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

Molecular and Cellular Biology

Volumn 16, Issue 1, 1996, Pages 302-308

  Iarovaia, Olga ^a,b   Hancock, Ronald ^c   Lagarkova, Maria ^b   Miassod, Raymond ^d   Razin, Sergey V ^a,b  

^a INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY   (Italy)

^b INSTITUTE OF GENE BIOLOGY   (Russian Federation)

^c LAVAL UNIVERSITY   (Canada)

^d LABORATOIRE DE BIOLOGIE CELLULAIRE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DROSOPHILA MELANOGASTER; MELANOGASTER;

DNA; DNA TOPOISOMERASE (ATP HYDROLYSING);

ANIMAL CELL; ARTICLE; BINDING SITE; CHROMOSOME SIZE; CHROMOSOME STRUCTURE; DNA STRUCTURE; DROSOPHILA MELANOGASTER; GENE LOCATION; GENE MAPPING; MARKER CHROMOSOME; NONHUMAN; PRIORITY JOURNAL; STRUCTURE ANALYSIS; X CHROMOSOME ABERRATION;

ANIMAL; BINDING SITES; CELL LINE; CHROMOSOME MAPPING; DNA; DNA TOPOISOMERASES, TYPE II; DNA, SUPERHELICAL; DROSOPHILA MELANOGASTER; NUCLEIC ACID CONFORMATION; SUPPORT, NON-U.S. GOV'T; X CHROMOSOME;

EID: 0029655715     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.16.1.302     Document Type: Article

References (45)

1. Berezney, R., and L. A. Buchholtz. 1981. Isolation and characterization of rat liver nuclear matrices containing high-molecular weight deoxyribonucleic acid. Biochemistry 20:4995-5002.
2. Berezney, R., and D. S. Coffey. 1974 Identification of a nuclear protein matrix Biochem. Biophys. Res. Commun 60:1410-1417.
3. Berezney, R., and D. S. Coffey. 1975. Nuclear protein matrix: association with newly synthesized DNA Science 189:291-293
4. Berrious, M., N. Osheroff, and P. Fisher. 1985. In situ localization of DNA topoisomerase II, a major polypeptide of Drosophila nuclear matrix. Proc. Natl. Acad. Sci. USA 82:4142-4146.
5. Brower, D. L., M. Wilcox, M. Piovant, R. J. Smith, and L. A. Reger. 1984. Related cell-surface antigens expressed with positional specificity in Drosophila imaginal discs Proc. Natl. Acad. Sci USA 81:7485-7489.
6. Brown, N. H., D. L. King, M. Wilcox, and C. Kafatos. 1989. Developmental regulated alternative splicing of Drosophila integrin PS2a transcripts. Cell 59:185-195
7. Brun, C., Q. Dang, and R. Miassod. 1990 Studies of an 800-kilobase DNA stretch of the Drosophila X chromosome: comparing of a subclass of scaffold-attached regions with sequences able to replicate autonomously in Saccharomyces cerevisiae. Mol. Cell. Biol. 10:5455-5463.
8. Chen, G. L., L. Yang, T. C. Rowe, B. D. Halligan, K. M. Tewey, and L. Liu. 1984. Nonintercalative antitumor drugs interfere with the breakage-reunion reaction of mammalian topoisomerase II J. Biol. Chem. 259:13560-13566.
9. Cockerill, P. N., and W. T. Garrard. 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, P. R., and I. A. Brazell. 1975 Supercoils in human DNA J. Cell Sci. 19:261-279.
11. Cook, P. R., and I. A. Brazell. 1976 Conformational constrains in human DNA. J Cell Sci. 22:287-302.
12. Cook, P. R., I. A. Brazell, and E. Jost. 1976. Characterization of nuclear structures containing superhelical DNA J Cell Sci. 22:303-324.
13. Earnshaw, W. C., B. Halligan, C. A. Cooke, M. M. S. Heck, and L. F. Liu. 1985. Topoisomerase II is a structural component of mitotic chromosome scaffolds. J. Cell Biol 100:1706-1715.
14. Farache, G., S. V. Razin, J. Rzeszowska-Wolny, J. Moreau, F. Recillas-Targa, and K. Scherrer. 1990. Mapping of structural and transcription-related matrix attachment sites in the α-globin gene domain of avian erythroblasts and erythrocytes. Mol Cell Biol 10:5349-5358.
15. Freud, J. N., W. Verges, P. Schedl, and B. P. Jarry. 1986. Molecular organization of the rudimentary gene of Drosophila melanogaster. J. Mol Biol. 189:25-36
16. Gasser, S. M., B. B. Amati, M. E. Cardenas, and J. F. Hofmann. 1989 Studies on scaffold attachment sites and their relation to genome function. Int Rev. Cytol 119:57-96
17. Georgiev, G. P., Y. S. Vassetzky, A. N. Luchnik, V. V. Chernokhvostov, and S.V. Razin. 1991. Nuclear skeleton, DNA domains and control of replication and transcription. Eur. J Biochem 200:613-624.
18. Getzenberg, R. H., K. J. Pienta, W. S. Ward, and D. S. Coffey. 1991. Nuclear structure and the three-dimensional organization of DNA J Cell. Biochem. 47:289-299.
19. Gromova, I. I., O. F. Nielsen, and S. V. Razin. 1995. 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. 270:18685-18690.
20. Gromova, I. I., B. Thompsen, and S. V. Razin. 1995. Different topoisomerase II antitumour 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 92:102-106.
21. Hancock, R. 1982. Topological organization of interphase DNA: the nuclear matrix and other skeletal structures. Biol. Cell 46:105-122
22. Hancock, R., and M. E. Hughes. 1982. Organization of DNA in the eukaryotic nucleus. Biol Cell 44:201-212.
23. Houde, M., M.-C. Tiverton, and F. Bregegere. 1989. Divergence of the nucleotide sequences encoding xanthine dehydrogenase in Calliphora vicina and Drosophila melanogaster. Gene 85:391-402.
24. Igo-Kemennes, T., and H. G. Zachau. 1977. Domains in chromatin structure. Cold Spring Harbor Symp. Quant. Biol. 42:109-118.
25. Izaurralde, E., J. Mirkovich, and U. K. Laemmli. 1988. Interaction of DNA with nuclear scaffolds in vitro. J. Mol. Biol 200:111-125
26. Jackson, D. A., and P. R. Cook. 1985 Transcription occurs at a nucleoskeleton. EMBO J. 4:919-925.
27. Jackson, D. A., and P. R. Cook. 1986 Replication occurs at a nucleoskeleton. EMBO J. 5:1403-1410.
28. Jackson, D. A., A. Dolle, G. Robertson, and P. R. Cook. 1992. The attachments of chromatin loops to the nucleoskeleton. Cell. Biol. Int. Rep. 16: 687-696.
29. Jackson, D. A., S. J. McCready, and P. R. Cook. 1981. RNA is synthesized at the nuclear cage. Nature (London) 292:552-555.
30. Jullien, N., et al. Submitted for publication.
31. Kirov, N., L. Djondjurov, and R. Tsanev. 1984. Nuclear matrix and transcriptional activity of the mouse α-globin gene. J. Mol. Biol. 180:603-614.
32. Laemmli, U. K., E. Kas, L. Poljak, and Y. Adachi. 1992 Scaffold-associated regions: cis-acting determinants of chromatin structural loops and functional domains. Curr. Opin. Genet. Dev. 2:275-285.
33. Lagarkova, M. A., O. V. Iarovaia, and S. V. Razin. 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. 270:20239-20241.
34. Leptin, M., R. Aebersold, and M. Wilcox. 1987. Drosophila position-specific antigenes resemble the vertebrate fibronectine-receptor family. EMBO J. 6: 1037-1043.
35. Marsden, M. P., and U. K. Laemmli. 1979. Metaphase chromosome structure: evidence for a radial loop model. Cell 17:849-858.
36. Miassod, R., et al. Unpublished data.
37. Mircovich, J., M. E. Mirault, and U. K. Laemmli. 1984. Organization of the higher-order chromatin loop: specific DNA attachment sites on nuclear scaffold. Cell 39:223-232.
38. Paulson, J. R., and U. K. Laemmli. 1977. The structure of histone-depleted metaphase chromosomes. Cell 12:815-828.
39. Razin, S. V. 1987. DNA interaction with the nuclear matrix and spatial organization of replication and transcription. BioEssays 6:19-23.
40. Razin, S. V., and I.I. Gromova. 1995. The channels model of nuclear matrix structure. BioEssays 17:443-450.
41. Razin, S. V., I.I. Gromova, and O. V. Iarovaia. 1995. Specificity and functional significance of DNA interaction with the nuclear matrix, new approaches to clarify the old questions. Int. Cytol. Rev. 1628:405-448
42. Razin, S. V., R. Hancock, O. Iarovaia, O. Westergaard, I. Gromova, and G. P. Georgiev. 1993. Structural-functional organization of chromosomal DNA domains. Cold Spring Harbor Symp. Quant. Biol. 58:25-35.
43. Razin, S. V., and Y. S. Vassetzky. 1992. Domain organization of the eukaryotic genome. Cell. Biol. Int. Rep. 16:697-708.
44. Sander, M., and T. S. Hsieh. 1985. Drosophila topoisomerase II double-strand DNA cleavage, analysis of DNA sequence homology at the cleavage site. Nucleic Acids Res 13:1057-1072.
45. Surdej, P., C. Got, R. Rosset, and R. Miassod. 1990. Supragenic loop organization: mapping in Drosophila embryos of scaffold-associated regions on a 800 kilobase continuum cloned from the 14B-15B first chromosome region. Nucleic Acids Res. 18:3713-3722.