Genetical Research

Conserved fragments of transposable elements in intergenic regions: evidence for widespread recruitment of MIR- and L2-derived sequences within the mouse and human genomes

J. C. SILVA a1c1p1, S. A. SHABALINA a1, D. G. HARRIS a2, J. L. SPOUGE a1 and A. S. KONDRASHOV a1
a1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
a2 National Security Agency, Fort Meade, MD 20755, USA

Article author query
silva j   [PubMed][Google Scholar] 
shabalina s   [PubMed][Google Scholar] 
harris d   [PubMed][Google Scholar] 
spouge j   [PubMed][Google Scholar] 
kondrashov a   [PubMed][Google Scholar] 


We analysed the distribution of transposable elements (TEs) in 100 aligned pairs of orthologous intergenic regions from the mouse and human genomes. Within these regions, conserved segments of high similarity between the two species alternate with segments of low similarity. Identifiable TEs comprise 40–60% of segments of low similarity. Within such segments, a particular copy of a TE found in one species has no orthologue in the other. Overall, TEs comprise only approximately 20% of conserved segments. However, TEs from two families, MIR and L2, are rather common within conserved segments. Statistical analysis of the distributions of TEs suggests that a majority of the MIR and L2 elements present in murine intergenic regions have human orthologues. These elements must have been present in the common ancestor of human and mouse and have remained under substantial negative selection that prevented their divergence beyond recognition. If so, recruitment of MIR- and L2-derived sequences to perform a function that increases host fitness is rather common, with at least two such events per host gene. The central part of the MIR consensus sequence is over-represented in conserved segments given its background frequency in the genome, suggesting that it is under the strongest selective constraint.

(Received April 30 2002)
(Revised October 22 2002)
(Revised January 29 2003)

c1 Corresponding author.
p1 Current address: The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. Tel: +1 (301) 8380200. Fax: +1 (301) 8380208. e-mail: