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

Genome Res. 2011 Mar;21(3):402-9. doi: 10.1101/gr.108563.110. Epub 2011 Jan 31.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5' Flanking Region / genetics
  • AT Rich Sequence
  • Animals
  • Base Sequence
  • Chloride Channels / genetics*
  • Chloride Channels / metabolism
  • Chromosome Breakage
  • Chromosome Mapping
  • Dosage Compensation, Genetic
  • Epigenomics
  • Evolution, Molecular
  • Female
  • Gene Dosage
  • Genes
  • Genome
  • Humans
  • Introns
  • Male
  • Mice
  • Molecular Sequence Data
  • Muridae
  • Protein Structure, Tertiary / genetics
  • Rats
  • Sequence Analysis, DNA
  • Species Specificity
  • X Chromosome / genetics


  • Chloride Channels

Associated data

  • GENBANK/HM053970
  • GENBANK/HM053971