Comparative genomics of vertebrate Fox cluster loci.
© Wotton and Shimeld; licensee BioMed Central Ltd. 2006 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
BACKGROUND: Vertebrate genomes contain numerous duplicate genes, many of which are organised into paralagous regions indicating duplication of linked groups of genes. Comparison of genomic organisation in different lineages can often allow the evolutionary history of such regions to be traced. A classic example of this is the Hox genes, where the presence of a single continuous Hox cluster in amphioxus and four vertebrate clusters has allowed the genomic evolution of this region to be established. Fox transcription factors of the C, F, L1 and Q1 classes are also organised in clusters in both amphioxus and humans. However in contrast to the Hox genes, only two clusters of paralogous Fox genes have so far been identified in the Human genome and the organisation in other vertebrates is unknown. RESULTS: To uncover the evolutionary history of the Fox clusters, we report on the comparative genomics of these loci. We demonstrate two further paralogous regions in the Human genome, and identify orthologous regions in mammalian, chicken, frog and teleost genomes, timing the duplications to before the separation of the actinopterygian and sarcopterygian lineages. An additional Fox class, FoxS, was also found to reside in this duplicated genomic region. CONCLUSION: Comparison of loci identifies the pattern of gene duplication, loss and cluster break up through multiple lineages, and suggests FoxS1 is a likely remnant of Fox cluster duplication.
We thank Peter Holland and Dave Ferrier for their discussions on this project and John Mulley for supplying the Amia calva genomic DNA, and for comments on the manuscript. This work was supported by the BBSRC.
Research Support, Non-U.S. Gov't
This is the final version of the article. Available from BioMed Central via the DOI in this record.
Vol. 7, pp. 271 -
Place of publication
Showing items related by title, author, creator and subject.
Genome-wide analysis reveals loci encoding anti-macrophage factors in the human pathogen Burkholderia pseudomallei K96243. Dowling, AJ; Wilkinson, PA; Holden, Matthew; Quail, MA; Bentley, SD; Reger, J; Waterfield, NR; Titball, Richard W.; ffrench-Constant, Richard (Public Library of Science, 2010-12-22)Burkholderia pseudomallei is an important human pathogen whose infection biology is still poorly understood. The bacterium is endemic to tropical regions, including South East Asia and Northern Australia, where it causes ...
Investigating the targets of MIR-15a and MIR-16-1 in patients with chronic lymphocytic leukemia (CLL). Hanlon, K; Rudin, CE; Harries, LW (Public Library of Science, 2009-09-25)BACKGROUND: MicroRNAs (miRNAs) are short, noncoding RNAs that regulate the expression of multiple target genes. Deregulation of miRNAs is common in human tumorigenesis. The miRNAs, MIR-15a/16-1, at chromosome band 13q14 ...
Cooper, JD; Simmonds, MJ; Walker, NM; Burren, O; Brand, OJ; Guo, H; Wallace, C; Stevens, H; Coleman, G; Wellcome Trust Case Control Consortium; Franklyn, JA; Todd, JA; Gough, SCL (Oxford University Press (OUP), 2012-12-01)Autoimmune thyroid disease (AITD), including Graves' disease (GD) and Hashimoto's thyroiditis (HT), is one of the most common of the immune-mediated diseases. To further investigate the genetic determinants of AITD, we ...