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

Shaun Mahony,Panayiotis V Benos,David L Corcoran,Eleanor Feingold

doi:10.1186/gb-2007-8-5-r84

Shaun Mahony, Panayiotis V Benos + Show 2 more

Open Access

https://doi.org/10.1186/gb-2007-8-5-r84

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Abstract

A study of conservation of non-coding sequences, cis-regulatory elements and biological functions of regulated genes in opossum and other vertebrates enables better estimation of promoter conservation and transcription factor binding site turnover among mammals

Highlights

Being the first noneutherian mammal sequenced, Monodelphis domestica offers great potential for enhancing our understanding of the evolutionary processes that take place in mammals
Distribution of conserved blocks in the upstream regions of protein coding and intergenic miRNA genes Conservation of the 5 kilobases upstream regions of all RefSeq protein coding genes as well as the known intergenic miRNA genes was calculated using the sliding window approach, as we describe in Materials and methods
Because little is known about the transcriptional regulation of non-intronic miRNA genes, we cannot assess the possible transcription factor binding sites (TFBSs) turnover

Summary

Introduction

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. One of the prime motivating factors driving the sequencing of vertebrate genomes is the expectation that the role played by the functional regions of the human genome may be discerned by finding molecular level commonalities with and differences from other animals. This is especially true of the newly sequenced opossum (Monodelphis domestica), which is the first completed marsupial genome. The increased conservation in the biologically more important parts of the promoter region has been explored by various phylogenetic footprinting algorithms, such as PhyloGibbs [3], ConSite [4], rVista [5], and FOOTER [6], to improve the prediction of transcription factor binding sites (TFBSs) in vertebrate genomes. Phylogenetic footprinting provides a way to reduce the sequence search space to regions that are conserved (and more likely to contain functional elements), thereby improving the specificity of TFBS prediction

Methods

Results

Conclusion