Chromosome 1q25-qter-specific NotI linking clones have been isolated from a NotI linking library that was constructed using DNA from MCH206.1 somatic cell hybrid cells. These cells contain chromosome 1q25-qter translocated to human chromosome Xp22 as the only human genetic material in mouse background. Sixty-eight NotI linking clones have been mapped by a combination of fluorescence in situ hybridization and R-banding to cytogenetic bands on the long arm of chromosome 1. The relative order of 11 Not I clones and their relation to known chromosome 1 markers have also been determined in 1q32 and 1q41, where the genes of Van der Woude and Usher syndrome type IIa have been previously mapped: cen-chr1.14-chr1.79-chr1.56-chr1.11-chr1.95-chr1.58 (chr1.74)-D1S70-chr1.15-chr1.82 (chr1, 143) -chr1.62-D1S81 -tel. The 1q32- and 1q41-specific NotI linking clones were sequenced in the vicinity of the Not I site. They were analyzed in terms of nucleotide composition, G+C content, frequency of CpG dinucleotides, and protein coding potentials. Most of the 1q32-q41-specific NotI linking clones were derived from CpG islands. Sequences of three NotI linking clones proved to be identical with known genes. Six of the remaining eight had a high potential for coding regions and shared short homologous regions with sequences in the GenBank database. The Not I linking clones and the identified CpG islands will provide valuable resources for constructing a long-range restriction map of chromosome 1q25-q44 and for the eventual isolation of disease genes of Van der Woude syndrome (1q32-q41) and Usher syndrome type Ha (1q41).
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