Biopolym. Cell. 1996; 12(3):67-76.
http://dx.doi.org/10.7124/bc.000430
The ordered disintegration of nuclear DNA as a specific genome reaction accompanying apoptosis, stress response and differentiation
1Solovyan V. T., 1Andreev I. O., 2Kolotova T. Yu., 3Pogrebnoy P. V., 3Tarnavsky D. V.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680
  2. Mechnikov Institute of Microbiology and Immunology AMS of Ukraine
    14, Pushkinska Str., Kharkiv, Ukraine, 61057
  3. R. E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, NAS of Ukraine
    45, Vasilkivska Str., Kyiv, Ukraine, 01022

Abstract

The treatment of agarose embedded nuclear or cellular preparations with protein denaturing agents resulted in ordered cleavage of intact nuclear DNA into high molecular weight fragments with the pattern of fragmentation being unityped for various eukaryotic representatives. We snowed that the set of DNA fragments represents the pre-existing DNA structural domains attributed to the higher levels of chromatin folding, and presented evidence allowing to interpret the nuclear DNA domain organization as a constituent component of topoisomerase III DNA complex with its ability to mediate the cleavage/religation reactions. We demonstrated that changes in the integrity of nuclear DNA, recognizable as an altered pattern of SDS-dependent cleavage of nuclear DNA into high molecular weight DNA fragments, took place at the early stage of apoptosis, upon number of stress challenges and in cells showing various proliferative status. The changes in the integrity of nuclear DNA affected by various influences were shown to be prompt and seem to be of transient nature. The results obtained allow to conclude that changes in the integrity of nuclear DNA revealed as an altered pattern of SDS-dependent high molecular weight DNA cleavage may present the specific genome reaction accompanying the physiological changes in the cells during apoptosis, stress response and differentiation.
Full text: (PDF, in English)

