Fig. 3

The dynamic of regulatory elements (REs) in the liver during ruminant evolution. A The fractions of REs that are highly conserved (AC), ruminant-specific (RS), and cattle-specific (CS) in cattle. B Specificity of liver REs determined by comparing to the other seven cattle tissues-adipose, cortex, cerebellum, hypothalamus, lung, spleen, and muscle. C Histone mark signals (H3K4me3 for cattle-specific promoters (CSP), H3K27ac for cattle-specific enhancers (CSE)), DNA methylation levels, and chromatin accessibility of tissue-specific CSE and CSP across eight cattle tissues. D GREAT Gene Ontology (GO) terms enrichment for six lineage-specific REs (FDR <0.01). E H3K27ac and H3K4me3 ChIP-seq profiles of PON1 gene (right) for six species, cattle, sheep, goat, pig, human, and mouse, at the loci of ruminant-specific enhancers (RSE). The expression levels of the PON1 gene (left) in the 28 organ systems of cattle. TPM, transcripts per kilobase million. F Transcription factor (TF) motifs enriched in six lineage-specific REs. The bubble plot shows the enrichment of TF motifs in six lineage-specific REs, and the heatmap shows the chromatin accessibility of TF promoters across five mammals. G The fraction of RE peaks harboring canonical PPARA motif (JASPAR – MA1148.1) as a function of distance from RE peaks to the summits