Chromosome rearrangement breakpoint clustering: The role of clonal selection

Molecular Biology

Volumn 39, Issue 3, 2005, Pages 313-320

  Umanskaya, O N ^a   Bystritskiy, A A ^a   Razin, S V ^a  

^a INSTITUTE OF GENE BIOLOGY   (Russian Federation)

Author keywords

Chimeric genes; Chromosome rearrangements; Double strand breaks; Nuclear architecture; Protein domains

Indexed keywords

CHIMERIC PROTEIN; DNA TOPOISOMERASE (ATP HYDROLYSING);

CHROMATIN STRUCTURE; CHROMOSOME REARRANGEMENT; DATA ANALYSIS; DNA STRAND BREAKAGE; EXON; FUSION GENE; GENE CLUSTER; GENETIC RECOMBINATION; NUCLEOTIDE SEQUENCE; PROTEIN DOMAIN; PROTEIN STRUCTURE; REVIEW;

EID: 21544444419     PISSN: 00268933     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11008-005-0044-6     Document Type: Review

References (43)

1. Mitelman F., Johansson B., Mertens F. 2003. Mitelman Database of Chromosome Aberrations in Cancer. [web page] http://cgap.nci.nih.gov/ Chromosomes/Mitelman.
2. Yoshino N., Kojima T., Asami S., Motohashi S., Yoshida Y., Chin M., Shichino H., Yoshida Y., Nemoto N., Kaneko M., Mugishima H., Suzuki T. 2003. Diagnostic significance and clinical applications of chimeric genes in Ewing's sarcoma. Biol. Pharm. Bull. 26, 585-588.
3. Mitelman F. 2000. Recurrent chromosome aberrations in cancer. Mutat. Res. 462, 247-253.
4. Ayton P.M., Cleary M.L. 2001. Molecular mechanisms of leukemogenesis mediated by MLL fusion proteins. Oncogene. 20, 5695-5707.
5. Kim J., Pelletier J. 1999. Molecular genetics of chromosome translocations involving EWS and related family members. Physiol. Genomics. 1, 127-138.
6. Rabbitts T.H. 1999. Perspective: Chromosomal translocations can affect genes controlling gene expression and differentiation-why are these functions targeted? J. Pathol. 187, 39-42.
7. Nikiforov Y.E. 2002. RET/PTC rearrangement in thyroid tumors. Endocrin. Pathol. 13, 3-16.
8. Bohlander S.K. 2000. Fusion genes in leukemia: An emerging network. Cytogenet. Cell Genet. 91, 52-56.
9. Strissel P.L., Strick R., Rowley J.D., Zeleznik-Le N.J. 1998. An in vivo topoisomerase II cleavage site and a DNase I hypersensitive site colocalize near exon 9 in the MLL breakpoint cluster region. Blood. 92, 3793-3803.
10. Rowley J.D. 1998. The critical role of chromosome translocations in human leukemias. Annu. Rev. Genet. 32, 495-519.
11. Nilson I., Reichel M., Ennas M.G., Greim R., Knorr C., Siegler G., Greil J., Fey G.H., Marschalek R. 1997. Exon/intron structure of the human AF-4 gene, a member of the AF-4/LAF- 4/FMR-2 gene family coding for a nuclear protein with structural alterations in acute leukaemia. Br. J. Haematol. 98, 157-169.
12. Strissel P.L., Strick R., Tomek R.J., Roe B.A., Rowley J.D., Zeleznik-Le N.J. 2000. DNA structural properties of AF9 are similar to MLL and could act as recombination hot spots resulting in MLL/AF9 translocations and leukemogenesis. Hum. Mol. Genet. 9, 1671-1679.
13. Okuda T., Nishimura M., Nakao M., Fujita Y. 2001. RUNX1/AML1: A central player in hematopoiesis. Int. J. Hematol. 74, 252-257.
14. Zhang Y., Strissel P., Strick R., Chen J., Nucifora G., Le Beau M.M., Larson R.A., Rowley J.D. 2002. Genomic DNA breakpoints in AML1/RUNX1 and ETO cluster with topoisomerase II DNA cleavage and DNase I hypersensitive sites in t(8;21) leukemia. Proc. Natl. Acad. Sci. USA. 99, 3070-3075.
