(A) Comparison of HNF4A ChIP-seq in WT and in Taf4ahep−/− liver and location of HNF4A occupied sites relative to the TSS. Comparison of the HNF4A consensus-binding sequence from our data generated by ChIP-MEME with the previously defined sequence. (B) Venn diagrams illustrate the number of genes with at least one HNF4A binding site either depleted or enriched in Taf4ahep−/− liver, within ±40 kb with respect to the TSS, intersected with up- or down-regulated genes. Graphs illustrate the locations of either the total, depleted or enriched HNF4A sites associated with the up and down-regulated genes within a window of ±40 kb with respect to the TSS. Total sites are shown in green and the sites associated with up- and down-regulated genes are shown in red and blue, respectively. (C) Upper panel shows the % of HNF4A-occupied sites enriched or depleted in Taf4ahep−/− liver that correspond to evolutionarily conserved or non-conserved CRMs. The lower panel shows the % of CRMs in each class that comprise sites for 1, 2, or 3 transcription factors in addition to HNF4A. (D) Location of HNF4A-occupied sites or CRMs, as indicated, enriched in WT or Taf4ahep−/− livers relative to the TSS corresponding to all peaks, all CRMs, or CRMs associated with down- and up-regulated genes.