title: Structural relationships between highly conserved elements and genes in vertebrate genomes.
abstract: Large numbers of sequence elements have been identified to be highly conserved among vertebrate genomes. These highly conserved elements (HCEs) are often located in or around genes that are involved in transcription regulation and early development. They have been shown to be involved in cis-regulatory activities through both in vivo and additional computational studies. We have investigated the structural relationships between such elements and genes in six vertebrate genomes human, mouse, rat, chicken, zebrafish and tetraodon and detected several thousand cases of conserved HCE-gene associations, and also cases of HCEs with no common target genes. A few examples underscore the potential significance of our findings about several individual genes. We found that the conserved association between HCE/HCEs and gene/genes are not restricted to elements by their absolute distance on the genome. Notably, long-range associations were identified and the molecular functions of the associated genes do not show any particular overrepresentation of the functional categories previously reported. HCEs in close proximity are found to be linked with different set of gene/genes. The results reflect the highly complex correlation between HCEs and their putative target genes.
authors.affiliation: Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Sun
authors.forename: Geir
authors.initials: G
authors.lastname: Skogerbø
authors.forename: Zhen
authors.initials: Z
authors.lastname: Wang
authors.forename: Wei
authors.initials: W
authors.lastname: Liu
authors.forename: Yixue
authors.initials: Y
authors.lastname: Li
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D017124:Conserved Sequence; D021901:DNA, Intergenic / Q000235:genetics; D008040:Genetic Linkage; D016678:Genome / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D014714:Vertebrates / Q000235:genetics*
chemical_list: D021901:DNA, Intergenic