Extended Data Fig. 8: NFI-TFs are Required to Maintain Bulge-SC Identity.
a, Replicate analysis of ATAC-seq experiments show correlation coefficients of >0.94, indicating good reproducibility. Correlation coefficients were calculated by Pearson’s method. b, Reduction of chromatin accessibility at bulge-SC TF-bound loci upon loss of NFI-TFs. Note loci co-occupied by NFIB and bulge-SC TFs show a greater decrease of chromatin accessibility. In boxplots, the median (line), first and third quartiles (box), and whiskers (highest and lowest values) are shown. TF bindings sites are based on prior in vivo ChIP-seq on bulge-SCs13,16,17,18,20,72. ATAC-seq (this study) was used to determine differential accessibility at bulge-SC TF ChIP-bound loci. Statistics was analyzed using unpaired, two-tailed t-test. Number of peaks analyzed: SOX9: n=1813 (NFIB-bound), n=1175 (no NFIB binding); LHX2: n=1363 (NFIB-bound), n=1453 (no NFIB binding); NFATc1: n=1503 (NFIB-bound), n=4199 (no NFIB binding); pSMAD1: n=1547 (NFIB-bound), n=1778 (no NFIB binding); TCF3: n=7840 (NFIB-bound), n=7668 (no NFIB binding); TCF4: n=5346 (NFIB-bound), n=4371 (no NFIB binding); TLE: n=2901 (NFIB-bound), n=2840 (no NFIB-binding); bulge SE H3K27ac: n=970 (NFIB-bound), and n=2017 (no NFIB binding). c, Comparison of bulge-SC-TF ChIP-peaks reveals high co-occupancy with NFIB. d, Differential chromatin accessibility at NFIB ChIP-occupied super-enhancers in WT vs. Nfib/Nfix-dKO bulge-SCs (measured by ATAC-seq). e, Immunofluorescence analysis shows gradual reduction in bulge-SC marker LHX2 over time. Scale bars = 20 μm. Bu, bulge. Dashed lines, HF-dermal border. Representative images for three biological replicates. f, Replicate analysis of 2 independent ChIP-seq experiments show correlation coefficients (r) of >0.94, indicating good reproducibility. Number of peaks analyzed: H3K4me1: n=128538 (WT), n=119965 (NFI-dKO); H3K27ac: n=65493 (WT), and n=82522 (NFI-dKO). Correlation coefficients were calculated by Pearson’s method. g, Heatmap of H3K4me1, H3K27ac and H3K27me3 ChIP-seq read densities centered on NFIB-bound peaks, depicting how they change with NFI status in bulge-SC chromatin. Note that Nfib/Nfix ablation associates with reduced H3K4me1 and H2K27ac but not H3K27me3 at NFIB-bound loci. See also Source Data.
