Research article

Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time

Dorota Retelska¹ , Emmanuel Beaudoing¹ , Cédric Notredame⁴ , C Victor Jongeneel^1,2 and Philipp Bucher^1,3

¹Computational Cancer Genomics Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland

²Office of Information Technology, Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland

³Computational Cancer Genomics Group, Swiss Institute for Experimental Cancer Research, Lausanne, Switzerland

⁴Structural and Genetic Information, Centre National de Recherche Scientifique, Marseille, France

author email corresponding author email

BMC Genomics 2007, 8:398doi:10.1186/1471-2164-8-398

Published:	31 October 2007

Abstract

Background

The comparison of complete genomes has revealed surprisingly large numbers of conserved non-protein-coding (CNC) DNA regions. However, the biological function of CNC remains elusive. CNC differ in two aspects from conserved protein-coding regions. They are not conserved across phylum boundaries, and they do not contain readily detectable sub-domains. Here we characterize the persistence length and time of CNC and conserved protein-coding regions in the vertebrate and insect lineages.

Results

The persistence length is the length of a genome region over which a certain level of sequence identity is consistently maintained. The persistence time is the evolutionary period during which a conserved region evolves under the same selective constraints.

Our main findings are: (i) Insect genomes contain 1.60 times less conserved information than vertebrates; (ii) Vertebrate CNC have a higher persistence length than conserved coding regions or insect CNC; (iii) CNC have shorter persistence times as compared to conserved coding regions in both lineages.

Conclusion

Higher persistence length of vertebrate CNC indicates that the conserved information in vertebrates and insects is organized in functional elements of different lengths. These findings might be related to the higher morphological complexity of vertebrates and give clues about the structure of active CNC elements.

Shorter persistence time might explain the previously puzzling observations of highly conserved CNC within each phylum, and of a lack of conservation between phyla. It suggests that CNC divergence might be a key factor in vertebrate evolution. Further evolutionary studies will help to relate individual CNC to specific developmental processes.