Fig. 2

Snake-diverged CNEs are associated with limb genes and limb regulatory elements. a Snake-diverged CNEs are significantly associated with genes annotated with limb-related functions. Left: Bars depict Benjamini & Hochberg adjusted p-values derived by a one-sided Fisher’s exact test. Middle: Observed (orange vertical bar) and expected number (gray violin plots, based on 10,000 random subsets sampled from all CNEs) of snake-diverged CNEs associated with genes in each set (the thick box inside the violin plot indicates the first quartile, the median and the third quartile). The Z-score measuring the number of standard deviations that the observed number is above the random expectation is indicated. Right panel: Many snake-diverged CNEs (dots) are far away from the transcription start site of genes in these sets. CNEs associated with the same gene have the same color. b Snake-diverged CNEs significantly overlap regulatory elements active in embryonic limb tissue of tegu lizard, green anole lizard, and mouse. Orange bars correspond to limb regulatory datasets. ATAC-seq datasets generated in this study are highlighted in green. Remaining visual representation as in a. All animal illustrations were taken from phylopic.org. c Genome browser screenshot shows that snake-diverged CNEs (orange) overlap tegu limb-specific ATAC-seq peaks. ATAC-seq signal tracks of limb, brain, and liver are shown. d Snake-diverged CNEs are broadly distributed in the limb patterning network. An asterisk marks the genes which are associated with at least one snake-diverged CNE that overlaps a limb regulatory element