References

[1] 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.
[2] Pardoll DM, Vogelstein B, Coffey DS. A fixed site of DNA replication in eucaryotic cells. Cell. 1980;19(2):527-36.
[3] Gasser SM, Laemmli UK. A glimpse at chromosomal order. Trends Genet 1987;3:16–22. :
[4] Paulson JR, Laemmli UK. The structure of histone-depleted metaphase chromosomes. Cell. 1977;12(3):817-28.
[5] Adolph KW, Cheng SM, Laemmli UK. Role of nonhistone proteins in metaphase chromosome structure. Cell. 1977;12(3):805-16.
[6] Benyajati C, Worcel A. Isolation, characterization, and structure of the folded interphase genome of Drosophila melanogaster. Cell. 1976;9(3):393-407.
[7] Cook PR, Brazell IA. Conformational constraints in nuclear DNA. J Cell Sci. 1976;22(2):287-302.
[8] Adolph KW. Isolation and structural organization of human mitotic chromosomes. Chromosoma. 1980;76(1):23-33.
[9] Lebkowski JS, Laemmli UK. Non-histone proteins and long-range organization of HeLa interphase DNA. J Mol Biol. 1982;156(2):325-44.
[10] Ward WS, Partin AW, Coffey DS. DNA loop domains in mammalian spermatozoa. Chromosoma. 1989;98(3):153-9.
[11] Vogelstein B, Pardoll DM, Coffey DS. Supercoiled loops and eucaryotic DNA replicaton. Cell. 1980;22(1 Pt 1):79-85.
[12] Earnshaw WC, Heck MM. Localization of topoisomerase II in mitotic chromosomes. J Cell Biol. 1985;100(5):1716-25.
[13] 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.
[14] 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.
[15] Sperry AO, Blasquez VC, Garrard WT. Dysfunction of chromosomal loop attachment sites: illegitimate recombination linked to matrix association regions and topoisomerase II. Proc Natl Acad Sci U S A. 1989;86(14):5497-501.
[16] Adachi Y, K?s E, Laemmli UK. Preferential, cooperative binding of DNA topoisomerase II to scaffold-associated regions. EMBO J. 1989;8(13):3997-4006.
[17] Sippel A, EStief A, Hecht A. et al. The structural and functional domain organization of the chicken lysozyme gene locus. Nucl. acids and mol. biol.. Eds F Eckstein, D. M. J. Lilley. Berlin; Heidelberg: Springer, 1989. Vol. 3: 133-47.
[18] Marilley M, Gassend-Bonnet G. Supercoiled loop organization of genomic DNA: a close relationship between loop domains, expression units, and replicon organization in rDNA from Xenopus laevis. Exp Cell Res. 1989;180(2):475-89.
[19] Cook PR. The nucleoskeleton and the topology of transcription. Eur J Biochem. 1989;185(3):487-501.
[20] Garrard W. T. Chromosomal loop organization in eukaryotic genomes. Nucl. acids and mol biol.. Eds F. Eckstein, D M. J. Lilley. Berlin; Heidelberg: Springer, 1989. Vol.4-P. 163-75.
[21] Georgiev GP, Vassetzky YS Jr, Luchnik AN, Chernokhvostov VV, Razin SV. A. E. Braunstein Plenary Lecture. Nuclear skeleton, DNA domains and control of replication and transcription. Eur J Biochem. 1991;200(3):613-24.
[22] Roberge M, Gasser SM. DNA loops: structural and functional properties of scaffold-attached regions. Mol Microbiol. 1992;6(4):419-23.
[23] Weintraub H, Groudine M. Chromosomal subunits in active genes have an altered conformation. Science. 1976;193(4256):848-56.
[24] Weisbrod S. Active chromatin. Nature. 1982;297(5864):289-95.
[25] Loc PV, Str?tling WH. The matrix attachment regions of the chicken lysozyme gene co-map with the boundaries of the chromatin domain. EMBO J. 1988;7(3):655-64.
[26] Bode J, Maass K. Chromatin domain surrounding the human interferon-beta gene as defined by scaffold-attached regions. Biochemistry. 1988;27(13):4706-11.
[27] Jarman AP, Higgs DR. Nuclear scaffold attachment sites in the human globin gene complexes. EMBO J. 1988;7(11):3337-44.
[28] Levy-Wilson B, Fortier C. The limits of the DNase I-sensitive domain of 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. 1989;264(35):21196-204.
[29] Berezney R, Coffey DS. Nuclear protein matrix: association with newly synthesized DNA. Science. 1975;189(4199):291-3.
[30] McCready SJ, Godwin J, Mason DW, Brazell IA, Cook PR. DNA is replicated at the nuclear cage. J Cell Sci. 1980;46:365-86.
[31] Robinson SI, Small D, Idzerda R, McKnight GS, Vogelstein B. The association of transcriptionally active genes with the nuclear matrix of the chicken oviduct. Nucleic Acids Res. 1983;11(15):5113-30.
[32] Gerdes MG, Carter KC, Moen PT Jr, Lawrence JB. Dynamic changes in the higher-level chromatin organization of specific sequences revealed by in situ hybridization to nuclear halos. J Cell Biol. 1994;126(2):289-304.
[33] Berezney R. The nuclear matrix: a heuristic model for investigating genomic organization and function in the cell nucleus. J Cell Biochem. 1991;47(2):109-23.
[34] Zlatanova JS, van Holde KE. Chromatin loops and transcriptional regulation. Crit Rev Eukaryot Gene Expr. 1992;2(3):211-24.
[35] Bodnar JW. A domain model for eukaryotic DNA organization: a molecular basis for cell differentiation and chromosome evolution. J Theor Biol. 1988;132(4):479-507.
[36] Walker PR, Kokileva L, LeBlanc J, Sikorska M. Detection of the initial stages of DNA fragmentation in apoptosis. Biotechniques. 1993;15(6):1032-40.
[37] Brown DG, Sun XM, Cohen GM. Dexamethasone-induced apoptosis involves cleavage of DNA to large fragments prior to internucleosomal fragmentation. J Biol Chem. 1993;268(5):3037-9.
[38] Oberhammer F, Wilson JW, Dive C, Morris ID, Hickman JA, Wakeling AE, Walker PR, Sikorska M. Apoptotic death in epithelial cells: cleavage of DNA to 300 and/or 50 kb fragments prior to or in the absence of internucleosomal fragmentation. EMBO J. 1993;12(9):3679-84.
[39] Cohen GM, Sun XM, Fearnhead H, MacFarlane M, Brown DG, Snowden RT, Dinsdale D. Formation of large molecular weight fragments of DNA is a key committed step of apoptosis in thymocytes. J Immunol. 1994;153(2):507-16.
[40] Solov'ian VT, Andreev IO, Kunakh VA. Fractionation of eukaryotic DNA in a pulsed electrical field. II. Discrete DNA fragments and level of structural organization of chromatin. Mol Biol (Mosk). 1991;25(6):1483-91.
[41] Laemmli UK, Cheng SM, Adolph KW, Paulson JR, Brown JA, Baumbach WR. Metaphase chromosome structure: the role of nonhistone proteins. Cold Spring Harb Symp Quant Biol. 1978;42 Pt 1:351-60.
[42] Filipski J, Leblanc J, Youdale T, Sikorska M, Walker PR. Periodicity of DNA folding in higher order chromatin structures. EMBO J. 1990;9(4):1319-27.
[43] Razin SV, Petrov P, Hancock R. 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 U S A. 1991;88(19):8515-9.
[44] Targa FR, Razin SV, de Moura Gallo CV, Scherrer K. Excision close to matrix attachment regions of the entire chicken alpha-globin gene domain by nuclease S1 and characterization of the framing structures. Proc Natl Acad Sci U S A. 1994;91(10):4422-6.
[45] Solov'yan VT, Andreyev IO, Kunakh VA. The functional organization of plant nuclear DNA. I. Evidence for a nuclear topoisomerae II DNA complex. Mol Biol (Mosk). 1993; 27(6):1245-51.
[46] Osheroff N. Biochemical basis for the interactions of type I and type II topoisomerases with DNA. Pharmacol Ther. 1989;41(1-2):223-41.
[47] Liu LF. DNA topoisomerase poisons as antitumor drugs. Annu Rev Biochem. 1989;58:351-75.
[48] Nelson EM, Tewey KM, Liu LF. Mechanism of antitumor drug action: poisoning of mammalian DNA topoisomerase II on DNA by 4'-(9-acridinylamino)-methanesulfon-m-anisidide. Proc Natl Acad Sci U S A. 1984;81(5):1361-5.
[49] Smith HC, Berezney R. Nuclear matrix-bound deoxyribonucleic acid synthesis: an in vitro system. Biochemistry. 1982;21(26):6751-61.
[50] Heller C, Pohl FM. A systematic study of field inversion gel electrophoresis. Nucleic Acids Res. 1989;17(15):5989-6003.
[51] Solov'yan VT, Andreev IO. The physiological significance of nuclear DNA structural domain disintegration: evidence for non-random DNA domain cleavage. Biopolym Cell. 1995; 11(5):51-5.