Fig. 6

FACT depletion has distinct effects on chromatin accessibility and nucleosome occupancy at SPT16-V5 binding sites and gene regulatory regions. A Differential chromatin accessibility visualized over TSS-distal DHSs, ± 2 kb, after 24-h IAA treatment. Higher signal indicates more accessible chromatin in IAA-treated samples than in EtOH-treated samples at the indicated timepoint, with the exception of untagged samples (log₂ IAA:IAA ratio) (n = 1 per cell line). Significance of altered chromatin accessibility at gene-distal DHSs (A) was analyzed by Friedman tests and corrected for multiple comparisons via Dunn’s test (p < 0.0001 overall, adj. p < 0.0001 for each individual comparison). B As in A but visualized over SPT16-V5 binding sites identified in Fig. 2. Significance of altered chromatin accessibility at SPT16-V5 binding sites was analyzed as in panel A (p < 0.0001 overall, adj. p < 0.0001 for each individual comparison). C As in A but visualized over RefSeq mRNA TSSs, ± 2 kb, after 24-h IAA treatment. Significance of altered chromatin accessibility was analyzed as in panel A (p < 0.0001 overall, adj. p < 0.0001 for both individual comparisons to Untagged. D Metaplot depicting change in chromatin accessibility at 24-h treatment over putative enhancer regions as defined in Fig. 5. Standard error is shaded in either direction. Significance of altered chromatin accessibility was analyzed as in panel A (p < 0.0001 overall, adj. p < 0.05 for each individual comparison except Untagged [adj. p = 0.4046]). E–H Differential nucleosome occupancy following 24-h IAA treatment (MNase-seq, n = 3 for untagged samples, n = 2 for each tagged cell line). Visualized over E TSS-distal DNaseI hypersensitive sites (DHSs) ± 2 kb (DNase-seq from GSM1014154) [83,84,85]. Significance of altered chromatin accessibility was analyzed as in panel A (p < 0.0001 overall, adj. p < 0.001 for each individual comparison). F Peaks called from SPT16-V5 CUT&RUN ± 2 kb. Significance of altered chromatin accessibility was analyzed as in panel A (p < 0.0001 overall, adj. p < 0.0001 for each individual comparison). G SOX2 ChIP-seq binding sites, ± 2 kb (ChIP-seq from GSE11724) [78]. Significance of altered chromatin accessibility was analyzed as in panel A (p < 0.0001 overall, adj. p < 0.0001 for each individual comparison). H OCT4 ChIP-seq binding sites, ± 2 kb (ChIP-seq from GSE11724) [78]. Significance of altered chromatin accessibility was analyzed as in panel A (p < 0.0001 overall, adj. p < 0.0001 for each individual comparison)