Analysis of 5' gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals

Abstract

Background: Phylogenetic footprinting is a comparative method based on the principle that functional sequence elements will acquire fewer mutations over time than non-functional sequences. Successful comparisons of distantly related species will thus yield highly important sequence elements likely to serve fundamental biological roles. RNA regulatory elements are less well understood than those in DNA. In this study we use the emerging model organism Nasonia vitripennis, a parasitic wasp, in a comparative analysis against 12 insect genomes to identify deeply conserved non-coding elements (CNEs) conserved in large groups of insects, with a focus on 5' UTRs and promoter sequences. Results: We report the identification of 322 CNEs conserved across a broad range of insect orders. The identified regions are associated with regulatory and developmental genes, and contain short footprints revealing aspects of their likely function in translational regulation. The most ancient regions identified in our analysis were all found to overlap transcribed regions of genes, reflecting stronger conservation of translational regulatory elements than transcriptional elements. Further expanding sequence analyses to non-insect species we also report the discovery of, to our knowledge, the two oldest and most ubiquitous CNE's yet described in the animal kingdom (700 MYA). These ancient conserved non-coding elements are associated with the two ribosomal stalk genes, RPLP1 and RPLP2, and were very likely functional in some of the earliest animals. Conclusions: We report the identification of the most deeply conserved CNE's found to date, and several other deeply conserved elements which are without exception, part of 5' untranslated regions of transcripts, and occur in a number of key translational regulatory genes, highlighting translational regulation of translational regulators as a conserved feature of insect genomes.