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

Background. Being the first non-eutherian mammal sequenced, Monodelphis domestica ( opossum) offers great potential in understanding the evolutionary processes taking place in mammals. This study focuses on the evolutionary relationships between conservation of non-coding sequences, cis-regulatory elements and biological functions of regulated genes in opossum and eight vertebrate species. Results. 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. Conclusions. Opossum facilitates better estimation of promoter conservation and TFBS turnover amongst mammals. The fact that substantial TFBS numbers are located in a small part of the human-opossum conserved sequences underlines the importance of marsupial genomes for phylogenetic footprinting-based motif discovery strategies. The BRPR measure is expected to help select genome combinations for optimal performance of these algorithms. Finally, although the etiology of the miRNA upstream increased conservation remains unknown, it is expected to have strong implications in understanding their expression regulation.