15. Zucman-Rossi J., Legoix P., Victor J.M., Lopez B., Thomas G. 1998. Chromosome translocation based on illegitimate recombination in human tumors. Proc. Natl. Acad. Sci. USA. 95, 11786-11791.
16. Obata K., Hiraga H., Nojima T., Yoshida M.C., Abe S. 1999. Molecular characterization of the genomic breakpoint junction in a t(11;22) translocation in Ewing sarcoma. Genes, Chromosomes, Cancer. 25, 6-15.
17. Taub R., Kirsch I., Morton C., Lenoir G., Swan D., Tronick S., Aaronson S., Leder P. 1982. Translocation of the c-myc gene into the immunoglobulin heavy chain locus in human Burkitt lymphoma and murine plasmacytoma cells. Proc. Natl. Acad. Sci. USA. 79, 7837-7841.
18. Butler M.P., Iida S., Capello D., Rossi D., Rao P.H., Nallasivam P., Louie D.C., Chaganti S., Au T., Gascoyne R.D., Gaidano G., Chaganti R.S., Dalla-Favera R. 2002. Alternative translocation breakpoint cluster region 5′ to BCL-6 in B-cell non-Hodgkin's lymphoma. Cancer Res. 62, 4089-4094.
19. Chen W., Iida S., Louie D.C., Dalla-Favera R., Chaganti R.S. 1998. Heterologous promoters fused to BCL6 by chromosomal translocations affecting band 3q27 cause its deregulated expression during B-cell differentiation. Blood. 91, 603-607.
20. Welzel N., Le T., Marculescu R., Mitterbauer G., Chott A., Pott C., Kneba M., Du M.Q., Kusec R., Drach J., Raderer M., Mannhalter C., Lechner K., Nadel B., Jaeger U. 2001. Templated nucleotide addition and immunoglobulin JH-gene utilization in t(11;14) junctions: Implications for the mechanism of translocation and the origin of mantle cell lymphoma. Cancer Res. 61, 1629-1636.
21. Baens M., Steyls A., Dierlamm J., De Wolf-Peeters C., Marynen P. 2000. Structure of the MLT gene and molecular characterization of the genomic breakpoint junctions in the t(11;18)(q21;q21) of marginal zone B-cell lymphomas of MALT type. Genes, Chromosomes, Cancer. 29, 281-291.
22. Hosaka T., Kanoe H., Nakayama T., Murakami H., Yamamoto H., Nakamata T., Tsuboyama T., Oka M., Kasai M., Sasaki M.S., Nakamura T., Toguchida J. 2000. Translin binds to the sequences adjacent to the breakpoints of the TLS and CHOP genes in liposarcomas with translocation t(12;6). Oncogene. 19, 5821-5855.
23. Razin S.V. 1999. Chromosomal DNA loops may constitute basic units of the eukaryotic genome organization and evolution. Crit. Rev. Eukaryot. Gene Expr. 9, 279-283.
24. Sperry A.O., Blasquez V.C., Garrard W.T. 1989. Dysfunction of chromosomal loop attachment sites: Illegitimate recombination linked to matrix association regions and topoisomerase II. Proc. Natl. Acad. Sci. USA. 86, 5497-5501.
25. Berrios M., Osheroff N., Fisher P.A. 1985. In situ localization of DNA topoisomerase II, a major polypeptide component of the Drosophila nuclear matrix fraction. Proc. Natl. Acad. Sci. USA. 82, 4142-4146.
26. Charron M., Hancock R. 1991. Chromosome recombination and defective genome segregation induced in Chinese hamster cells by the topoisomerase II inhibitor VM-26. Chromosoma. 100, 97-102.
27. Asami Y., Jia D.W., Tatebayashi K., Yamagata K., Tanokura M., Ikeda H. 2002. Effect of the DNA topoisomerase II inhibitor VP-16 on illegitimate recombination in yeast chromosomes. Gene. 291, 251-257.
