Пространственная организация ДНК в ядре и индуцированные ДНК-топоизомеразой II хромосомные перестройки тема диссертации и автореферата по ВАК РФ 03.00.03, кандидат биологических наук Кантидзе, Омар Леванович

• Кантидзе, Омар Леванович
• кандидат биологических наук
• 2007

Оглавление диссертации кандидат биологических наук Кантидзе, Омар Леванович

СПИСОК СОКРАЩЕНИЙ.

Введение.

1. Обзор литературы.

1.1. Пространственная организация ДНК в ядре.

1.1.1. Уровни компактизации ДНК.

1.1.2. Доменная структура генома.

1.1.2.1. Ядерный матрикс.

1.1.2.2. Прикрепленная к ядерному матриксу ДНК.

1.1.2.3. Функции ДНК ядерного матрикса.

1.1.3. Хромосомные территории.

1.2. Незаконная рекомбинация и хромосомные перестройки.

1.2.1. Двухчепочечные разрывы ДНК (ДЦР) и их репарация.

1.2.2. Кластеризация точек разрыва при транслокациях, ассоциированных с лейкозами.

1.2.3. Структура хроматина как причина кластеризации первичных точек разрыва.

1.2.4. Участие топоизомеразы II в незаконной рекомбинации.

1.2.5. Пространственная организация ядра способствует образованию определённых транслокаций.

Постановка задачи и методические подходы.

2. Материалы и методы.

2.1. Материалы.

2.1.1. Клеточные линии.

2.1.2. Антитела.

2.1.3. Химические реактивы.

2.2. Методы.

2.2.1. Культивирование человеческих клеток.

2.2.2. Электрофорез в пульсирующем поле.

2.2.3. Приготовление препаратов ядерных матриксов in situ.

2.2.4. Иммуноцитохимия.

2.2.5. Определение относительной представленности различных участков ДНК во фракции ДНК ядерного матрикса.

2.2.6. Метод остановки полимеразной цепной реакции (PCR-stop assay).

2.2.7. Иммунопреципитация хроматина.

2.2.7.1. Растворы:.

2.2.7.2. Методика.

3. Результаты исследований.

3.1. Подавление активности ДНК-топоизомеразы II приводит к образованию двухцепочечных разрывов ДНК.

3.1.1. Обработка клеток этопозидом приводит к образованию ДЦР.

3.1.2. Количество ДЦР зависит от концентрации этопозида.

3.1.3. Индуцированные monollДЦР эффективно репарируются.

3.2. РОЛЬ ядерного матрикса в репарации ДЦР, индуцированных ДНК-топоизомеразой II.

3.2.1. Индуцированные этопозидом фокусы гистона уН2АХассоциированы с ядерным матриксом.

3.2.2. Участки кластеризации точек разрыва (bcr) ассоциированы с ядерным матриксом.

3.3. Негомологичное соединение концов ДНК, как механизм хромосомных перестроек, индуцированных ДНК-топоизомеразой II.

3.3.1. Цитологический подход.

3.3.2. Молекулярно-биологический подход.

3.3.2.1. Выбор геномной модели.

3.3.2.2. Контрольные эксперименты.

3.3.2.3. Иммунопреципитация хроматина.

4. Обсуждение результатов.

Выводы.

Введение диссертации (часть автореферата) на тему «Пространственная организация ДНК в ядре и индуцированные ДНК-топоизомеразой II хромосомные перестройки»

Уже достаточно давно в химиотерапии различных опухолей используются ингибиторы ДНК-топоизомеразы II, и нередки случаи, когда использование этих препаратов приводит к развитию вторичных лейкозов, в основе которых лежат те или иные хромосомные перестройки (Auxenfants et al., 1992; Super et al., 1993). Известно также, что обработка клеток высших эукариот ингибиторами топоизомеразы II (например, этопозидом или амсакрином) может приводить к возникновению таких перестроек, как делеции, инсерции и транслокации (Maraschin et al., 1990; Shibuya et al., 1994). Более того, показано, что топоизомераза II обладает межмолекулярной ДНК-лигазной активностью и может осуществлять незаконную рекомбинацию ДНК in vitro (Gale, 1992). Не менее важным нам представляется тот факт, что образование ковалентных комплексов топоизомеразы и ДНК, вызванное подавлением лигирующей активности топоизомеразы II, может приводить к запуску систем репарации двухцепочечных разрывов ДНК. В клетках эукариот существуют два основных пути репарации ДЦР: гомологичная рекомбинация, играющая большую роль в клетках низших эукариот, и негомологичное соединение концов ДНК (NHEJ, non-homologous end joining). Существует множество косвенных данных о том, что именно NHEJ является основным механизмом репарации ДЦР, индуцированных топоизомеразой II (Adachi et al., 2003; Adachi et al., 2004).

Известно, что транслокации, ассоциированные с развитием некоторых лейкозов, имеют характерную черту - точки разрыва сосредоточены в достаточно узких участках генома, названных кластерами точек разрыва (bcr, breakpoint cluster region). Во многих из этих участков обнаружены сайты гиперчувствительности к

ДНКазе I и топоП. Ранее было показано, что основной мишенью ингибиторов топоизомеразы II является нерастворимая форма фермента, связанная с ядерным матриксом и взаимодействующая с участками прикрепления ДНК к матриксу. Исходя из представленных данных логично предположить, что связанная с ядерным матриксом топоизомераза может играть важную роль в запуске систем репарации ДЦР, в результате действия которых возможно появление различных транслокаций.

