Genetic, physical, and comparative map of the subtelomeric region of mouse Chromosome 4

Abstract

The subtelomeric region of mouse chromosome (Chr) 4 harbors loci with effects on behavior, development, and disease susceptibility. Regions near the telomeres are more difficult to map and characterize than other areas because of the unique features of subtelomeric DNA. As a result of these problems, the available mapping information for this part of mouse Chr 4 was insufficient to pursue candidate gene evaluation. Therefore, we sought to characterize the area in greater detail by creating a comprehensive genetic, physical, and comparative map. We constructed a genetic map that contained 30 markers and covered 13.3 cM; then we created a 1.2-Mb sequence-ready BAC contig, representing a 5.1-cM area, and sequenced a 246-kb mouse BAC from this contig. The resulting sequence, as well as approximately 40 kb of previously deposited genomic sequence, yielded a total of 284 kb of sequence, which contained over 20 putative genes. These putative genes were confirmed by matching ESTs or cDNA in the public databases to the genomic sequence and/or by direct sequencing of cDNA. Comparative genome sequence analysis demonstrated conserved synteny between the mouse and the human genomes (1p36.3). DNA from two strains of mice (C57BL/6ByJ and 129P3/J) was sequenced to detect single nucleotide polymorphisms (SNPs). The frequency of SNPs in this region was more than threefold higher than the genome-wide average for comparable mouse strains (129/Sv and C57BL/6J). The resulting SNP map, in conjunction with the sequence annotation and with physical and genetic maps, provides a detailed description of this gene-rich region. These data will facilitate genetic and comparative mapping studies and identification of a large number of novel candidate genes for the trait loci mapped to this region.

Fig. 1

(A) Linkage map of the distal part of mouse Chr 4. Distances between markers were estimated in cM based on data from the B6 × 129 F₂ intercross (n = 628). The genetic interval from D4Mit33 to D4Ertd296e is 13.3 cM. Thick line indicates region that was physically mapped. (B) Physical map and the BAC contig of the subtelomeric region of mouse Chr 4 between D4Mit256 and K00231. BAC sizes (kb) are shown in parentheses. Dots indicate the presence of markers detected by hybridization and PCR, and in some cases, by direct sequencing.

Fig. 2

Mouse and human comparative 1.2-Mb map. The minimum tiling paths of the human BACs (upper) and mouse BACs (lower) are shown. Human BACs are identified by Accession number, and mouse BACs are identified by clone name. Mouse and human genes are denoted by approved gene symbols, if available. If no approved symbol was available in either species, Accession numbers were given. If no Accession number was found, but there was a sequence identity (see Fig. 3) the “like” suffix was added to the human gene name (KIAA1716-like).

Fig. 3

Percentage identity plot-based comparative map of mouse and human genomes. The mouse genomic sequence is upper, and the human genomic draft sequence is lower, assembled from three overlapping human BAC clones (Accession # AC026283, AL139287, and AL162741). Both the mouse and human sequences are oriented from the centromere (left) to telomere (right), and the percentage identity is shown on the vertical axis (50–100%). The portions of the figure corresponding to exons with exact matches to known genes are yellow; those with exact matches to cDNAs are blue. Mouse cDNA sequences with no homology to human genomic sequence are not included. Mouse genes are denoted as described in Fig. 2.

Fig. 3

Percentage identity plot-based comparative map of mouse and human genomes. The mouse genomic sequence is upper, and the human genomic draft sequence is lower, assembled from three overlapping human BAC clones (Accession # AC026283, AL139287, and AL162741). Both the mouse and human sequences are oriented from the centromere (left) to telomere (right), and the percentage identity is shown on the vertical axis (50–100%). The portions of the figure corresponding to exons with exact matches to known genes are yellow; those with exact matches to cDNAs are blue. Mouse cDNA sequences with no homology to human genomic sequence are not included. Mouse genes are denoted as described in Fig. 2.

Fig. 3

Percentage identity plot-based comparative map of mouse and human genomes. The mouse genomic sequence is upper, and the human genomic draft sequence is lower, assembled from three overlapping human BAC clones (Accession # AC026283, AL139287, and AL162741). Both the mouse and human sequences are oriented from the centromere (left) to telomere (right), and the percentage identity is shown on the vertical axis (50–100%). The portions of the figure corresponding to exons with exact matches to known genes are yellow; those with exact matches to cDNAs are blue. Mouse cDNA sequences with no homology to human genomic sequence are not included. Mouse genes are denoted as described in Fig. 2.