Highly conserved syntenic blocks at the vertebrate Hox loci and conserved regulatory elements within and outside Hox gene clusters - PubMed (original) (raw)

Highly conserved syntenic blocks at the vertebrate Hox loci and conserved regulatory elements within and outside Hox gene clusters

Alison P Lee et al. Proc Natl Acad Sci U S A. 2006.

Abstract

Hox genes in vertebrates are clustered, and the organization of the clusters has been highly conserved during evolution. The conservation of Hox clusters has been attributed to enhancers located within and outside the Hox clusters that are essential for the coordinated "temporal" and "spatial" expression patterns of Hox genes in developing embryos. To identify evolutionarily conserved regulatory elements within and outside the Hox clusters, we obtained contiguous sequences for the conserved syntenic blocks from the seven Hox loci in fugu and carried out a systematic search for conserved noncoding sequences (CNS) in the human, mouse, and fugu Hox loci. Our analysis has uncovered unusually large conserved syntenic blocks at the HoxA and HoxD loci. The conserved syntenic blocks at the human and mouse HoxA and HoxD loci span 5.4 Mb and 4 Mb and contain 21 and 19 genes, respectively. The corresponding regions in fugu are 16- and 12-fold smaller. A large number of CNS was identified within the Hox clusters and outside the Hox clusters spread over large regions. The CNS include previously characterized enhancers and overlap with the 5' global control regions of HoxA and HoxD clusters. Most of the CNS are likely to be control regions involved in the regulation of Hox and other genes in these loci. We propose that the regulatory elements spread across large regions on either side of Hox clusters are a major evolutionary constraint that has maintained the exceptionally long syntenic blocks at the HoxA and HoxD loci.

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Conflict of interest statement

Conflict of interest statement: No conflicts declared.

Figures

Fig. 1.

Conserved syntenic blocks at the fugu and human Hox loci. Fugu has two duplicate loci for human HoxA, HoxB, and HoxD loci. Hexagons represent genes. MicroRNA genes are shown as borderless hexagons and pseudogenes with dotted borders. Genes that are present in only fugu or human locus are shown as open hexagons. Dark colored hexagons in the fugu (linked with their human orthologs with a diagonal line) represent genes that have undergone rearrangements.

Fig. 2.

Profiles of CNS at the human HoxA, HoxB, HoxC, and HoxD loci. x axis represents chromosomal coordinates, and y axis represents CNS. Genes at each locus are shown at the top as red boxes (Hox genes) or open boxes (non-Hox genes) linked with a thin line. Names of some genes are indicated. The previously identified 5′ global enhancers at HoxD and HoxA loci (3, 5) are represented by purple oval shapes.

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Highly conserved syntenic blocks at the vertebrate Hox loci and conserved regulatory elements within and outside Hox gene clusters - PubMed (original) (raw)