An unusual extended DNA loop attachment region is located in the human dystrophin gene

Journal of Cellular Physiology

Volumn 209, Issue 2, 2006, Pages 515-521

  Iarovaia, Olga V ^a   Borounova, Victoria ^a,b   Vassetzky, Yegor S ^b,c   Razin, Sergey V ^a,c  

^a INSTITUTE OF GENE BIOLOGY   (Russian Federation)

^b CNRS   (France)

^c INSTITUT GUSTAVE ROUSSY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA TOPOISOMERASE (ATP HYDROLYSING); DYSTROPHIN;

ARTICLE; BIOCHEMISTRY; CELL NUCLEUS MATRIX; CHROMOSOMAL LOCALIZATION; CONTROLLED STUDY; DNA CLEAVAGE; DNA DETERMINATION; DNA LOOP; DNA RECOMBINATION; DNA REPLICATION ORIGIN; DNA SEQUENCE; DNA STRUCTURE; DP427M GENE; DYSTROPHIN GENE; EXON; GENE; GENE LOCATION; GENE MAPPING; HUMAN; HUMAN CELL; INTERACTIONS WITH DNA; INTRON; LOOP ANCHORAGE REGION; MICROSCOPY; MOLECULAR MODEL; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RECOMBINATION HOT SPOT;

CHROMOSOME MAPPING; DNA; DNA TOPOISOMERASES, TYPE II; DYSTROPHIN; GENOME, HUMAN; HUMANS; MATRIX ATTACHMENT REGIONS; NUCLEAR MATRIX; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TUMOR CELLS, CULTURED;

EID: 33749259810     PISSN: 00219541     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcp.20759     Document Type: Article

References (43)

1. Aelen JM, Opstelten RJ, Wanka F. 1983. Organization of DNA replication in Physarum polycephalum. Attachment of origins of replicons and replication forks to the nuclear matrix. Nucleic Acids Res 11(4):1181-1195.
2. Aplan PD, Chervinsky DS, Stanulla M, Burhans WC. 1996. Site-specific DNA cleavage within the MLL breakpoint cluster region induced by topoisomerase II inhibitors. Blood 87(7):2649-2658.
3. Balajee AS, Dominguez I, Bohr VA, Natarajan AT. 1996. Immunofluorescent analysis of the organization of telomeric DNA sequences and their involvement in chromosomal aberrations in hamster cells. Mutat Res 372(2):163-172.
4. Berrios M, Osheroff N, Fisher PA. 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.
5. Blonden LA, Grootscholten PM, den Dunnen JT, Bakker E, Abbs S, Bobrow M, Boehm C, van Broeckhoven C, Baumbach L, Chamberlain J, et al. 1991. 242 breakpoints in the 200-kb deletion-prone P20 region of the DMD gene are widely spread. Genomics 10(3):631-639.
6. Bode J, Benham C, Ernst E, Knopp A, Marschalek R, Strick R, Strissel P. 2000. Fatal connections: When DNA ends meet on the nuclear matrix. J Cell Biochem Suppl 35:3-22.
7. Boulikas T. 1995. Chromatin domains and prediction of MAR sequences. Int Rev Cytol 162A:279-388.
8. Buongiorno-Nardelli M, Micheli G, Carri MT, Marilley M. 1982. A relationship between replicon size and supercoiled loop domains in the eukaryotic genome. Nature 298(5869):100-102.
9. Cockerill PN, Garrard WT. 1986. Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites. Cell 44:273-282.
10. Cook PR, Brazell IA. 1976. Conformational constraints in nuclear DNA. J Cell Sci 22(2):287-302.
11. Den Dunnen JT, Grootscholten PM, Dauwerse JG, Walker AP, Monaco AP, Butler R, Anand R, Coffey AJ, Bentley DR, Steensma HY, et al. 1992. Reconstruction of the 2.4 Mb human DMD-gene by homologous YAC recombination. Hum Mol Genet 1(1):19-28.
12. Earnshaw WC, Halligan B, Cooke CA, Heck M, Liu LF. 1985. Topoisomerase II is a structural component of mitotic chromosome scaffolds. J Cell Biol 100(5):1706-1715.
13. Fajkus J, Nicklas JA, Hancock R. 1998. DNA loop domains in a 1.4-Mb region around the human hprt gene mapped by cleavage mediated by nuclear matrix-associated topoisomerase II. Mol Gen Genet 260(5):410-416.
14. Gerdes MG, Carter KC, Moen PT, Jr., Lawrence JB. 1994. Dynamic changes in the higher-level chromatin organization of specific sequences revealed by in situ hybridization to nuclear halos. J Cell Biol 126(2):289-304.
15. Gillard EF, Chamberlain JS, Murphy EG, Duff CL, Smith B, Burghes AH, Thompson MW, Sutherland J, Oss I, Bodrug SE, et al. 1989. Molecular and phenotypic analysis of patients with deletions within the deletion-rich region of the Duchenne muscular dystrophy (DMD) gene. Am J Hum Genet 45(4):507-520.
16. Gromova II, Nielsen OF, Razin SV. 1995a. Long-range fragmentation of the eukaryotic genome by exogenous and endogenous nucleases proceeds in a specific fashion via preferential DNA cleavage at matrix attachment sites. J Biol Chem 270(31):18685-18690.
17. Gromova II, Thomsen B, Razin SV. 1995b. Different topoisomerase II antitumor drugs direct similar specific long-range fragmentation of an amplified c-MYC gene locus in living cells and in high-salt-extracted nuclei. Proc Natl Acad Sci USA 92(1):102-106.
18. Iarovaia O, Hancock R, Lagarkova M, Miassod R, Razin SV. 1996. Mapping of genomic DNA loop organization in a 500-kilobase region of the Drosophila X chromosome by the topoisomerase II-mediated DNA loop excision protocol. Mol Cell Biol 16(1):302-308.
19. Iarovaia OV, Bystritskiy A, Ravcheev D, Hancock R, Razin SV. 2004a. Visualization of individual DNA loops and a map of loop domains in the human dystrophin gene. Nucleic Acids Res 32(7):2079-2086.
20. Iarovaia OV, Shkumatov P, Razin SV. 2004b. Breakpoint cluster regions of the AML-1 and ETO genes contain MAR elements and are preferentially associated with the nuclear matrix in proliferating HEL cells. J Cell Sci 117(Pt 19):4583-4590.
21. Ioudinkova E, Petrov A, Razin SV, Vassetzky YS. 2005. Mapping long-range chromatin organization within the chicken alpha-globin gene domain using oligonucleotide DNA arrays. Genomics 85(1):143-151.
22. Jackson DA, Dickinson P, Cook PR. 1990. The size of chromatin loops in HeLa cells. EMBO J 9(2):567-571.
23. Kantidze OL, Iarovaia OV, Razin SV. 2006. Assembly of nuclear matrix-bound protein complexes involved in non-homologous end joining is induced by inhibition of DNA topoisomerase II. J Cell Physiol 207(3):660-667.
24. Lagarkova MA, Iarovaia OV, Razin SV. 1995. Large-scale fragmentation of mammalian DNA in the course of apoptosis proceeds via excision of chromosomal DNA loops and their oligomers. J Biol Chem 270(35):20239-20241.
25. Lemaitre JM, Danis E, Pasero P, Vassetzky Y, Mechali M. 2005. Mitotic remodeling of the replicon and chromosome structure. Cell 123(5):787-801.
26. Mirkovitch J, Mirault ME, Laemmli UK. 1984. Organization of the higher-order chromatin loop: Specific DNA attachment sites on nuclear scaffold. Cell 39(1):223-232.
27. Muntoni F, Torelli S, Ferlini A. 2003. Dystrophin and mutations: One gene, several proteins, multiple phenotypes. Lancet Neurol 2(12):731-740.
28. Paulson JR, Laemmli UK. 1977. The structure of histone-depleted metaphase chromosomes. Cell 12(3):817-825.
29. Petrov A, Pirozhkova I, Laoudj D, Carnac G, Lipinski M, Vassetzky YS. 2006. Chromatin loop domain organization within the 4q35 locus in facioscapulo-humeral dystrophy patients versus normal human myoblasts. Proc Natl Acad Sci USA 103(18):6982-6987.
30. Razin SV. 1999. Chromosomal DNA loops may constitute basic units of the eukaryotic genome organization and evolution. Crit Rev Eukaryot Gene Expr 9(3-4):279-283.
31. Razin SV, Gromova II. 1995. The channels model of nuclear matrix structure. Bioessays 17(5):443-450.
32. Razin SV, Mantieva VL, Georgiev GP. 1979. The similarity of DNA sequences remaining bound to scaffold upon nuclease treatment of interphase nuclei and metaphase chromosomes. Nucleic Acids Res 7(6):1713-1735.
33. Razin SV, Petrov P, Hancock R. 1991. Precise localization of the alpha-globin gene cluster within one of the 20- to 300-kilobase DNA fragments released by cleavage of chicken chromosomal DNA at topoisomerase II sites in vivo: Evidence that the fragments are DNA loops or domains. Proc Natl Acad Sci USA 88(19):8515-8519.
34. Sperry AO, Blasquez VC, Garrard WT. 1989. Dysfunction of chromosomal loop attachment sites: Illegitimate recombination linked to matrix association regions and topoisomerase II. Proc Natl Acad Sci USA 86(14):5497-5501.
35. Stanulla M, Wang J, Chervinsky DS, Aplan PD. 1997a. Topoisomerase II inhibitors induce DNA double-strand breaks at a specific site within the AML1 locus. Leukemia 11(4):490-496.
36. Stanulla M, Wang J, Chervinsky DS, Thandla S, Aplan PD. 1997b. DNA cleavage within the MLL breakpoint cluster region is a specific event which occurs as part of higher-order chromatin fragmentation during the initial stages of apoptosis. Mol Cell Biol 17(7):4070-4079.
37. Svetlova EY, Razin SV, Debatisse M. 2001. Mammalian recombination hot spot in a DNA loop anchorage region: A model for the study of common fragile sites. J Cell Biochem 81(S36):170-178.
38. Umanskaya ON, Lebedeva SS, Gavrilov AA, Bystritskiy AA, Razin SV. 2006. Inhibition of DNA topoisomerase II may trigger illegitimate recombination in living cells: Experiments with a model system. J Cell Biochem Epub May 4, 2006.
39. Vassetzky Y, Hair A, Mechali M. 2000a. Rearrangement of chromatin domains during development in Xenopus. Genes Dev 14(12):1541-1552.
40. Vassetzky Y, Lemaitre JM, Mechali M. 2000b. Specification of chromatin domains and regulation of replication and transcription during development. Crit Rev Eukaryot Gene Expr 10(1):31-38.
41. Verbovaia LV, Razin SV. 1997. Mapping of replication origins and termination sites in the Duchenne muscular dystrophy gene. Genomics 45(1):24-30.
42. Vogelstein B, Pardoll DM, Coffey DS. 1980. Supercoiled loops and eucaryotic DNA replication. Cell 22(79):79-85.
43. Wapenaar MC, Kievits T, Hart KA, Abbs S, Blonden LA, den Dunnen JT, Grootscholten PM, Bakker E, Verellen-Dumoulin C, Bobrow M, et al. 1988. A deletion hot spot in the Duchenne muscular dystrophy gene. Genomics 2(2):101-108.