Conserved distances between vertebrate highly conserved elements

High numbers of sequence element with very high (>95%) sequence conservation between the human and other vertebrate genomes have been reported and ascribed putative cis-regulatory functions. We have investigated the structural relationships between such elements in mammalian genomes and find that not only their sequences, but also the distances between them are significantly (P<2.2x10(-16)) more conserved than corresponding distances between orthologous protein-coding genes or between exons within these genes. Regions of largely conserved distance between consecutive highly conserved elements (HCE) generally overlap previously identified HCE clusters, but may be far longer (up to 20 Mb) and possibly cover close to 25% of the human genome sequence. Similar conservation of distance is found between bird (chicken) and mammalian genomes and is also discernible in comparisons between fish and mammals. The data suggest either that a substantial amount of essential (functionally active) elements with lower sequence conservation occupy the space between the HCEs or that distance itself is an important factor in transcriptional regulation or chromatin modelling.