Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse (original) (raw)
- Ann-Marie Mallon1,4,
- Laurens Wilming2,4,
- Joseph Weekes1,
- James G.R. Gilbert2,
- Jennifer Ashurst2,
- Sandrine Peyrefitte2,
- Lucy Matthews2,
- Matthew Cadman1,
- Richard McKeone1,
- Chris A. Sellick1,
- Ruth Arkell1,
- Marc R.M. Botcherby3,
- Mark A. Strivens1,
- R. Duncan Campbell3,
- Simon Gregory2,5,
- Paul Denny1,
- John M. Hancock1,6,
- Jane Rogers2, and
- Steve D.M. Brown1
- 1_Medical Research Council Mammalian Genetics Unit, Harwell, Oxfordshire, United Kingdom_
- 2_Wellcome Trust Sanger Institute, Hinxton Genome Campus, United Kingdom_
- 3_Medical Research Council Rosalind Franklin Centre for Genomics Research, Hinxton Genome Campus, United Kingdom_
Abstract
Del(13)_Svea_36H (Del36H) is a deletion of ∼20% of mouse chromosome 13 showing conserved synteny with human chromosome 6p22.1-6p22.3/6p25. The human region is lost in some deletion syndromes and is the site of several disease loci. Heterozygous Del36H mice show numerous phenotypes and may model aspects of human genetic disease. We describe 12.7 Mb of finished, annotated sequence from Del36H. Del36H has a higher gene density than the draft mouse genome, reflecting high local densities of three gene families (vomeronasal receptors, serpins, and prolactins) which are greatly expanded relative to human. Transposable elements are concentrated near these gene families. We therefore suggest that their neighborhoods are gene factories, regions of frequent recombination in which gene duplication is more frequent. The gene families show different proportions of pseudogenes, likely reflecting different strengths of purifying selection and/or gene conversion. They are also associated with relatively low simple sequence concentrations, which vary across the region with a periodicity of ∼5 Mb. Del36H contains numerous evolutionarily conserved regions (ECRs). Many lie in noncoding regions, are detectable in species as distant as Ciona intestinalis, and therefore are candidate regulatory sequences. This analysis will facilitate functional genomic analysis of Del36H and provides insights into mouse genome evolution.
Footnotes
Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2478604\. Article published online before print in September 2004.
↵4 These two authors contributed equally to this work.
↵5 Present address: Center for Human Genetics, Duke University Medical Center, Durham, 27710 NC, USA.
↵6 Corresponding author. E-MAIL j.hancock{at}har.mrc.ac.uk; FAX 44-1235-834-776.
- Accepted July 21, 2004.
- Received March 4, 2004.
Cold Spring Harbor Laboratory Press