Настоящая работа посвящена определению и изучению механизма возникновения хромосомных перестроек, индуцированных ДНК-топоизомеразой II. Отдельное внимание уделяется роли ядерного матрикса в этом процессе.

1. Обзор литературы

Заключение диссертации по теме «Молекулярная биология», Кантидзе, Омар Леванович

Выводы:

1. Продемонстрировано, что стабилизированные ингибиторами комплексы топоизомеразы II с ДНК конвертируются в клетке в двухцепочечные разрывы, которые узнаются системами мониторинга целостности ДНК.

2. Показано, что при подавлении лигирующей активности ДНК-топоизомеразы II разрывы вносятся предпочтительно в участки прикрепления ДНК к ядерному матриксу.

3. Продемонстрировано, что участок кластеризации хромосомных разрывов, присутствующий в гене AMLI, прикреплен к ядерному матриксу

4. Впервые продемонстрировано, что репарация двухцепочечных разрывов, вносимых в ДНК топоизомеразой II, осуществляется преимущественно системой негомологичного соединения концов ДНК.

Список литературы диссертационного исследования кандидат биологических наук Кантидзе, Омар Леванович, 2007 год

1. Abranches R, Beven AF, Aragon-Alcaide L, Shaw PJ (1998) Transcription sites are not correlated with chromosome territories in wheat nuclei. J Cell Biol. 143(1):5-12.

2. Adachi N, Iiizumi S, So S, Koyama H (2004) Genetic evidence for involvement of two distinct nonhomologous end-joining pathways in repair of topoisomerase II-mediated DNA damage. Biochem. Biophys. Res. Commun. 318, 856--861.

3. Adachi N., Suzuki H., Iiizumi S., Koyama H. (2003) Hypersensitivity of nonhomologous DNA end-joining mutants to VP-16 and ICRF-193: implications for the repair of topoisomerase II-mediated DNA damage. J. Biol. Chem. 278, 35897-35902.

4. Adam M, Robert F, Larochelle M & Gaudreau L (2001) H2A.Z is required for global chromatin integrity and for recruitment of RNA polymerase II under specific condition. Mol Cell Biol 21: 6270-6279.

5. Ahmad K. & Henikoff S (2002) Histone H3 variants specify modes of chromatin assembly. Proc Natl Acad Sci USA 99: 16477-16484.

6. Ahnesorg P, Smith P, Jackson SP (2006) XLF interacts with the XRCC4-DNA ligase IV complex to promote DNA nonhomologous end-joining. Cell 124(2):301-13.

7. Alvelo-Ceron D, Niu L & Collart DG (2000) Growth regulation of human variant histone genes and acetylation of the encoded proteins. Mol Biol Report 27: 61-71.

8. Andersen MK, Johansson B, Larsen SO, Pedersen-Bjergaard J (1998) Chromosomal abnormalities in secondary MDS and AML. Relationship to drugsand radiation with specific emphasis on the balanced rearrangements. Haematologica 83(6):483-8.

9. Andoh T, Ishida R (1998) Catalytic inhibitors of DNA topoisomerase II. Biochim BiophysActa 1400(1-3):155-71.

10. Angelov D, Verdel A, An W, Bondarenko V, Hans F, Doyen C-M, Studitsky VM, Hamiche A, Roeder RG, Bouvet P & Dimitrov S (2004) SWI/SNF remodeling and p300-dependent transcription of histone variant H2A.Bbd nucleosomal arrays. EMBOJ 23:3815-3824.

11. Apian PD (2006) Chromosomal translocations involving the MLL gene: molecular mechanisms. DNA Repair (Amst) 5(9-10): 1265-72.

12. Apian, P.D., Chervinsky, D.S., Stanulla, M., Burhans, W.C. (1996) Sitespecific DNA cleavage within the MLL breakpoint cluster region induced by topoisomerase II inhibitors. Blood 87, 2649-2658.

13. Ausio J & Abbott DW (2002) The many tales of a tail: carboxyl terminal tail heterogeneity specializes histone H2A variants for defined chromatin function. Biochemistry 41: 5945-5949.

14. Auxenfants E., Morel P., Lai J.L., Sartiaux C., Detourmignies L., Bauters F., Fenaux P. (1992) Secondary acute lymphoblastic leukemia with t (4; 11): report on two cases and review of the literature. Ann. Hematol. 65, 143-146.

15. Ayton PM & Cleary ML (2001) Molecular mechanisms of Ieukemogenesis mediated by MLL fusion proteins. Oncogene 20:5695-5707.

16. Bae YS, Kawasaki I, Ikeda H, Liu LF (1988) Illegitimate recombination mediated by calf thymus DNA topoisomerase II in vitro. Proc Natl Acad Sci USA 85(7):2076-80.

17. Bakshi RP, Galande S, Muniyappa К (2001) Functional and regulatory characteristics of eukaryotic type II DNA topoisomerase. Crit Rev Biochem Mol Biol. 36(1): 1-37.

18. Bao Y, Konesky K, Park Y-J, Rosu S, Dyer PN, Rangasamy D, Tremethick DJ, Laybourn PJ & Lugcr К (2004) Nucleosomes containing the histone variant H2A.Bbd organize only 118 base pairs of DNA. EMBOJ23: 3314-3324.

19. Basler J, Hastie ND, Pietras D, Matsui SI, Sandberg AA, Berezney R. (1981) Hybridization of nuclear matrix attached deoxyribonucleic acid fragments. Biochemistry 20(24):6921 -9.

20. Baumann P & West SC (1998) DNA end joining catalyzed by human cell-free extracts. Proc. Natl. Acad. Sci. USA 95(24): 14066-14070.

