Highly conserved regulatory elements around the SHH gene may contribute to the maintenance of conserved synteny across human chromosome 7q36.3.
Comparative genomic analysis reveals an exceptionally large section of conserved shared synteny between the human 7q36 chromosomal region and the pufferfish (Fugu rubripes) genome. Remarkably, this conservation extends not only to gene order across 16 genes, but also to the position and orientation of a number of prominent conserved noncoding elements (CNEs). A functional assay using zebrafish has shown that most of the CNEs have reproducible and specific enhancer activity. This enhancer activity is often detected in a subset of tissues which reflect the endogenous expression pattern of a proximal gene, though some CNEs may act over a long range. We propose that the distribution of CNEs, and their probable association with a number of genes throughout the region, imposes a critical constraint on genome architecture, resulting in the maintenance of such a large section of conserved synteny across the vertebrate lineage.
Goode
Debbie K
DK
Comparative Genomics Group, MRC Rosalind Franklin Centre for Genomics Research, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK.
Snell
Philip
P
Smith
Sarah F
SF
Cooke
Julie E
JE
Elgar
Greg
G
D000818:Animals; D002874:Chromosome Mapping; D002897:Chromosomes, Human, Pair 7; D017124:Conserved Sequence; D017931:DNA Primers / Q000737:chemistry; D004742:Enhancer Elements, Genetic; D015894:Genome, Human; D049452:Green Fluorescent Proteins / Q000378:metabolism; D053823:Hedgehog Proteins; D006801:Humans; D008957:Models, Genetic; D008969:Molecular Sequence Data; D012045:Regulatory Sequences, Nucleic Acid; D012689:Sequence Homology, Nucleic Acid; D026801:Synteny; D014018:Tissue Distribution; D015534:Trans-Activators / Q000235:genetics*; D015027:Zebrafish
D017931:DNA Primers; D053823:Hedgehog Proteins; C509239:SHH protein, human; D015534:Trans-Activators; D049452:Green Fluorescent Proteins