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Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans

Tanya Vavouri12*, Klaudia Walter3, Walter R Gilks4, Ben Lehner5 and Greg Elgar2

Author Affiliations

1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK

2 School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK

3 MRC Biostatistics Unit, Institute of Public Health, Cambridge CB2 2SR, UK

4 Department of Statistics, University of Leeds, Leeds LS2 9JT, UK

5 EMBL/CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), UPF, C/Dr. Aiguader 88, Barcelona 08003, Spain

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Genome Biology 2007, 8:R15  doi:10.1186/gb-2007-8-2-r15

Published: 2 February 2007

Abstract

Background

The human genome contains thousands of non-coding sequences that are often more conserved between vertebrate species than protein-coding exons. These highly conserved non-coding elements (CNEs) are associated with genes that coordinate development, and have been proposed to act as transcriptional enhancers. Despite their extreme sequence conservation in vertebrates, sequences homologous to CNEs have not been identified in invertebrates.

Results

Here we report that nematode genomes contain an alternative set of CNEs that share sequence characteristics, but not identity, with their vertebrate counterparts. CNEs thus represent a very unusual class of sequences that are extremely conserved within specific animal lineages yet are highly divergent between lineages. Nematode CNEs are also associated with developmental regulatory genes, and include well-characterized enhancers and transcription factor binding sites, supporting the proposed function of CNEs as cis-regulatory elements. Most remarkably, 40 of 156 human CNE-associated genes with invertebrate orthologs are also associated with CNEs in both worms and flies.

Conclusion

A core set of genes that regulate development is associated with CNEs across three animal groups (worms, flies and vertebrates). We propose that these CNEs reflect the parallel evolution of alternative enhancers for a common set of developmental regulatory genes in different animal groups. This 're-wiring' of gene regulatory networks containing key developmental coordinators was probably a driving force during the evolution of animal body plans. CNEs may, therefore, represent the genomic traces of these 'hard-wired' core gene regulatory networks that specify the development of each alternative animal body plan.