Fig. 4

FACT and pluripotency factors colocalize at putative enhancers genome-wide. A–C SPT16-V5 CUT&RUN data visualized as one-dimensional heatmaps [47]. Each row represents the average of technical replicates, while biological replicates are displayed separately (n = 3 for untagged and n = 2 for each V5-tagged clone). Visualized at A H3K27ac ChIP-seq peaks ± 2 kb (GSE32218), B H3K4me1 ChIP-seq peaks ± 2 kb (GSE31039), C TSS-distal DNaseI hypersensitive sites ± 2 kb (GSM1014154) [83,84,85]. D SPT16-V5 CUT&RUN data visualized at SPT16-V5-bound putative enhancers, defined as DHSs (GSM1014154) overlapping H3K4me1 or H3K27ac ChIP-seq peaks (GSE32218 and GSE31039) ± 2 kb [83,84,85]. E SPT16-V5 CUT&RUN binding over TSS-distal OCT4 ChIP-seq peaks (ChIP-seq from GSE11724 [78]). Merged replicates are shown as heatmaps ± 2 kb from the center of the OCT4 ChIP-seq peak (n = 3 for untagged, n = 2 for each V5-tagged clone). F OCT4, SOX2, or NANOG enrichment over SPT16-V5 CUT&RUN peaks. Averaged replicates shown (n = 1 for OCT4, n = 2 for SOX2 and NANOG; ChIP-seq from GSE11724) [78]. Significance of overlap between pluripotency factor binding and SPT16-V5 binding was assessed via two-tailed Fisher’s exact tests (p = 0 for all remodelers, ratio = 61.597, 94.475, and 93.779 for OCT4, SOX2, and NANOG overlap with SPT16-V5, respectively). G Heatmaps displaying overlap between OCT4 ChIP-seq and SPT16-V5 CUT&RUN peaks. Clusters were assigned by direct overlap between peak datasets and are individually sorted by strength of SPT16-V5 binding (ChIP-seq from GSE11724) [78]. Merged replicates are shown as heatmaps ± 2 kb from the center of the peak (n = 3 for untagged, n = 2 for each V5-tagged clone, n = 1 for OCT4 ChIP-seq, n = 2 for other ChIP-seq experiments; ChIP-seq from GSE11724) [78]