Extended Data Fig. 4: Repressive motifs in CREs exhibiting decreasing accessibility across keratinocyte differentiation.
From: The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation
(a) Top: dynamics of negative contribution scores of predictive motif instances of CEPBA and KLF4 across time averaged over all CREs exhibiting decreasing accessibility across the timecourse. Bottom: dynamic expression patterns of CEBP and KLF family TFs that exhibit strong anticorrelation with motif activity dynamics across the timecourse. (b) A closing CRE (chr10:60192514-60203992) shows progressively increasing negative contributions of nucleotides in CEBPA motif across the timecourse in concordance with an increasing negative effect on accessibility. Assay ranges are ATAC-seq: 0-500; H3K27ac: 0-20; H3K4me1: 0–50. (c) Functional enrichments for gene sets linked to CREs containing predictive instances of CEBPA and KLF4 motifs with strong negative contribution scores. Left: enrichments linked to closing CREs with negative CEBPA motif scores. Right: enrichments linked to closing CREs with negative KLF4 motif scores.
