Yeast artificial chromosome cloning of 3.2 megabases within chromosomal band 11q24 closely linking c-ets 1 and Fli-1 and encompassing the Ewing sarcoma breakpoint.

Human chromosome 11 harbors many genes of medical significance and cancer-related rearrangements. The availability of cloned DNA in cosmids and in yeast artificial chromosomes (YACs), combined with fluorescence in situ hybridization analysis, has led to the cloning of genes at sites of chromosomal breakpoints in acute leukemias in 11q23 and in Ewing tumors in 11q24. YAC cloning has facilitated the construction of contigs covering large portions of chromosomes for the detailed analysis of disease gene regions. Here we have cloned in YACs approximately 3.2 Mb of DNA within band 11q24, spanning the Ewing sarcoma breakpoint. Landmark cosmids 23.2 (D11S374) and 5.8 (D11S372), shown by FISH to flank the breakpoint within a 1.5- to 1.8-Mb segment, were used to seed two YAC "walks" both centromeric and telomeric to the breakpoint by YAC-end cloning and screening of two total genomic YAC libraries. The centromeric YAC contig, which consists of 23 overlapping YACs and orders 19 sequence-tagged sites (STSs), covers a minimum of 2.2 Mb and spans the Ewing sarcoma breakpoint. c-ets 1 and Fli-1, two members of the ets family, have been linked within 400 kb of intervening DNA within this contig, which also comprises a polymorphic microsatellite, D11S912 (CA)n, which we have localized within the Fli-1 gene. The telomeric YAC contig, which consists of 11 overlapping YACs, comprises 5 STSs and covers a minimum of 1 Mb distal to the breakpoint. Taken together, the two contigs, which consist of a total of 34 YACs and comprise 24 STSs, are separated by a maximum gap of 200-400 kb and cover as a whole 3.2 Mb of DNA. This represents about 70% of human chromosomal band 11q24, which extends over approximately 4.4 Mb of DNA.