Biopolym. Cell. 1997; 13(4):314-322.
http://dx.doi.org/10.7124/bc.000491
Genome and Its Regulation
SDS-dependent cleavage of nuclear DNA into high molecular weight DNA fragments: a signal to the engagement of apoptosis?
1Solov'yan V. T.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

In this paper we employed an extraction of the cells with high concentration of sodium chloride (a procedure commonly used for preparation of histone-depleted nuclei) to investigate the genesis of nuclear DNA degradation during apoptosis. We demonstrated that apoptosis in primary culture of murine thymocytes and in continuously growing Swiss 3T3 fibroblasts is associated with progressive disintegration of nuclear DNA into high molecular weight (HMW) DNA fragments of about 50–150 kb followed by the development of oligonucleosomai DNA ladder. In apoptotic cells both HMW DNA cleavage and internucleosomal DNA fragmentation can be detected cither by cell treatment with ionic detergents (SDS) or by extraction with high concentration of sodium chloride. However, at the early stage of apoptosis only SOS-detected HMW-DNA cleavage can be observed which precedes the sodium-chloride-detected nuclear DNA degradation. SDS-detected but not sodium-chloride-detected formation of HMW-DNA fragments occurs in apoptotic cells as early as before detachment. It may be observed also in nonapoptotic cells after they reach t/ic confluent state and is reversible. On the basis of obtained results it is possible to suggest thai SDS-detected HMW-DNA cleavage represents a physiological reaction of alive cells that accompanies an early commitment step of apoptosis.
Full text: (PDF, in English)