28. Felix C.A. 1998. Secondary leukemias induced by topoisomerase-targeted drugs. Biochim. Biophys. Acta. 1400, 233-255.
29. Elliott B., Jasin M. 2002. Double-strand breaks and translocations in cancer. Cell Mol. Life Sci. 59, 373-385.
30. Onno M., Nakamura T., Hillova J., Hill M. 1992. Rearrangement of the human tre oncogene by homologous recombination between Alu repeats of nucleotide sequences from two different chromosomes. Oncogene. 7, 2519-2523.
31. Taki T., Kano H., Taniwaki M., Sako M., Yanagisawa M., Hayashi Y. 1999. AF5q31, a newly identified AF4-related gene, is fused to MLL in infant acute lymphoblastic leukemia with ins(5;11)(q31;q13q23). Proc. Natl. Acad. Sci. USA. 96, 14535-14540.
32. Monaco C., Visconti R., Barone M.V., Pierantoni G.M., Berlingieri M.T., de Lorenzo C., Mineo A., Vecchio G., Fusco A., Santoro M. 2001. The RFG oligomerization domain mediates kinase activation and re-localization of the RET/PTC3 oncoprotein to the plasma membrane. Oncogene. 20, 599-608.
33. Nowell P.C. 1976. The clonal evolution of tumor cell populations. Science. 194, 23-28.
34. Marschalek R., Nilson I., Lochner K., Greim R., Siegler G., Greil J., Beck J.D., Fey G.H. 1997. The structure of the human ALL-1/MLL/HRX gene. Leuc. Lymphoma. 27, 417-428.
35. Iarovaia O.V., Bystritskiy A., Ravcheev D., Hancock R., Razin S.V. 2004. Visualization of individual DNA loops and a map of loop domains in the human dystrophin gene. Nucleic Acids Res. 32, 2079-2086.
36. Broeker P.L., Super H.G., Thirman M.J., Pomykala H., Yonebayashi Y., Tanabe S., Zeleznik-Le N., Rowley J.D. 1996. Distribution of 11q23 breakpoints within the MLL breakpoint cluster region in de novo acute leukemia and in treatment-related acute myeloid leukemia: Correlation with scaffold attachment regions and topoisomerase II consensus binding sites. Blood. 87, 1912-1922.
37. Kozubek S., Lukasova E., Jirsova P., Koutna I.I., Kozubek M., Ganova A., Bartova E., Falk M., Pasekova R. 2002. 3D Structure of the human genome: Order in randomness. Chromosoma. 111, 321-331.
38. Cremer M., von Hase J., Volm T., Brero A., Kreth G., Walter J., Fischer C., Solovei I., Cremer C., Cremer T. 2001. Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells. Chromosome Res. 9, 541-567.
39. Neves H., Ramos C., da Silva M.G., Parreira A., Parreira L. 1999. The nuclear topography of ABL, BCR, PML, and RARalpha genes: Evidence for gene proximity in specific phases of the cell cycle and stages of hematopoietic differentiation. Blood. 93, 1197-1207.
40. Kozubek S., Lukasova E., Mareckova A., Skalnikova M., Kozubek M., Bartova E., Kroha V., Krahulcova E., Slotova J. 1999. The topological organization of chromosomes 9 and 22 in cell nuclei has a determinative role in the induction of t(9.22) translocations and in the pathogenesis of t(9.22) leukemias. Chromosoma. 108, 426-435.
41. Parada L.A., McQueen P.G., Munson P.J., Misteli T. 2002. Conservation of relative chromosome positioning in normal and cancer cells. Curr. Biol. 12, 1692-1697.
42. Barrow J.D. 2001. Cosmology, life, and the anthropic principle. Ann. N.Y. Acad. Sci. 950, 139-153.
43. Kaessmann H., Zollner S., Nekrutenko A., Li W.H. 2002. Signatures of domain shuffling in the human genome. Genome Res. 12, 1642-1650.