Biopolym. Cell. 1990; 6(6):63-68.
Mapping DNA attachment sites on nuclear frame by graphic representation of long DNA sequences
1Schmatchenko V. V., 1Berezhnev A. B.
  1. Institute of Biochemistry and Physiology of Microorganisms, Academy of Sciences of the USSR
    Pushchino, Moscow Region, USSR

Abstract

Characteristic (S-form) curves corresponding to nuclear matrix association regions have been revealed by graphically represented DNA sequences. The curves reflect AT and GC distribution along the sequence length. The method is applicable for mapping DNA attachment sites on nuclear frame. Functionally identical nonhomologous DNA regions in long sequences can be detected which is impossible using other computer-assisted methods of nucleotide sequence analysis.

References

[1] Hamori E, Ruskin J. H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences. J Biol Chem. 1983;258(2):1318-27.
[2] Ikemura T, Aota S. Global variation in G+C content along vertebrate genome DNA. Possible correlation with chromosome band structures. J Mol Biol. 1988;203(1):1-13.
[3] Benyajati C, Worcel A. Isolation, characterization, and structure of the folded interphase genome of Drosophila melanogaster. Cell. 1976;9(3):393-407.
[4] Paulson JR, Laemmli UK. The structure of histone-depleted metaphase chromosomes. Cell. 1977;12(3):817-28.
[5] Vogelstein B, Pardoll DM, Coffey DS. Supercoiled loops and eucaryotic DNA replicaton. Cell. 1980;22(1 Pt 1):79-85.
[6] Georgiev GP, Nedospasov SA, Bakayev VV. Supranucleosomal levels of chromatin organization. The Cell Nucleus. 1978; 6(1):3-34
[7] Mirkovitch J, Mirault ME, Laemmli UK. Organization of the higher-order chromatin loop: specific DNA attachment sites on nuclear scaffold. Cell. 1984;39(1):223-32.
[8] Cockerill PN, Garrard WT. Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites. Cell. 1986;44(2):273-82.
[9] Gasser SM, Laemmli UK. Cohabitation of scaffold binding regions with upstream/enhancer elements of three developmentally regulated genes of D. melanogaster. Cell. 1986;46(4):521-30.
[10] Dijkwel PA, Hamlin JL. Matrix attachment regions are positioned near replication initiation sites, genes, and an interamplicon junction in the amplified dihydrofolate reductase domain of Chinese hamster ovary cells. Mol Cell Biol. 1988;8(12):5398-409.
[11] Hamori E, Varga G. DNA sequence (H) curves of the human immunodeficiency virus 1 and some related viral genomes. DNA. 1988;7(5):371-8.
[12] Cockerill PN, Yuen MH, Garrard WT. The enhancer of the immunoglobulin heavy chain locus is flanked by presumptive chromosomal loop anchorage elements. J Biol Chem. 1987;262(11):5394-7.
[13] K?s E, Chasin LA. Anchorage of the Chinese hamster dihydrofolate reductase gene to the nuclear scaffold occurs in an intragenic region. J Mol Biol. 1987;198(4):677-92.
[14] Greenstein RJ. Constitutive attachment of murine erythroleukemia cell histone-depleted DNA loops to nuclear scaffolding is found in the beta-major but not the alpha 1-globin gene. DNA. 1988;7(9):601-7.
[15] Berrios M, Osheroff N, Fisher PA. In situ localization of DNA topoisomerase II, a major polypeptide component of the Drosophila nuclear matrix fraction. Proc Natl Acad Sci U S A. 1985;82(12):4142-6.
[16] Gasser SM, Laroche T, Falquet J, Boy de la Tour E, Laemmli UK. Metaphase chromosome structure. Involvement of topoisomerase II. J Mol Biol. 1986;188(4):613-29.
[17] Max EE, Maizel JV Jr, Leder P. The nucleotide sequence of a 5.5-kilobase DNA segment containing the mouse kappa immunoglobulin J and C region genes. J Biol Chem. 1981;256(10):5116-20.
[18] Emorine L, Max EE. Structural analysis of a rabbit immunoglobulin kappa 2 J-C locus reveals multiple deletions. Nucleic Acids Res. 1983;11(24):8877-90.
[19] Sander M, Hsieh T. Double strand DNA cleavage by type II DNA topoisomerase from Drosophila melanogaster. J Biol Chem. 1983;258(13):8421-8.