Sequences contacted by promoters are conserved during evolution. (A) Phylogenetic tree for the analyzed species. (B) Sequence conservation levels, derived from pairwise alignments, for contacted restriction fragments. Violin plots represent the distribution of the percentage of aligned nucleotides between human and other species. Vertical segments represent median values; white dots represent mean values. (C) Sequence conservation levels for contacted ENCODE enhancers. (D) Conservation of contacted restriction fragments between human and mouse, as a function of the median genomic distance between restriction fragments and contacting baits. (E) Same as D, for ENCODE enhancers. (F) Conservation of contacted restriction fragments between human and mouse, as a function of the number of genes found within at most 500 kb from the restriction fragment. (G) Same as F, for ENCODE enhancers. (D–G) Dots represent mean values; vertical segments represent 95% confidence intervals of the mean, obtained with a nonparametric bootstrap approach (Methods). Filled dots represent nonrepetitive sequences; empty dots represent repetitive sequences.
