Identification of a rearrangement in the 5' upstream region of the poly(ADP-ribose) polymerase pseudogene on chromosome 13 in Ewing's sarcoma cells.

We have cloned a 3.0 kb SalI-Sau3AI fragment containing 5' upstream sequences of a human poly(ADP-ribose) polymerase (PARR) pseudogene from the Ewing's sarcoma (ES) cell line A4573. The nucleotide sequence of the entire cloned fragment has been determined. Nucleotide sequence homology and Southern hybridization analysis of a panel of human/hamster somatic cell hybrids allowed us to map the PARP 5' sequences to human chromosome 13. Because it has been reported that the duplication of a 193 bp within the PARP sequences on chromosome 13 results in a 2.7/2.5 kb HindIII restriction fragment length polymorphism (RFLP), defined as A/B allele polymorphism, and that an elevated B allele frequency has been proposed to be associated with predisposition to cancer, we have analyzed ES cell lines for the presence of PARR-linked polymorphisms on chromosome 13. Using a probe from the cloned 5' PARP sequences, we found that ES cells homozygous (A/A) and heterozygous (A/B) for the 2.7/2.5 kb HindIII RFLP also differ in the organization of the genomic region upstream of the PARP pseudogene sequences. HindIII fragments of about 6.3, 10.5 and 22.0 kb were detected in A/B heterozygous cell lines (A4573 and SK-ES-1), whereas the A/A homozygous TC-106 ES cells showed fragments of about 6.6, 11.0 and 24.0 kb. This novel rearrangement on chromosome 13 may provide an additional marker to investigate cancer predisposition in human populations.