In a key set of experiments, the researchers used a technique called spectral karyotyping to analyze in detail the breakage and rearrangements of the chromosomes in the lymphomas. "Basically, this technique traces chromosome rearrangements by 'painting' individual chromosomes with fluorescent probes targeted to specific DNA sequences," said Alt. "If you paint different chromosomes different colors, you can figure out where the rearrangements came from."
Their analyses revealed that all the tumors showed a complex translocation -- a complicon -- that involved specific regions of chromosomes 12 and 15 that became embedded in a third chromosome. "We found that the amplified c-myc genes, as well as parts of the IgH locus, were somewhere else," said Alt. "They were on another chromosome that often had just pieces of chromosomes 12 and 15 attached. That was a surprise, because when we originally detected such a translocation between the two chromosomes, it resembled those of Burkitt's lymphoma which just involve human equivalents of 12 and 15, so we thought that was where the action would be in this case; but it wasn't."
Furthermore, said Alt, the chromosome breakages that caused amplification of the genes were not found in a location where one might expect them to trigger c-myc activation. "It was striking that every c-myc gene that we found to be amplified was located far away from the breakpoint, instead of adjacent to it, as is found in Burkitt's lymphoma." The adjacent breakage classically damages the regulatory region upstream of the gene, switching it on, explained Alt. "The mechanism that we have uncovered activates c-myc by leading to the amplification of the region of the chromosome in which it resides," he said.