Fig. 1

Schematic of Experimental Design. a We identified potential hominoid-specific enhancers by intersecting hominoid-specific ChIP-seq predicted enhancers from primary human liver with ChromHMM-predicted strong enhancers in HepG2 cells (screenshot from http://genome.ucsc.edu) [54]. We then tiled across each candidate enhancer using 194 nt sequences and identified 697 tiles that were active in the STARR-seq reporter assay in HepG2 cells. b We located orthologous sequences in 11 primates and computationally reconstructed 9 ancestral sequences for 348 of the active tiles, using New World monkeys as an outgroup. c We then cloned all 20 present-day or ancestral orthologs per tile and performed STARR-seq again in HepG2 cells. After collecting DNA and RNA from cells, we calculated enrichment scores as the log₂ ratio of RNA to DNA for each ortholog. Each shade of red represents a different ortholog tested