Selection and sequencing of interchromosomal rearrangements from gamma-irradiated normal human fibroblasts

To determine the sequences that flank sites of interchromosomal DNA rearrangements and to determine the relative frequency of inter- and intrachromosomal rearrangements induced by 30 Gy gamma-irradiation in a region 5' from exon I of the c-myc gene in normal human fibroblasts (IMR-90).

A modification of an inverse polymerase chain reaction (PCR) procedure, developed previously to detect rearrangements, was used. Inverse PCR products were re-amplified using primers designed to determine whether the product was a result of an inter- or intrachromosomal rearrangement. Possible interchromosomal rearrangements were then sequenced.

Four of 12 different products analyzed were potentially derived from interchromosomal rearrangements, while the remainder derived from intrachromosomal rearrangements. For three of the potential interchromosomal rearrangements, the sequence recombining with c-myc was unidentified, while in the other case the sequence was homologous to an L1 element. The frequencies of inter- and intrachromosomal rearrangements induced by 30 Gy gamma-irradiation in a 2 kbp region flanking the c-myc gene of IMR-90 cells were calculated to be at least 1.6x10(-4) and 3.3x10(-4) respectively. No clear association between sequence context and sites of radiation-induced rearrangement was found; however, two of the four sequenced rearrangements involved breakpoints in the 5'-flanking region of c-myc that occurred immediately after the sequence AAAGG.