Fig. 4

Sequence divergence results in widespread loss of transcription factor (TF) binding sites. a Difference in the median motif scores of limb-related TFs between 933 snake-diverged CNEs that overlap limb regulatory data and all other CNEs (excess score, x-axis). A positive excess score as observed for limbed species reflects a preference to preserve motifs of limb-related TFs. P-values comparing the distribution of motif scores of diverged and all other CNEs were computed with a one-sided Wilcoxon rank sum test and corrected for multiple testing. b Mutations in snakes in a CNE overlapping a limb-specific ATAC-seq peak weaken or destroy binding sites for key limb transcription factors. The binding preference of the TFs is visualized as a sequence logo, motif scores were computed with SWAN⁷⁴. c As panel a, but using motifs of eye-related TFs to compare CNEs that are diverged in subterranean mammals and overlap eye regulatory data with all other CNEs. d Mutations in two subterranean mammals in a CNE overlapping a lens-specific ATAC-seq peak weaken a binding site for c-Maf, a crystallin-inducing TF that is required for lens fiber cell differentiation⁷⁵