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Aim: Today it is known that treatment of cells with topoisomerase poisons leads to the formation of double stranded DNA breaks in breakpoint cluster regions (BCRs) of known proto-oncogenes such as MLL or AML1. And that incorrect repair of these breaks may cause chromosomal rearrangements which in turn may induce the so-called treatment-related leukaemias. But the exact mechanisms of these rearrangements remain unclear. Methods: We have treated cultured human lymphoid cells (Jurkat) with etoposide or camptothecin and visualized the chromosome territories and proto-oncogene parts upstream and downstream of BCR then used 3D-FISH method to. Confocal images were processed by computer application that detects labeled parts of proto-oncogene and chromosomal territories. Results: We found that after etoposide treatment parts of some MLL or AML1 alleles are distanced from each other in the nuclear space. We analyzed interposition of labeled parts of proto-oncogenes and chromosomal territories where this genes normally lie. We obtained that separated parts of proto-oncogene are localized outside the chromosome territory more frequently than non-broken proto-oncogene. Camptothecin treatment does not affect on integrity of AML1 and MLL. Conclusion: Parts of breaking proto-oncogenes have high mobility in the nuclear space and tend to be outside or on the edge of chromosome territory. There is no difference between 5'- and 3'-part of proto-oncogene. For AML1 this effect is more noticeable than for MLL, because normally MLL lie more proximately in chromosome 11 territory, than AML1 in chromosome 21 territory. The work was supported by the Ministry of Science and Education of the Russian Federation (grant P1339), by RFBR (grant 10-04-00305-а), by Carl Zeiss grant and by the “Grant of the President of Russian Federation” (MK-222.2011.4).