PUBLICATION

Structural relationships between highly conserved elements and genes in vertebrate genomes

Authors
Sun, H., Skogerbo, G., Wang, Z., Liu, W., and Li, Y.
ID
ZDB-PUB-081121-10
Date
2008
Source
PLoS One   3(11): e3727 (Journal)
Registered Authors
Liu, Wei
Keywords
Mammalian genomics, Human genomics, Comparative genomics, DNA-binding proteins, Genomic databases, Chromosomes, Gene regulation, Zebrafish
MeSH Terms
  • Animals
  • Cluster Analysis
  • Conserved Sequence*
  • DNA, Intergenic/genetics
  • Genetic Linkage
  • Genome/genetics*
  • Genome, Human/genetics
  • Humans
  • Regulatory Sequences, Nucleic Acid/genetics*
  • Vertebrates/genetics*
PubMed
19008958 Full text @ PLoS One
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.
Genes / Markers
Figures
Show all Figures
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes