DNA loop domains in a 1.4-Mb region around the human hprt gene mapped by cleavage mediated by nuclear matrix-associated topoisomerase II

Molecular and General Genetics

Volumn 260, Issue 5, 1998, Pages 410-416

  Fajkus, J ^a,b   Nicklas, J A ^c   Hancock, R ^a  

^a UNIVERSITÉ LAVAL   (Canada)

^b INSTITUTE OF BIOPHYSICS   (Czech Republic)

^c UNIVERSITY OF VERMONT   (United States)

Author keywords

DNA loop domains; Human hprt gene; Nuclear matrix; Topoisomerase II

Indexed keywords

DNA TOPOISOMERASE (ATP HYDROLYSING); HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE;

ARTICLE; CELL NUCLEUS MATRIX; CELL STRAIN K 562; DELETION MUTANT; DNA CLEAVAGE; DNA STRAND BREAKAGE; DNA STRUCTURE; GENE MAPPING; HUMAN; HUMAN CELL; LYMPHOCYTE; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS; RESTRICTION FRAGMENT;

CELL NUCLEUS; CHROMOSOME MAPPING; DNA; DNA TOPOISOMERASES, TYPE II; HUMANS; HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE; NUCLEIC ACID CONFORMATION; RECOMBINATION, GENETIC; RESTRICTION MAPPING; X CHROMOSOME;

EID: 0032413236     PISSN: 00268925     EISSN: None     Source Type: Journal    
DOI: 10.1007/s004380050911     Document Type: Article

References (44)

1. Beggs AH, Migeon BR (1989) Chromatin loop structure of the human X chromosome: relevance to X inactivation and CpG clusters. Mol Cell Biol 9:2322-2331
2. Benyajati C, Worcel A (1976) Isolation, characterisation, and structure of the folded interphase genome of Drosophila melanogaster. Cell 9:393-407
3. Berrios M, Osheroff N, Fisher P (1985.) In situ localisation of DNA topoisomerase II, a major polypeptide of the Drosophila nuclear matrix. Proc Natl Acad Sci USA 82:4142-4146
4. Blasquez VC, Sperry AO, Cockerill PN, Garrard WT (1989) Protein: DNA interactions at chromosomal loop attachment sites. Genome 31:503-509
5. Bode J, Maass K (1988) Chromatin domain surrounding the human interferon-β gene as defined by scaffold attached regions. Biochemistry 27:4706-4711
6. Bode J, Kohwi Y, Dickinson L, Joh T, Klehr D, Mielke C, Kohwi-Shigematsu T (1992) Biological significance of unwinding capability of nuclear matrix-associating DNA. Science 255:195-197
7. Bodley AL, Huang HC, Yu CA, Liu LF (1993) Integration of SV40 virus into cellular DNA occurs at or near topoisomerase II cleavage hot spots induced by VM-26. Mol Cell Biol 13:6190-6200
8. Broeker PLS, Super HG, Thirman MJ, Pomykala H, Yonebayashi V, Tanabe S, Zeleznikle N, Rowley JD (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
9. Buongiorno-Nardelli M, Gioacchino M, Carri MT, Marriley M (1982) A relationship between replicon size and supercoiled loop domains in the eukaryotic genome. Nature 298:100-102
10. Charron M, Hancock R (1991) Chromosome recombination and defective genome segregation induced in CHO cells by the lopoisomerase II inhibitor VM-26. Chromosoma 100:97-102
11. Chong SY, Taylor KA, Piper AA (1995) Intragenic matrix attachment and DNA-protein interactions in the human X-linked HPRT gene. Biochim Biophys Acta 1264:103-114
12. Cutting GR, Antonarakis SE, Youssoufian H, Kazazian HH (1988) Accuracy and limitations of pulsed field gel electrophoresis in sizing partial deletions of the factor VIII gene. Mol Biol Med 5:173-184
13. Felix CA, Lange BJ, Hosler MR, Fertala J, Bjornsti MA (1995) Chromosome band 11Q23 translocation breakpoints are DNA topoisomerase II cleavage sites. Cancer Res 55:4287-4292
14. Georgiev GP, Vassetzky YS, Luchnik AN, Chernovostok VV, Razin SV (1991) Nuclear skeleton, DNA domains, and control of replication and transcription. Eur J Biochem 200:613-624
15. Gromova II, Thomsen B, Razin SV (1995a) Different topoisomerase II antitumour drugs direct similar specific long-range fragmentation of an amplified c-myc gene region in living cells and in high salt-extracted nuclei. Proc Natl Acad Sci USA 92:102-106
16. Gromova II, Nielsen OF, Razin SV (1995b) Long-range fragmentation of the eukaryotic genome by exogenous and endogenous nucleuses proceeds in a specific fashion via preferential DNA cleavage at matrix attachment sites. J Biol Chem 270:18685-18690
17. Hancock R, Hughes M (1982) Organisation of DNA in the interphase nucleus. Biol Cell 46:105-122
18. Hanson RD, Ley T J (1992) A-T-rich scailbld attachment regions flank the hematopoietic serine protease genes clustered on chromosome 14q11.2. Blood 79:610-618
19. Hartwig M (1982) Organisation of mammalian chromosomal DNA: supercoiled and folded circular DNA subunits from interphase nuclei. Acta Biol Med Germ 37:421-432
20. Iarovaia OM, Lagarkova M, Razin SV (1995) The specificity of human lymphocyte nucleolar DNA long-range fragmentation by endogenous topoisomerase II and exogenous Bal 31 nuclease depends on cell proliferation status. Biochemistry 34:4133-4138
21. Ilarovaia OM, Hancock R, Lagarkova M, Miassod R, Razin SV (1996) Mapping of genomic DNA loop organisation in a 500-kb region of the Drosophila X chromosome using the topoisomerase II-mediated DNA loop excision protocol. Mol Cell Biol 16:302-308
22. Igo-Kemenes T, Zachau HG (1977) Domains in chromatin structure. Cold Spring Harbor Symp Quant Biol 42:109-118
23. Jackson DA, Dickinson P, Cook PR (1990) The size of chromatin loops in HeLa cells. EMBO J 9:567-571
24. Laemmli UK, Käs E, Poljak L, Adachi Y (1992) Scaffold-associated regions: civ-acting determinants of chromatin structural loops and functional domains. Curr Opin Genet Dev 2:275-285
25. Levy-Wilson B, Fortier C (1990) The limits of the DNase I-sensitive domain in the human apolipoprotein B gene coincide with the locations of chromosomal anchorage loops and define the 5' and 3' boundaries of the gene. J Biol Chem 264:21196-21204
26. Lippert MJ, Albertini RJ, Nicklas JA (1995a) Physical mapping of the human hprt chromosomal region Xq26. Mut Res 326:39-49
27. Lippert MJ, Nicklas JA, Hunter TC, Albertini RJ (1995b) Pulsed field analysis of hprt T-cell large deletions: telomeric region breakpoint spectrum. Mut Res 326:51-64
28. Little RD, Pilia G, Johnson S, D'Urso M, Schlessinger D (1992) Yeast artificial chromosomes spanning 8 megabases and 10-15 centimorgans of human cytogenetic band Xq26. Proc Natl Acad Sci USA 89:177-181
29. Marilley M, Gassend-Bonnet G (1989) Supercoiled loop organisation of genomic DNA: a close relationship between loop domains, expression units, and replicon organisation in rDNA from Xenopus laevis. Exp Cell Res 180:475-489
30. Micheli G, Luzzatto ARC, Carri MT, Decapoa A, Pelliccia F (1993) Chromosome length and DNA loop size during early embryonic development of Xenopus laevis. Chromosoma 102:478-483
31. Morris T, Thacker J (1993) Formation of large deletions by illegitimate recombination in the hprt gene of primary human fibroblasts. Proc Natl Acad Sci USA 90:1392-1396
32. Phi-Van L, Strätling WH (1988) The matrix attachment regions of the chicken lysozyme gene comap with the boundaries of the chromatin domain. EMBO J 7:655-664
33. Rainville IR, Albertini RJ., Nicklas JA (1995) Breakpoints and junctional regions of intragenic deletions in the hprt gene in human T-cells. Somatic Cell Mol Genet 21:309-326
34. Ralph RK, Hancock R (1985) Chromosomal DNA fragments from mouse cells exposed to an intercalating agent contain a 175 kDa terminal polypeptide. Can J Biochem Cell Biol 63:780-783
35. Razin SV, Petrov P, Hancock R (1991) Precise localisation of the α-globin gene cluster within one of the 20-300-kb 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 88:8515-8519
36. Razin SV, Hancock R, Iarovaia O, Westergaard O, Gromova I, Georgiev GP (1994) Structural-functional organisation of chromosomal DNA domains. Cold Spring Harbor Symp Quant Biol 58:25-35
37. Razin SV, Gromova I, Iarovaia O (1995) Specificity and functional significance of DNA interaction with the nuclear matrix: new-approaches to clarify old questions. Int Rev Cytol 162B:405-448
38. Roberge M, Gasser SM (1992) DNA loops: structural and functional properties of scaffold-attached regions. Mol Microbiol 6:419-423
39. Rowe TC, Wang JC, Liu LF (1986) In vivo localisation of DNA topoisomerase II cleavage sites on Drosophila heat shock chromatin. Mol Cell Biol 6:985-992
40. Sperry AO, Blasquez VC, Garrard WT (1989) Dysfunction of chromosomal loop attachment sites: illegitimate recombination linked to matrix attachment regions and topoisomerase II. Proc Natl Acad Sci USA 86:5497-5501
41. Sykes RC, Lin D, Hwang SJ, Framson PE, Chinault AC (1988) Yeast ARS function and nuclear matrix association coincide in a short sequence from the human hprt gene region. Mol Cell Genet 212:301-309
42. Udvardy A, Schedl P, Sander M, Hsieh T (1986) Topoisomerase II cleavage in chromatin. J Mol Biol 191:231-246
43. Yu YJ, Xu ZD, Hsie AW (1994) Adriamycin induces large deletions as a major type of mutation in CHO cells. Mut Res Lett 325:91-98
44. Wang JC (1996) DNA topoisomerases. Annu Rev Biochem 65:635-692