21. Belmont AS & Bruce К (1994) Visualization of G1 chromosomes: a folded, twisted, supercoiled chromonema model of interphase chromatid structure. J. Cell Biol 127: 287-302.

22. Belmont AS, Sedat JW & Agard DA (1987) A three-dimensional approach to mitotic chromosome structure: evidence for a complex hierarchical organization. J. Cell Biol. 105: 77-92.

23. Benyajati С & Worcel A (1976) Isolation, characterization, and structure of the folded interphase genome of Drosophila melanogaster. Cell 9(3): 393-407.

24. Berezney R & Coffey DS (1974) Identification of a nuclear protein matrix. Biochem. Biophys. Res. Commun. 60: 1410-1417.

25. Berezney R & Coffey DS (1977) Nuclear matrix. Isolation and characterization of a framework structure from rat liver nuclei. J Cell Biol. 73(3):616-37.

26. Berrios M., Osheroff N., Fisher P. (1985) In situ localization of DNA topoisomerase II, a major polypeptide component of the Drosophila nuclear matrix fraction. Proc Natl Acad Sci USA, 82,4142-6.

27. Bicknell GR, Snovvden RT, & Cohen GM (1994) Formation ofhigh molecular mass DNA fragments is a marker of apoptosis in the human leukaemic cell line, U937.J Cell Sci. 107: 2483-9.

28. Bode J, Schlake T, Rios-Ramirez M, Mielke C, Stengert M, Kay V, Klehr-Wirth D (1995) Scaffold/matrix-attached regions: structural properties creating transcriptionally active loci. Int Rev Cytol. 162A: 389-454.

29. Bode J., Benham C., Ernst E., Knopp A., Marschalek R., Strick R., Strissel P. (2000) Fatal connections: when DNA ends meet on the Nuclear Matrix. J Cellular Biochem, 3, 3-22.

30. Bolzer A, Kreth G, Solovei I, Koehler D, Saracoglu K, Fauth C, Muller S, Eils R, Cremer C, Speicher MR, Cremer T.(2005) Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol. 3(5):el57.

31. Boulikas T (1993). Nature of DNA sequences at the attachment regions of genes to the nuclear matrix. J Cell Biochem. 52(1): 14-22.

32. Boulikas T (1995) Chromatin domains and prediction of MAR sequences. Int Rev Cytol 162A: 279-388.

33. Boy de la Tour, E & Laemmli UK (1988) The metaphase scaffold is helically folded: sister chromatids have predominantly opposite helical handedness. Cell 55: pp. 937-944.

34. Brotherton Т., Zenk D., Kahanic S., Renecer J. (1991). Avian nuclear matrix proteins bind very tightly to cellular DNA of the beta-globin gene enhancer in a tissue-specific fashion. Biochemistry 30(24): 5845-50.

35. Bryans M, Valenzano MC, Stamato TD (1999) Absence of DNA ligase IV protein in XR-1 cells: evidence for stabilization by XRCC4. Mutat Res. 433(l):53-8.

36. Buongiorno-Nardelli M, Micheli G, Carri MT, Marilley M (1982) A relationship between replicon size and supercoiled loop domains in the eukaryotic genome. Nature 298:100-2.

37. Burma S, Chen BP, Murphy M, Kurimasa A & Chen DJ (2001) ATM phosphorylates histone H2A.X in response to DNA double-strand breaks. J Biol Chem 276: 42462-42467.

38. Bystritskiy A. & Razin S. (2004) Breakpoint clusters: reason or consequence? Crit Rev Eukaryot Gene Expr, 14, 65-78.

39. Calsou P, Delteil C, Frit P, Drouet J, Salles В (2003) Coordinated assembly of Ku and p460 subunits of the DNA-dependent protein kinase on DNA ends is necessary for XRCC4-ligase IV recruitment. J. Mol. Biol 326(1):93-103.

40. Carruthers LM & Hansen JC (2000) The core histone N termini function independently of linker histones during chromatin condensation. J. Biol. Chem. 275: 37285-37290.

41. Chadwick BP & Willard HF (2002) Cell cycle-dependent localization of macroH2A in chromatin of the inactive X chromosome. J Cell Biol 157: 11131123.

42. Chadwick BP & Willard HF (2003) Chromatin of the Barr body: histone and nonhistone proteins associated with or excluded from the inactive X chromosome. Human Mol Genet 12: 2167-2178.

43. Chaly N., Little J.E., Brown D.L. (1985) Localization of nuclear antigens during preparation of nuclear matrices in situ. Can. J. Biochem. Cell Biol. 63, 644-653.

44. Champoux J. (2001) DNA topoisomerases: structure, function, and mechanism. Annu Rev Biochem, 70, 369-413.

45. Chappell C, Hanakahi LA, Karimi-Busheri F, Weinfeld M, West SC (2002) Involvement of human polynucleotide kinase in double-strand break repair by non-homologous end joining, EMBOJ. 21(11): 2827-2832.

46. Charron M. & Hancock R. (1991) Chromosome recombination and defective genome segregation induced in Chinese hamster cells by the topoisomerase II inhibitor VM-26. Chromosoma, 100, 97-102.

47. Chen HT, Bhandoola A, Difilippantonio MJ, Zhu J, Brown MJ, Tai X et al. (2000) Response to RAG-mediated VDJ cleavage by NBS1 and gamma-H2AX. Science 290: 1962-1965.

