Extended Data Fig. 9: Differentially occupied nucleotides reflect aggregate DNase I cleavage profiles.

a, Differential footprint testing within thousands of accessible DHSs between nervous and non-nervous related biosamples. The vast majority of tested DHSs encode a single TF binding topology. Top, percentage of the DHSs tested that containing one or more differentially occupied element. Bottom left, distribution of differentially footprinted elements per DHS. Bottom right, selected TF recognition sequences significantly enriched in differentially occupied footprints (binomial test P < 0.01). Indicated in parenthesis is the fold-enrichment vs expected (based on prevalence of footprinted motif in tested regions). b, Density histograms of relative footprint occupancy between nervous-system derived and non-nervous-system derived samples for the TF recognition sequences of REST, NFIB, ZIC1 and EBF1. Grey indicates distribution of all motif instances tested. Black indicates differentially footprinted. c, Per-nucleotide aggregate plots of the mean relative DNase I protection (top) and differential test P value (–log₁₀, bottom) around differential occupied motifs. d, Cell- and tissue-specific expression of genes nearby differentially occupied REST footprints. Enrichment was performed using Enrichr²⁷. Shown are cell and tissues with an adjusted Fisher exact test P value <0.01.