Research

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

Shaun Mahony¹ , David L Corcoran² , Eleanor Feingold^2,3 and Panayiotis V Benos^1,2,4

¹Department of Computational Biology, School of Medicine, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15260, USA

²Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, DeSoto Street, Pittsburgh, PA 15261, USA

³Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, DeSoto Street, Pittsburgh, PA 15261, USA

⁴University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Centre Avenue, Pittsburgh, PA 15232, USA

author email corresponding author email

Genome Biology 2007, 8:R84doi:10.1186/gb-2007-8-5-r84

Published:	16 May 2007

Subject areas: Evolution, Molecular biology, Genome studies

Abstract

Background

Being the first noneutherian mammal sequenced, Monodelphis domestica (opossum) offers great potential for enhancing our understanding of the evolutionary processes that take place in mammals. This study focuses on the evolutionary relationships between conservation of noncoding sequences, cis-regulatory elements, and biologic 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 among mammals, except in the first 500 base pairs, where the conservation is similar. Comparison of 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 conserved between human and opossum. Some core biologic processes exhibited significantly fewer conserved TFBSs in human-opossum comparisons, suggesting greater functional divergence. A new measure of efficiency in multigenome phylogenetic footprinting (base regulatory potential rate [BRPR]) shows that including human-opossum conservation increases specificity in finding human TFBSs.

Conclusion

Opossum facilitates better estimation of promoter conservation and TFBS turnover among mammals. The fact that substantial TFBS numbers are located in a small proportion of the human-opossum conserved sequences emphasizes 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 microRNA upstream increased conservation remains unknown, it is expected to have strong implications for our understanding of regulation of their expression.