Supplementary Figure 7: CTCF BS are enriched at regenerative genes. | Nature Neuroscience

Supplementary Figure 7: CTCF BS are enriched at regenerative genes.

From: Epigenomic signatures underpin the axonal regenerative ability of dorsal root ganglia sensory neurons

Supplementary Figure 7

(A) Stacked bar plot illustrating the number of genes with CTCF BS in the TSS +/-1Kb region with a differential chromatin accessibility and occupancy of the indicated histone marks upon SNA vs sham, or DCA vs lam (N=3 for ATACseq, and N=2 for ChIPseq, independent samples; Pvalue<0.05). (B) Stacked bar plot illustrating the number of enhancers with CTCF BS with a differential chromatin accessibility and occupancy of the indicated histone marks upon SNA vs sham, or DCA vs lam (N=3 for ATACseq, and N=2 for ChIPseq, independent samples; Pvalue<0.05). (C) Bar plot of the number of DE genes after SNA vs sham, or DCA vs lam with a CTCF BS (TSS and enhancers +/-1 Kb) (N=3 independent samples; Pvalue<0.05). (D) Heatmap comparing the GO enrichment analysis of the upregulated and downregulated genes upon SNA, with that of subset of genes with CTCF BS at their TSS or enhancer +/-1Kb, and with that of the upregulated and downregulated genes in mouse CTCF-cKO hippocampus (GSE84175) (BP:biological process, Modified Fisher Exact Pvalue<0.05). (E) Heatmap showing the upregulated RAGs, ranked by fold change; in purple the ones displaying CTCF BS at their TSS or enhancer +/-1Kb. (F) DNA quantification by RT-PCR of the recovered DNA after microccocal nuclease (MNase) treatment at different concentrations (U=units), relative to Input. The Fos TSS +/-1 Kb region has been tested following SNA (top) or DCA (bottom) vs their controls (mean+s.e.m. of N=3 independent experiments). (G) Ratio of the recovered DNA after MNase treatment at different concentrations upon SNA vs sham (top), or DCA vs lam (bottom) for the indicated TSS +/-1 Kb regions (mean±s.e.m. of; N=3 independent experiments for Klf16 and Bdnf upon SNA, for Bdnf upon DCA, for Klf16 and b2m at 1.5 U of MNase; N=4 for all the other conditions;2-way ANOVA, Sidak’s multiple comparison test; ns=not significant; full statistics in Supplementary Data 15. The red line represents a ratio=1, meaning no difference between conditions.

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