Fig. 3

Differences in TF-binding site accessibility occur in putative enhancers at every stage of differentiation in HD cells. a Heatmap depicting differential ATAC-seq signal in HD and WT cells at macaque brain enhancers containing the RFX2, RFX3, and RFX5 binding sequences (N = 125). The red color represents enrichment and the blue color indicates depletion of THSSs containing this RFX motif in HD cells. b RFX2, RFX3, and RFX5 motif found by de novo motif analysis at enhancers showing differential ATAC-seq. c, d Bar graphs generated from RNA-seq data depicting differential expression of RFX2 (c) and RFX3 (d) showing differential expression corresponding with motif accessibility. Average FPKM for each sample was plotted. Error bars show 95% confidence intervals (**p < 0.001 and *p < 0.01, differential expression analysis). e, f Heatmap depicting differential THSSs at macaque brain enhancers containing FOSL2 (N = 47; e) and JUN (N = 204; f) binding sequences. Red represents HD enrichment and blue represents HD depletion. g The motif for FOSL2 and JUN found at enhancers showing differential ATAC-seq enrichment. h, i Bar graphs generated from RNA-seq for FOSL2 (h) and JUN (i) expression across differentiation. Error bars show 95% confidence intervals (**p < 0.001 and *p < 0.01, differential expression analysis)