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

Nathaniel J Davies,Eran Tauber,Peter Krusche,Sascha Ott

doi:10.1186/s12862-015-0499-6

Nathaniel J Davies, Eran Tauber + Show 2 more

Open Access

https://doi.org/10.1186/s12862-015-0499-6

Copy DOI

Abstract

BackgroundPhylogenetic 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.ResultsWe 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.ConclusionsWe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0499-6) contains supplementary material, which is available to authorized users.

Highlights

Phylogenetic footprinting is a comparative method based on the principle that functional sequence elements will acquire fewer mutations over time than non-functional sequences
Using straightforward computational methods for prediction of regulatory elements presents issues; for example, prediction of transcription factor binding sites is usually accomplished by scanning a sequence of interest for matches to position-specific scoring matrices (PSSMs)
These two ancient coding elements (CNEs) are located in the 5’ UTRs of two genes that are known to interact with one another; RPLP1 and RPLP2

Summary

Introduction

Phylogenetic footprinting is a comparative method based on the principle that functional sequence elements will acquire fewer mutations over time than non-functional sequences. One of the most well-characterized of these mechanisms is regulation of transcription through the binding of transcription factors to regulatory DNA sequence [1]. The DNA sequences bound by transcription factors are generally short, the average binding site length being around 10 bp in eukaryotes [2]. Using straightforward computational methods for prediction of regulatory elements presents issues; for example, prediction of transcription factor binding sites is usually accomplished by scanning a sequence of interest for matches to position-specific scoring matrices (PSSMs). These PSSMs [5] describe the kinds of, generally short [2] sequence motifs bound by these

Objectives

Methods

Results

Discussion

Conclusion