48. Chen L, Trujillo K, Sung P, Tomkinson AE (2000) Interactions of the DNA Iigase IV-XRCC4 complex with DNA ends and the DNA-dependent protein kinase. J. Biol. Chem. 275(34):26196-26205.

49. Cleary H, Boulton E, Plumb M (2001) Allelic loss on chromosome 4 (Lyr2/TLSR5) is associated with myeloid, B-lymph-myeloid and lymphoid (B & T) mouse radiation-induced leukemias. Blood 98:1549-1554.

50. Cleary ML (1991) Oncogenic conversion of transcription factors by chromosomal translocations. Cell 66:619-622.

51. Cockerill PN & Garrard WT (1986). Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites. Cell 44(2): 273-82.

52. Cohen GM, Sun XM, Fearnhead I I, MacFarlane M, Brown DG, Snowden RT, & Dinsdale D (1994) Formation of large molecular weight fragments of DNA is a key committed step of apoptosis in thymocytes. J Immunol 153(2): 507-16.

53. Comings DE (1968) The rationale for an ordered arrangement of chromatin in the interphase nucleus. Am J Hum Genet. 20(5):440-60.

54. Cook P. (1999). The organization of replication and transcription. Science, 284, 1790-5.

55. Cook PR & Brazell IA (1976) Conformational constraints in nuclear DNA. J Cell Sci 22(2): 287-302.

56. Cook PR & Brazell IA (1980). Mapping sequences in loops of nuclear DNA by their progressive detachmcnt from the nuclear cage. Nucleic Acids Res 8(13): 2895-906.

57. Cremer M, von Hase J, Volm T, Brero A, Kreth G, Walter J, Fischer C, Solovei I, Cremer C, Cremer T (2001) Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells. Chromosome Res. 9(7):541-67.

58. Cremer T. and Cremer C. (2001) Chromosome territories, nuclear architechture and gene regulation in mammalian cells. Nat Rev Genet. 2(4):292-301.

59. Daban JR (2000) Physical constraints in the condensation of eukaryotic chromosomes. Local concentration of DNA versus linear packing ratio in higher order chromatin structures. Biochemistiy 39: 3861-3866.

60. Dang Q., Auten J., Plavec I. (2000). Human beta interferon scaffold attachment region inhibits de novo methylation and confers long-term, copy number-dependent expression to a retroviral vector. J Virol 74(6): 2671-8

61. DeFazio LG, Stansel RM, Griffith JD, Chu G. (2002) Synapsis of DNA ends by DNAdependent protein kinase. EMBOJ. 21(12): 3192-3200.

62. Downs JA, Lowndes NF & Jackson SP (2000) A role for Saccharomyces cerevisiae histone H2A in DNA repair. Nature 408: 1001-1004.

63. Dvir A, Peterson SR, Knuth MW, Lu H, Dynan WS (1992) Ku autoantigen is the regulatory component of a template-associated protein kinase that phosphorylates RNA polymerase II, Proc. Natl. Acad. Sci. USA 89:11920-11924

64. Dynan WS & Yoo S (1998) Interaction of Ku protein and DNA-dependent protein kinase catalytic subunit with nucleic acids. Nucl. Acids Res. 26(7): 1551-1559.

65. Eickbush TH & Moudrianakis EN (1978) The histone core complex: an octamer assembled by two sets of protein-protein interactions. Biochemistry 17:49554964.

66. Elliott B. & Jasin M. (2002) Double-strand breaks and translocations in cancer. Cell Mol Life Sci, 59,373-85.

67. Fabry S, Muller K, Lindauer A, Park PB, Cornelius T, Schmitt R. (1995) The organization structure and regulatory elements of Chlamydomonas histone genes reveal features linking plant and animal genes. Curr Genet. 28(4):333-45

68. Felix C. (1998) Secondary leukemias induced by topoisomerase-targeted drugs. Biochim Biophys Acta, 1400,233-55.

69. Felsenfeld G. & Bell A. (1999) Stopped at the border: boundaries and insulators. Curr Opin Genet Dev, 9, 191-8.

70. Fernandes DJ & Catapano CV (1995) The nuclear matrix as a site of anticancer drug action. Int Rev Cytol 162A:539-76.

71. Finch JT and Klug A (1976) Solenoidal model for superstructure in chromatin. Proc. Natl. Acad. Sci. USA 73: 1897-1901.

72. Fiorini A, Gouveia Fde S, Fernandez MA (2006) Scaffold/Matrix Attachment Regions and intrinsic DNA curvature. Biochemistry (Mosc) 71(5):481-8.

73. Gale КС & Osheroff N (1992) Intrinsic intermolecular DNA ligation activity of eukaryotic topoisomerase II. Potential roles in recombination. J. Biol. Chem. 267, 12090-12097.

74. Gasser SM, Walter R, Dang Q, Cardenas ME (1992) Topoisomerase II: its functions and phosphorylation. Antonie Van Leeuwenhoek. 62(1-2): 15-24.

75. Gerlich D., Beaudouin J., Kalbfuss В., Daigle N., Eils R., Ellenberg J. (2003) Global chromosome positions are transmitted through mitosis in mammalian cells. Cell. 112(6):751-64.

76. Goldberg GI, Collier I, Cassel A (1983) Specific DNA sequences associated with the nuclear matrix in synchronized mouse 3T3 cells. Proc Natl Acad Sci USA. 80(22):6887-91.

77. Gottlieb TM & Jackson SP (1993) The DNA-dependent protein kinase: requirement for DNA ends and association with Ku antigen. Cell 72(1): 131-142.

