Molecular Mechanisms for Chromosome Deletion

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1. Molecular processes causing chromosome interstitial deletion

Chromosome interstitial deletion is a critical genetic event for the inactivation of tumor suppressor genes in human cells. The deletion at chromosome 9p21 removing the p16 tumor suppressor gene is a genetic alteration frequently observed in a variety of human cancers. Thus, structural analyses of breakpoints for p16 deletions in several types of human cancers have been performed to elucidate the molecular process of chromosome interstitial deletion, consisting of formation of DNA double strand breaks (DSBs) and subsequent joining of DNA ends in human cells. In lymphoid leukemia, it was indicated that deletions were caused by illegitimate VDJ recombination triggered by DSBs formed by the RAG complex at a few defined RSS (recombination-signal-sequence)-like sequences. In solid tumors, it was indicated that deletions were caused by non-homologous end joining of DNA ends for DSBs generated at unspecific sites in or near the p16 locus by unspecified factors.



2. Genomic/chromosomal feature(s) responsible for the susceptibility to DSBs

Breakpoint clustering in human cancer makes us consider that a genomic/chromosomal feature(s) other than nucleotide sequences also affects the susceptibility of genomic segments of the p16 locus to DSBs. To address the issue, we introduced a restriction enzyme, MspI, into HeLa cells to investigate the differences in the susceptibility to DSB along the genome in vivo. Three regions containing the promoters for the p16, p14ARF and p15 genes, respectively, were found to be sensitive to MspI digestion. Breakpoint cluster sites/region identified in lymphoid leukemia and solid tumors co-localized with these sensitive regions. Thus, it was considered that these three regions form unique architectures making DNA susceptible to the attack of DNA damaging agents, including DNA end nucleases.