Sequence Analysis of a 685-kb Genomic Region on Chromosome 3p22-p21.3 That Is Homozygously Deleted in a Lung Carcinoma Cell Line

Abstract

Frequent chromosomal aberrations and/or losses of heterozygosity involving the short arm of chromosome 3 in carcinomas of the lung, kidney and other tissues imply that multiple putative tumor suppressor genes may be present on this chromosomal arm. To search for one of these genes, we determined DNA sequences in the genomic region at 3p22–21.3 where we had previously detected a homozygous deletion in a lung cancer cell line. The DNA sequence results of an about 685-kb region indicated that the size of the homozygously deleted segment was 638,489 bp, in which we identified only four genes including the integrin αRLC and the trans -Golgi p230 genes, both reported previously. The predicted amino acid sequences of one of the two novel genes showed high homology to villin, a human cytoskeleton protein; those of the other gene, termed HYA22, revealed significant homology to YA22, a hypothetical protein predicted from DNA sequences of Schizosaccharomyces pombe . The computer programs HEXON or GRAIL were able to predict three-fourths of the exons; the smallest exon predicted by either program was 46 base pairs. Repetitive sequences contained in the genomic region included 151 copies of the Alu sequence (1 copy/every 4.5 kb), 19 copies of the L1 sequence (1 copy/every 36 kb) , and 10 copies of the THE sequence.