78. Gravel S, Larrivee M, Labrecque P, Wellinger RJ (1998) Yeast Ku as a regulator of chromosomal DNA end structure. Science 280:741-4.

79. Grawunder U, Wilm M, Wu X, Kulesza P, Wilson ТЕ, Mann M, Lieber MR (1997) Activity of DNA ligase IV stimulated by complex formation with XRCC4 protein in mammalian cells. Nature 388:492-5.

80. Grawunder U, Zimmer D, Kulesza P, Lieber MR (1998) Requirement for an interaction of XRCC4 with DNA ligase IV for wild-type V(D)J recombination and DNA double-strand break repair in vivo .J Biol Chem. 273(38):24708-14.

81. Gu Y, Cimino G, Alder H, Nakamura T, Prasad R, Canaani 0, Moir DT, Jones C, Nowell PC, Croce CM, et al. (1992) The (4;11)(q21;q23) chromosome translocations in acute leukemias involve the VDJ recombinase. Proc. Natl. Acad. Sci. USA 89(21): 10464-8.

82. Haluska FG, Tsujimoto Y, Croce CM (1987) The t(8;14) chromosome translocation of the Burkitt lymphoma cell line Daudi occurred during immunoglobulin gene rearrangement and involved the heavy chain diversity region. Proc Natl Acad Sci USA 84(19):6835-9.

83. Hanakahi LA & West SC (2002) Specific interaction of IP6 with human Ku70/80, the DNA-binding subunit of DNA-PK. EMBOJ. 21(8):2038-2044.

84. Hancock R (2000) A new look at the nuclear matrix. Chromosoma 109(4):219-25.

85. Hand R (1978) Eucaryotic DNA: Organization of the genome for replication. Cell 15(2): 317-325.

86. Hansen JC (2002) Conformational dynamics of the chromatin fiber in solution: determinants, mechanisms and functions. Annu. Rev. Biophys. Biomol. Struct. 31: 361-392.

87. Hayes JJ and Hansen JC (2001) Nucleosomes and the chromatin fiber. Curr. Opin. Genet. Dev. 11: 124-129.

88. Hayes JJ, Clark DJ, Wolffe AP (1991) Histone contributions to the structure of DNA in the nucleosome Proc. Natl. Acad. Sci. USA 88: 6829-6833.

89. Hilliker AJ & Appels R (1989) The arrangement of interphase chromosomes: structural and functional aspects. Exp Cell Res. 185(2):267-318.

90. Hochstrasser M, Mathog D, Gruenbaum Y, Saumweber H, Sedat JW (1986) Spatial organization of chromosomes in the salivary gland nuclei of Drosophila melanogaster. J Cell Biol. 102(1): 112-23.

91. Hochstrasser M., Mathog D., Gruenbaum Y., Saumweber H., Sedat J.W. (1986) Spatial organization of chromosomes in the salivary gland nuclei of Drosophila melanogaster. J Cell Biol. 102(1): 112-23.

92. Huang C.H., Mirabelli C.K., Jan Y., Crooke S.T. (1981) Single-strand and double-strand deoxyribonucleic acid breaks produced by several bleomycin analogues. Biochemistry. 20, 233—238.

93. Jackson DA & Cook PR (1985). A general method for preparing chromatin containing intact DNA. EMBOJ4(4): 913-8.

94. Jackson DA, Dolle A, Robertson G, Cook PR (1992) The attachments of chromatin loops to the nucleoskeleton. Cell Biol Int Rep 16 (8), 687-96.

95. Junop MS, Modesti M, Guarne A, Ghirlando R, Gellert M, Yang W (2000) Crystal structure of the Xrcc4 DNA repair protein and implications for end joining. EMBOJ. 19(22):5962-70.

96. Karimi-Busheri F, Daly G, Robins P, Canas B, Pappin DJ, Sgouros J, Miller GG, Fakhrai H, Davis EM, Le Beau MM, Weinfeld M (1999) Molecular characterization of a human DNA kinase. J. Biol. Chem. 274(34): 24187-24194.

97. Kim J & Pelletier J (1999) Molecular genetics of chromosome translocations involving EWS and related family members. Physiol Genomics 1:127-138.

98. Koch CA, Agyei R, Galicia S, Metalnikov P, O'Donnell P, Starostine A,

99. Kozubek S., Lukasova E., Jirsova P., Koutna I., Kozubek M., Ganova A., Bartova E., Falk M., Pasekova R. (2002) 3D structure of the human genome: order in randomness. Chromosoma, 111, 321-31.

100. Kuhne M, Rothkamm K, Lobrich M (2002) Physical and biological parameters affecting DNA double strand break misrejoining in mammalian cells. Radiat. Prot. Dosim. 99:129-132.

101. M.Kuhne, M., Riballo, E., Rief, N., Rothkamm, K., Jeggo, P.A. and Lobrich, M. (2004) A double-strand break repair defect in ATM-deficient cells contributes to radiosensitivity. Cancer Res, 64, 500-508.

102. Laemmli UK (1978) Levels of organization of the DNA in eucaryotic chromosomes. Pharmacol Rev. 30(4):469-76

103. Lagarkova M, Iarovaia O, Razin S (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(35): 20239-41.

104. Leach TJ, Mazzeo M, Chotkowski HL, Madigan JP, Wotring MG & Glaser RL (2001) Histone H2A.Z is widely but non-randomly distributed in chromosomes of Drosophila melanogaster. J Biol Chem 275: 23267-23272.

