The 1.4-Mb CMT1A duplication/HNPP deletion genomic region reveals unique genome architectural features and provides insights into the recent evolution of new genes.

Duplication and deletion of the 1.4-Mb region in 17p12 that is delimited by two 24-kb low copy number repeats (CMT1A-REPs) represent frequent genomic rearrangements resulting in two common inherited peripheral neuropathies, Charcot-Marie-Tooth disease type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsy (HNPP). CMT1A and HNPP exemplify a paradigm for genomic disorders wherein unique genome architectural features result in susceptibility to DNA rearrangements that cause disease. A gene within the 1.4-Mb region, PMP22, is responsible for these disorders through a gene-dosage effect in the heterozygous duplication or deletion. However, the genomic structure of the 1.4-Mb region, including other genes contained within the rearranged genomic segment, remains essentially uncharacterized. To delineate genomic structural features, investigate higher-order genomic architecture, and identify genes in this region, we constructed PAC and BAC contigs and determined the complete nucleotide sequence. This CMT1A/HNPP genomic segment contains 1,421,129 bp of DNA. A low copy number repeat (LCR) was identified, with one copy inside and two copies outside of the 1.4-Mb region. Comparison between physical and genetic maps revealed a striking difference in recombination rates between the sexes with a lower recombination frequency in males (0.67 cM/Mb) versus females (5.5 cM/Mb). Hypothetically, this low recombination frequency in males may enable a chromosomal misalignment at proximal and distal CMT1A-REPs and promote unequal crossing over, which occurs 10 times more frequently in male meiosis. In addition to three previously described genes, five new genes (TEKT3, HS3ST3B1, NPD008/CGI-148, CDRT1, and CDRT15) and 13 predicted genes were identified. Most of these predicted genes are expressed only in embryonic stages. Analyses of the genomic region adjacent to proximal CMT1A-REP indicated an evolutionary mechanism for the formation of proximal CMT1A-REP and the creation of novel genes by DNA rearrangement during primate speciation.

Mouse molecular cytogenetic resource: 157 BACs link the chromosomal and genetic maps.

We have established a collection of strong molecular cytogenetic markers that span the mouse autosomes and X chromosome at an average spacing of one per 19 Mb and identify 127 distinct band landmarks. In addition, this Mouse Molecular Cytogenetic Resource relates the ends of the genetic maps to their chromosomal locations. The resource consists of 157 bacterial artificial chromosome (BAC) clones, each of which identifies specific mouse chromosome bands or band borders, and 42 of which are linked to genetic markers that define the centromeric and telomeric ends of the Whitehead/MIT recombinational maps. In addition, 108 randomly selected and 6 STS-linked BACs have been assigned to single chromosome bands. We have also developed a high-resolution fluorescent reverse-banding technique for mouse chromosomes that allows simultaneous localization of probes by fluorescence in situ hybridization (FISH) with respect to the cytogenetic landmarks. This approach integrates studies of the entire mouse genome. Moreover, these reagents will simplify gene mapping and analyses of genomic fragments in fetal and adult mouse models. As shown with the MMU16 telomeric marker for the trisomy 16 mouse model of Down syndrome, these clones can obviate the need for metaphase analyses. The potential contribution of this resource and associated methods extends well beyond mapping and includes clues to understanding mouse chromosomes and their rearrangements in cancers and evolution. Finally it will facilitate the development of an integrated view of the mouse genome by providing anchor points from the genetic to the cytogenetic and functional maps of the mouse as we attempt to understand mutations, their biological consequences, and gene function.