Phylogenetic footprinting was first used and published by Tagle et al. in 1988, which allowed researchers to predict evolutionary conserved cis-regulatory elements responsible for embryonic ε and γ globulin gene expression in primates [REF].
Before phylogenetic footprinting, DNase footprinting was used, where protein would be bound to DNA transcription factor binding sites (TFBS) protecting it from DNase digestion.