105. Lee JW, Blanco L, Zhou T, Garcia-Diaz M, Bebenek K, Kunkel ТА, Wang Z, Povirk LF (2004) Implication of DNA polymerase lambda in alignment-based gap-filling for non-homologous DNA end joining in human nuclear extracts. J. Biol. Chem. 279(1):805-811.

106. Levy-Wilson B. & Fortier C. (1989) The limits of the DNase I-sensitive domain of the human apolipoprotein В gene coincide with the locations of chromosomal anchorage loops and define the 5' and 3' boundaries of the gens. J Biol Chem, 264,21196-204.

107. Li HJ (1976) A model for chromatin structure. Nucleic Acids Res. 2(8): 1275-89.

108. Li TK, Chen AY, Yu С, Mao Y, Wang H, & Liu LF (1999) Activation of topoisomerase II-mediated excision of chromosomal DNA loops during oxidative stress. Genes Dev 13(12): 1553-60.

109. Look AT (1997) Oncogenic transcription factors in the human acute leukemias. Science 278:1059-1064.

110. Losa R, Thoma F & Koller T (1984) Involvement of the globular domain of histone HI in the higher order structures of chromatin. J. Mol. Biol. 175: pp. 529— 551.

111. Luger К & Richmond T J (1998) DNA binding within the nucleosome core. Curr. Opin. Struct. Biol. 8: 33-40.

112. Luger K, Mader AW, Richmond RK et al. (1997) Crystal structure of the nucleosome core particle at 2.8 A0 resolution. Nature 389: pp. 251-260.

113. Ma H., Siegel A.J., Berezney R. (1999) Association of chromosome territories with the nuclear matrix. Disruption of human chromosome territoriescorrelates with the release of a subset of nuclear matrix proteins. J Cell Biol. 146(3):531-42.

114. Ma Y,. Lieber MR (2002) Binding of inositol hexakisphosphate (IP6) to Ku but not to DNA-PKcs. J. Biol. Chem. 277(13): 10756-10759.

115. Mahadevaiah SK, Turner JMA, Baudat F, Rogakou EP, de Boer P, Bianco-Rodriguez J et al. (2001) Recombinational DNA double-strand breaks in mice precede synapsis. Nat Genet 27: 271-276.

116. Mahajan KN, Nick McElhinny SA, Mitchell BS, Ramsden DA (2002) Association of DNA polymerase mu (pol mu) with Ku and ligase IV: role for pol mu in end joining double-strand break repair. Mol. Cell. Biol. 22(14): 5194-5202

117. Malik HS & Henikoff S (2003) Phylogenomics of the nucleosome. Nat Struct Biol 10: 882-891.

118. Maraschin J, Dutrillaux B, Aurias A (1990) Chromosome aberrations induced by etoposide (VP-16) are not random. Int. J. Cancer 46, 808-812.

119. Marchetti F, Bishop JB, Lowe X, Generoso WM, Hozier J, Wyrobek AJ (2001) Etoposide induces heritable chromosomal aberrations and aneuploidy during male meiosis in the mouse. Proc Natl Acad Sci USA 98(7):3952-7.

120. Marie С & Hyrien О (1998) Remodeling of chromatin loops does not account for specification of replication origins during Xenopus development. Chromosoma, 107, 155-65.

121. Marsde MP & Laemmli U К (1979) Metaphase chromosome structure: evidence for a radial loop model. Cell 17: 849-858.

122. Marshall WF, Dernburg AF, Harmon B, Agard DA, Sedat JW (1996) Specific interactions of chromatin with the nuclear envelope: positional determination within the nucleus in Drosophila melanogaster. Mol Biol Cell. 7(5):825-42.

123. Mathog D, Hochstrasser M, Gruenbaum Y, Saumweber H, Sedat J (1984) Characteristic folding pattern of polytene chromosomes in Drosophila salivary gland nuclei. Nature 308:414-21.

124. Maya-Mendoza A, Aranda-Anzaldo A (2003) Positional mapping of specific DNA sequences relative to the nuclear substructure by direct polymerase chain reaction on nuclear matrix-bound templates. Analyt. Biochem. 313, 196-207.

125. McCready SJ, Akrigg A, Cook PR (1979) Electron-microscopy of intact nuclear DNA from human cells. J Cell Sci 39: 53-62.

126. Mersfelder EL & Parthun MR (2006) The tale beyond the tail: histone core domain modifications and the regulation of chromatin structure. Nucleic Acids Res. 34(9):2653-62.

127. Mirkovitch J, Gasser SM & Laemmli UK (1988) Scaffold attachment of DNA loops in metaphase chromosomes. J Mol Biol 200(1): 101-9.

128. Mirkovitch J, Mirault ME & Laemmli UK (1984). Organization of the higher-order chromatin loop: specific DNA attachment sites on nuclear scaffold. Cell 39(1): 223-32.

129. Modesti M, Hesse JE, Gellert M (1999) DNA binding of Xrcc4 protein is associated with V(D)J recombination but not with stimulation of DNA ligase IV activity. EMBO J. 18(7):2008-18.

130. Moneypenny CG, Shao J, Song Y, Gallagher EP (2006) MLL rearrangements are induced by low doses of etoposide in human fetal hematopoietic stem cells. Carcinogenesis 27(4):874-81.

131. Morgan WF, Corcoran J, Hartmann Л, Kaplan MI, Limoli CL, Ponnaiya В (1998) Double strand breaks, chromosomal rearrangements, and genomic instability. Mutat. Res. 404:125-128.

132. Nakanishi M, Tanaka K, Shintani T, Takahashi T, Kamada N (1999) Chromosomal instability in acute myelocytic leukemia and myelodysplastic syndrome patients among atomic bomb survivors. J. Radial Res. 40:159-167.

