Clcn4-2 genomic structure differs between the X locus in Mus spretus and the autosomal locus in Mus musculus: AT motif enrichment on the X
- Di Kim Nguyen1,8,
- Fan Yang1,8,
- Rajinder Kaul2,3,
- Can Alkan2,4,
- Anthony Antonellis5,6,
- Karen F. Friery1,
- Baoli Zhu7,
- Pieter J. de Jong7 and
- Christine M. Disteche1,2,9
- 1Department of Pathology, University of Washington, Seattle, Washington 98195, USA;
- 2Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA;
- 3Department of Medicine, University of Washington, Seattle, Washington 98195, USA;
- 4Howard Hughes Medical Institute, Seattle, Washington 98195, USA;
- 5Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA;
- 6Department of Neurology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA;
- 7Children's Hospital, Oakland Research Institute, Oakland, California 94609, USA
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↵8 These authors contributed equally to this work.
Abstract
In Mus spretus, the chloride channel 4 gene Clcn4-2 is X-linked and dosage compensated by X up-regulation and X inactivation, while in the closely related mouse species Mus musculus, Clcn4-2 has been translocated to chromosome 7. We sequenced Clcn4-2 in M. spretus and identified the breakpoints of the evolutionary translocation in the Mus lineage. Genetic and epigenetic differences were observed between the 5′ends of the autosomal and X-linked loci. Remarkably, Clcn4-2 introns have been truncated on chromosome 7 in M. musculus as compared with the X-linked loci from seven other eutherian mammals. Intron sequences specifically preserved in the X-linked loci were significantly enriched in AT-rich oligomers. Genome-wide analyses showed an overall enrichment in AT motifs unique to the eutherian X (except for genes that escape X inactivation), suggesting a role for these motifs in regulation of the X chromosome.
Footnotes
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↵9 Corresponding author.
E-mail cdistech{at}u.washington.edu; fax (206) 543-3644.
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[Supplemental material is available for this article. The sequencing data from this study have been submitted to GenBank (http://www.ncbi.nlm.nih.gov/Genbank/) under accession nos. HM053970 and HM053971.]
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Article published online before print. Article, Supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.108563.110.
- Received March 30, 2010.
- Accepted December 15, 2010.
- Copyright © 2011 by Cold Spring Harbor Laboratory Press
