Analysis of a 69-kb Contiguous Genomic Sequence at a Putative Tumor Suppressor Gene Locus on Human Chromosome 6q27

• Published in: DNA sequence 1998, Vol.9 (4), p.189-204
• Main Authors: Qu, Xiao-Yan, Hauptschein, Robert S., Rzhetsky, Andrey, Scotto, Luigi, Chien, Ming-Cheng, Ye, Xiaolu, Frigeri, Ferdinando, Rao, Pulivarthi H., Pasqualucci, Laura, Gamberi, Barbara, Deaven, Larry L., Zhang, Peisen, Chaganti, R. S. K., Dalla-favera, Riccardo, Russo, James J.
• Format: Article
• Language: English
• Subjects: 6q27; Alu Elements; Base Sequence; Breast Neoplasms - genetics; Chromosome Deletion; Chromosome Mapping; Chromosomes, Human, Pair 6 - genetics; Cloning, Molecular; DNA - genetics; Exon trapping; Exons; Female; GC Rich Sequence; Genes, Tumor Suppressor; Genetic Variation; Genome, Human; Humans; Lymphoma, B-Cell - genetics; Molecular Sequence Data; Ovarian Neoplasms - genetics; Promoter Regions, Genetic; Repetitive Sequences, Nucleic Acid; sequence annotation; shotgun sequencing; Tumor Cells, Cultured; tumor suppressor gene
• ISSN: 1042-5179; 1029-2365
• DOI: 10.3109/10425179809105206

Multiple neoplasias including B-cell non-Hodgkin's lymphoma, breast carcinoma, and ovarian carcinoma, have been associated with frequent deletions of the distal region on the long arm of human chromosome 6, suggesting the presence of one or more tumor suppressor gene(s) at this locus. Loss of heterozygosity analysis of breast and ovarian tumors has further restricted the minimal region of loss within 6q27. To further characterize this genomic region for gene content including putative tumor suppressor genes as well as other elements that may contribute to tumorigenesis, a 68940-bp contiguous sequence, encompassing markers D6S193 and D6S297, was generated by random shotgun sequencing of a cos-mid, PI, and PAC contig. In addition, exon trapping was performed utilizing a subset of these clones. Sixteen trapped exons, ranging in size from 44 to 399 bp, span this approximately 69-kb region. Many other putative exons have been identified computationally. Further analysis has identified 13 potential promoters and 13 putative polyadenylation sites in the region. Northern analysis identified a transcript mapping within this interval that is expressed in ovarian, breast, and lymphoid-derived tumor cell lines. Consideration of these data, together with the demonstration of several regions of high CpG content, suggests the possibility of several genes at this locus.