133. Olins AL and Olins DE (1974) Spheroid Chromatin Units (nu Bodies). Science 183: 330- 332

134. Olive P.L., Banath J.P. (1993) Detection of DNA double-strand breaks through the cell cycle after exposure to X-rays, bleomycin, etoposide and 125IdUrd. Int. J. Radial Biol. 64, 349-358.

135. Olive PL (2000) The role of single and double strand breaks in cell killing by ionizing radiation. Radiat. Res. 150: 42-51.

136. Oshita F, Yamada K, Nomura I, Noda К (1998) Gene-specific damage produced by topoisomerase inhibitors in human lung cancer cells and peripheral mononuclear cells as assayed by polymerase chain reaction-stop assay. Anticancer Res. 18:3389-3393

137. Parsons CA, Baumann P, Van Dyck E, West SC (2000) Precise binding of single-stranded DNA termini by human RAD52 protein. EMBOJ. 19:4175-4181.

138. Paull TT, Rogakou EP, Yamazaki V, Kirchgessner CU, Gellert M & Bonner WM (2000) A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage. Curr Biol 10: 886-895.

139. Pehrson JR & Fried VA (1992) MacroH2A, a core histone containing a large nonhistone region. Science 257: 1398-1400.

140. Perche P-Y, Vourch C, Konecny L, Souchier C, Nicoud MR, Dimitrov S & Khochbin S (2000) Higher concentrations of histone macroH2A in the Barr body are correlated with higher nucleosome density. Curr Biol 10: 1531-1534.

141. Peterson CL, Laniel MA. (2004) Histones and histone modifications. Curr Biol. 14(14): 546-51.

142. Pfeiffer P., Goedecke W., Obe G. (2000) Mechanisms of DNA double strand break repair and their potential to induce chromosomal aberrations. Mutagenesis, 15, 289-302.

143. Philip P & Pedersen-Bjergaard J (1988) Cytogenetic, clinical, and cytologic characteristics of radiotherapy-related leukemias. Cancer Genet. Cytogenet. 31:227-236.

144. Pilch DR, Sedelnikova OA, Redon C, Celeste A, Nussenzweig A, Bonner WM (2003) Characteristics of gamma-H2AX foci at DNA double-strand breaks sites. Bioch Cell Biology 81(3): 123-9.

145. Rabl C. (1885) Uber Zellteilung. In Morphologisches Jahrbuch, G. C., ed., pp. 214-258.

146. Ramakrishnan V (1995) The Histone Fold: Evolutionary Questions. ProcNatl Acad Sci US A. 92: 11328-11330

147. Rangasamy D, Berven L, Ridgway P & Tremethick DJ (2003) Pericentric heterochromatin becomes enriched with H2A.Z during early mammalian development. EMBOJ22: 1599-1607.

148. Rassool F.V. (2003) DNA double strand breaks (DSB) and non-homologous end joining (NHEJ) pathways in human leukemia. Cancer Letters, 193, 1-9.

149. Rattner J В and Lin CC (1985). Radial loops and helical coils coexist in metaphase chromosomes. Cell 42: 291-296.

150. Razin S & Gromova I (1995) The channels model of nuclear matrix structure. Bioessays, 17,443-50.

151. Razin S (1999) Chromosomal DNA loops may constitute basic units of the eukaryotic genome organization and evolution. Crit Rev Eukaryot Gene Expr, 9, 279-83.

152. Razin S, Farrell C, Recillas-Targa F (2003) Genomic domains and regulatory elements operating at the domain level. Int Rev Cytol 226: 63-125.

153. Razin SV (2001) The nuclear matrix and chromosomal DNA loops: is their any correlation between partitioning of the genome into loops and functional domains? Cell Mol Biol Lett. 6(l):59-69.

154. Razin SV, Kekelidze MG, Lukanidin EM, Scherrer K, Georgiev GP (1986) Replication origins are attached to the nuclear skeleton. Nucleic Acids Res. 14(20):8189-207.

155. Razin SV, Mantieva VL, Georgiev GP (1978) DNA adjacent to attachment points of deoxyribonucleoprotein fibril to chromosomal axial structure is enriched in reiterated base sequences. Nucleic Acids Res. 5(12):4737-51.

156. Redon C, Pilch D, Rogakou EP, Orr AH, Lowndes NF, Bonner WM (2003) Yeast histone 2A serine 129 is essential for the efficient repair of checkpoint-blind DNA damage. EMBO Report 4: 678-684.

157. Redon C, Pilch D, Rogakou EP, Sedelnikova O, Newrock K, Bonner WM (2002) Histone H2A variants H2AX and H2AZ. Curr Opin Genet Dev 12: 162-169.

158. Riballo E, Kuhne M, RiefN, Doherty A, Smith GC, Recio MJ, Reis C, Dahm K, Fricke A, Krempler A et al. (2004) A pathway of double-strand break rejoining dependent upon ATM, Artemis, and proteins locating to gamma-H2AX foci. Mol. Cell 16: 715-24.

159. Richardson С & Jasin M(2000) Frequent chromosomal translocations induced by DNA double strand breaks. Nature 405: 697-700.

160. Richmond, T J and Davey, С A (2003) The structure of DNA in the nucleosome core. Nature 423: 145-150.

161. Rivera-Calzada A, Maman JD, Spagnolo L, Pearl LH, Llorca О (2005) Three-dimensional structure and regulation of the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). Structure 13(2):243-55.