References

[1] Ellis RE, Yuan JY, Horvitz HR. Mechanisms and functions of cell death. Annu Rev Cell Biol. 1991;7:663-98. Review.
[2] Kerr JF, Wyllie AH, Currie AR. Apoptosis: a basic biological phenomenon with wide-ranging implications in tissue kinetics. Br J Cancer. 1972;26(4):239-57. Review.
[3] Wyllie AH, Kerr JF, Currie AR. Cell death: the significance of apoptosis. Int Rev Cytol. 1980;68:251-306. Review.
[4] McConkey DJ, Orrenius S, Jondal M. Cellular signalling in programmed cell death (apoptosis). Immunol Today. 1990;11(4):120-1. Review.
[5] Barry MA, Eastman A. Endonuclease activation during apoptosis: the role of cytosolic Ca2+ and pH. Biochem Biophys Res Commun. 1992;186(2):782-9.
[6] Caron-Leslie LM, Schwartzman RA, Gaido ML, Compton MM, Cidlowski JA. Identification and characterization of glucocorticoid-regulated nuclease(s) in lymphoid cells undergoing apoptosis. J Steroid Biochem Mol Biol. 1991;40(4-6):661-71.
[7] Arends MJ, Wyllie AH. Apoptosis: mechanisms and roles in pathology. Int Rev Exp Pathol. 1991;32:223-54. Review.
[8] Das SK, Berger NA. Alterations in deoxynucleoside triphosphate metabolism in DNA damaged cells: identification and consequences of poly(ADP-ribose) polymerase dependent and independent processes. Biochem Biophys Res Commun. 1986;137(3):1153-8.
[9] Berger NA, Berger SJ, Sudar DC, Distelhorst CW. Role of nicotinamide adenine dinucleotide and adenosine triphosphate in glucocorticoid-induced cytotoxicity in susceptible lymphoid cells. J Clin Invest. 1987;79(6):1558-63.
[10] Denisenko MF, Soldatenkov VA, Belovskaya LN, Filippovich IV. Is the NAD-poly (ADP-ribose) polymerase system the trigger in radiation-induced death of mouse thymocytes? Int J Radiat Biol. 1989;56(3):277-85.
[11] Patel T, Gores GJ, Kaufmann SH. The role of proteases during apoptosis. FASEB J. 1996;10(5):587-97. Review.
[12] Takahashi A, Earnshaw WC. ICE-related proteases in apoptosis. Curr Opin Genet Dev. 1996;6(1):50-5. .
[13] Kaufmann SH, Desnoyers S, Ottaviano Y, Davidson NE, Poirier GG. Specific proteolytic cleavage of poly(ADP-ribose) polymerase: an early marker of chemotherapy-induced apoptosis. Cancer Res. 1993;53(17):3976-85.
[14] Lazebnik YA, Cole S, Cooke CA, Nelson WG, Earnshaw WC. Nuclear events of apoptosis in vitro in cell-free mitotic extracts: a model system for analysis of the active phase of apoptosis. J Cell Biol. 1993;123(1):7-22.
[15] Zweyer M, Bareggi R, Grill V, Soranzo MR, Marugg RA, Riederer BM, Narducci P, Martelli AM. Behavior of nuclear matrix proteins during camptothecin-induced apoptosis in HL-60 human leukemia cells. Exp Cell Res. 1995;221(1):27-40.
[16] Weaver VM, Carson CE, Walker PR, Chaly N, Lach B, Raymond Y, Brown DL, Sikorska M. Degradation of nuclear matrix and DNA cleavage in apoptotic thymocytes. J Cell Sci. 1996;109 ( Pt 1):45-56.
[17] Lazebnik YA, Takahashi A, Moir RD, Goldman RD, Poirier GG, Kaufmann SH, Earnshaw WC. Studies of the lamin proteinase reveal multiple parallel biochemical pathways during apoptotic execution. Proc Natl Acad Sci U S A. 1995;92(20):9042-6.
[18] Hara S, Halicka HD, Bruno S, Gong J, Traganos F, Darzynkiewicz Z. Effect of protease inhibitors on early events of apoptosis. Exp Cell Res. 1996;223(2):372-84.
[19] Oberhammer F, Fritsch G, Schmied M, Pavelka M, Printz D, Purchio T, Lassmann H, Schulte-Hermann R. Condensation of the chromatin at the membrane of an apoptotic nucleus is not associated with activation of an endonuclease. J Cell Sci. 1993;104 ( Pt 2):317-26.
[20] 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.
[21] Walker PR, Kokileva L, LeBlanc J, Sikorska M. Detection of the initial stages of DNA fragmentation in apoptosis. Biotechniques. 1993;15(6):1032-40.
[22] 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.
[23] 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.
[24] Beere HM, Chresta CM, Alejo-Herberg A, Skladanowski A, Dive C, Larsen AK, Hickman JA. Investigation of the mechanism of higher order chromatin fragmentation observed in drug-induced apoptosis. Mol Pharmacol. 1995;47(5):986-96.
[25] Cohen GM, Sun XM, Snowden RT, Dinsdale D, Skilleter DN. Key morphological features of apoptosis may occur in the absence of internucleosomal DNA fragmentation. Biochem J. 1992;286 ( Pt 2):331-4.
[26] Schulze-Osthoff K, Walczak H, Dr?ge W, Krammer PH. Cell nucleus and DNA fragmentation are not required for apoptosis. J Cell Biol. 1994;127(1):15-20.
[27] Jacobson MD, Burne JF, Raff MC. Programmed cell death and Bcl-2 protection in the absence of a nucleus. EMBO J. 1994;13(8):1899-910.
[28] Berezney R, Coffey DS. Identification of a nuclear protein matrix. Biochem Biophys Res Commun. 1974;60(4):1410-7.
[29] Benyajati C, Worcel A. Isolation, characterization, and structure of the folded interphase genome of Drosophila melanogaster. Cell. 1976;9(3):393-407.
[30] Cook PR, Brazell IA. Conformational constraints in nuclear DNA. J Cell Sci. 1976;22(2):287-302.
[31] Adolph KW, Cheng SM, Laemmli UK. Role of nonhistone proteins in metaphase chromosome structure. Cell. 1977;12(3):805-16.
[32] 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.
[33] Pardoll DM, Vogelstein B, Coffey DS. A fixed site of DNA replication in eucaryotic cells. Cell. 1980;19(2):527-36.
[34] 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.
[35] Earnshaw WC, Heck MM. Localization of topoisomerase II in mitotic chromosomes. J Cell Biol. 1985;100(5):1716-25.
[36] 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.
[37] 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.
[38] 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.
[39] 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.
[40] 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.
[41] Gasser SM, Laemmli UK. A glimpse at chromosomal order. Trends Genet. 1987;3:16–22.
[42] Poljak L, K?s E. Resolving the role of topoisomerase II in chromatin structure and function. Trends Cell Biol. 1995;5(9):348-54.
[43] Vosberg HP. DNA topoisomerases: enzymes that control DNA conformation. Curr Top Microbiol Immunol. 1985;114:19-102.
[44] Wang JC. DNA topoisomerases. Annu Rev Biochem. 1985;54:665-97. Review.
[45] Osheroff N. Biochemical basis for the interactions of type I and type II topoisomerases with DNA. Pharmacol Ther. 1989;41(1-2):223-41. Review.
[46] Liu LF. DNA topoisomerase poisons as antitumor drugs. Annu Rev Biochem. 1989;58:351-75. Review.
[47] Heller C, Pohl FM. A systematic study of field inversion gel electrophoresis. Nucleic Acids Res. 1989;17(15):5989-6003.
[48] Kaufmann SH. Induction of endonucleolytic DNA cleavage in human acute myelogenous leukemia cells by etoposide, camptothecin, and other cytotoxic anticancer drugs: a cautionary note. Cancer Res. 1989;49(21):5870-8.
[49] Solovyan VT, Andreev IO, Kolotova TYu, Pogrebnoy PV, Tarnavsky DV. The ordered disintegration of nuclear DNA as a specific genome reaction accompanying apoptosis, stress response and differentiation. Biopolym Cell. 1996; 12(3):67-76.
[50] Ucker DS. Death by suicide: one way to go in mammalian cellular development? New Biol. 1991;3(2):103-9. Review.
[51] Sen S, D'Incalci M. Apoptosis. Biochemical events and relevance to cancer chemotherapy. FEBS Lett. 1992;307(1):122-7. Review.
[52] 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. Russian.
[53] 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.
[54] Razin SV, Hancock R, Iarovaia O, Westergaard O, Gromova I, Georgiev GP. Structural-functional organization of chromosomal DNA domains. Cold Spring Harb Symp Quant Biol. 1993;58:25-35.
[55] Solovyan VT, Andreev IO, Kunakh VA. Functional organization of plant nuclear DNA. I. Evidence for a DNA- Topoisomerase II complex. Mol Biol. (Mosk). 1993; 27: 770-4.
[56] Solovyan VT, Andreyev IO. Structural domains of plant nuclear DNA as a constitutive component of the topoisomerase II/DNA complex. Acta Biochim Pol. 1995;42(2):201-4.
[57] Lichtenstein AV, Zaboikin MM, Sjakste NI, Alechina RP. Differential dissociation of chromatin digests: a novel approach revealing a hierarchy of DNA-protein interactions within chromatin domains. J Cell Sci. 1991;99 ( Pt 3):503-13.
[58] Hsiang YH, Liu LF. Evidence for the reversibility of cellular DNA lesion induced by mammalian topoisomerase II poisons. J Biol Chem. 1989;264(17):9713-5.