters. g ChIP-seq enrichment plots for MAT gene promoters. h Example tracks of a histone promoter signature for an SAT gene promoter and looped enhancers, as well as an MAT gene promoter. i Violin plots of fusion enrichment at promoters and enhancers with different patterns of intersected peaks called for histone marks or randomly selected promoters across the genome. Any column missing a plus or minus was simply not specified for ChIP-seq in that category (Violin plots show data distribution with embedded box plots indicating median, 25th–75th percentiles, and whiskers for minimum and maximum. Sample sizes by types of loci: triple positive, n = 3381; random, n = 977; negative, n = 940; bivalent, n = 325. Kruskal–Wallis test for unbalanced data, rank-based). Source data are provided as a Source Data file.
