Regulatory conservation of protein coding and miRNA genes in vertebrates: lessons from the opossum genom

"Analysis of 145 intergenic microRNA and all protein coding genes revealed that the upstream sequences of the former are up to twice as conserved as the latter amongst mammals, except in the first 500 bp where the conservation is similar. Comparison of the promoter conservation in 513 protein coding genes and related transcription factor binding sites (TFBSs) showed that 41% of the known human TFBSs are located in the 6.7% of promoter regions that are human-opossum conserved. Some core biological processes showed significantly smaller number of conserved TFBSs in human-opossum comparisons, suggesting greater functional divergence. A new measure of efficiency in multi-genome phylogenetic footprinting (BRPR) shows that including human-opossum conservation increases the specificity in finding human TFBSs."