162. Rogakou EP, Boon C, Redon C, Bonner WM (1999) Megabase chromatin domains involved in DNA double-strand breaks in vivo. J. Cell. Biol. 146, 905916.

163. Rogakou EP, Pilch DR, Orr AH, Ivanova VS, Bonner WM (1998) DNA double stranded breaks induce H2AX phosphorylation on serine-139. J Biol Chem 273: 5858-5868.

164. Rothkamm K, Lobrich M (2002) Misrepair of radiation-induced DNA double-strand breaks and its relevance for tumorigenesis and cancer treatment. Int. J. Oncol. 2: 433-440.

165. Rzeszowska-Wolny J, Razin S, Puvion E, Moreau J, Scherrer К (1988) Isolation and characterization of stable nuclear matrix preparations and associated DNA from avian erythroblasts. Biol. Cell. 64, 13-22.

166. Sandman K, Krzycki JA, Dobrinski B, Lurz R, Reeve JN (2000) HMf, a DNA binding protein isolated from the hyperthermophilic archeon Methanothermus fervidus, is most closely related to histones. Proc Natl Acad Sci USA 7: 57885757.

167. Santisteban MS, Kalashnikova T, Smith MM (2000) Histone H2A.Z regulates transcription and is partially redundant with nucleosome remodeling complexes. Cell 103: 411^22.

168. Schaefer C, Grouse L, Buetow K, Strausberg RL (2001) A new cancer genome anatomy project web resource for the community. Cancer J. 7:52-60.

169. Schar P (2001) Spontaneous DNA damage, genome instability, and cancer when DNA replication escapes control. Cell 104:329-332.

170. Schwarz PM, Felthauser A, Fletcher TM, Hansen JC (1996) Reversible oligonucleosome self-association: dependence on divalent cations and core histone tail domains. Biochemistry 35: 4009-4015.

171. Sedelnikova OA, Rogakou EP, Panuytin IG, Bonner WM (2002) Quantitative detection of 125IUdr-induced DNA double-strand breaks with y-H2AX antibody. Radiation Research 158:486-92.

172. Sekiguchi JM & Alt FW (1999) Non homologous endjoining proteins are required for V(D)J recombination, normal growth and neurogenesis. Cold Spring Harbor Symp. Quant. Biol. 64:169-181.

173. Sellos D, Krawetz SA, Dixon GH (1990) Organization and complete nucleotide sequence of the core-histone-gene cluster of the annelid Platynereis dumerilii. Eur J Biochem. 190(1): 21-29.

174. Shibuya ML, Ueno AM, Vannais DB, Craven PA, Valdren CA (1994) Megabase pair deletions in mutant mammalian cells following exposure to amsacrine, an inhibitor of DNA topoisomerase II. Cancer Res. 54, 1092-1097.

175. Sibanda BL, Critchlow SE, Begun J, Pei XY, Jackson SP, Blundell TL, Pellegrini L (2001) Crystal structure of an Xrcc4-DNA ligase IV complex. Nat Struct Biol. 8(12): 1015-9.

176. Sigurdson AJ & Jones IM (2003) Second cancers after radiotherapy: any evidence for radiation-induced genomic instability? Oncogene, 22, 7018-7027.

177. Singer RH & Green MR (1997) Compartmentalization of eukaryotic gene expression: causes and effects. Cell. 91(3):291-4.

178. Smith MA, McCaffrey RP, Karp JE (1996) The secondary leukemias: challenges and research directions. J Natl Cancer Inst. 88(7):407-18

179. Spagnolo L, Rivera-Calzada A, Pearl LH, Llorca О (2006) Three-dimensional structure of the human DNA-PKcs/Ku70/Ku80 complex assembled on DNA and its implications for DNA DSB repair. Mol Ce//.22(4):511-9.

180. Staufenbiel M., Deppert W. (1984) Preparation of nuclear matrices from cultured cells: subfractionation of nuclei in situ. J. Cell. Biol. 98, 1886-1894.

181. Strick R, Zhang Y, Emmanuel N, Strissel PL (2006) Common chromatin structures at breakpoint cluster regions may lead to chromosomal translocations found in chronic and acute leukemias. Hum Genet. 119(5):479-95.

182. Strissel PL, Strick R, Rowley JD, Zeleznik-Le NJ (1998) An in vivo topoisomerase II cleavage site and a DNase I hypersensitive site colocalize near exon 9 in the MLL breakpoint cluster region. Blood 92:3793-3803

183. Strout MP, Marcucci G, Bloomfield CD, Caligiuri МЛ (1998) The partial tandem duplication of ALL1 (MLL) is consistently generated by Alu-mediated homologous recombination in acute myeloid leukemia. Proc Natl Acad Sci USA 95(5):2390-5.

184. Sullivan KF, Hechenberger M & Masri К (1994) Human CENP-A contains a histone H3 related histone fold domain that is required for targeting to the centromere. J Cell Biol 127: 581-592.

185. Sung P & Klein H (2006) Mechanism of homologous recombination: mediators and helicases take on regulatory functions. Nat Rev Mol Cell Biol. 7(10):739-50.

186. Taylor EM, Lehmann AR (1998) Conservation of eukaryotic DNA repair mechanisms. Int J Radiat Biol. 74(3):277-86.

187. Thompson LH, Schild D (2001) Homologous rccombinational repair of DNA ensures mammalian chromosome stability. Mutat Res. 477(1-2): 131-53.

188. Turner JMA, Aprelikova O, Xu X, Wang R, Kim S, Chandramouli GVA, Barratt CJ, Burgoyne PS & Deng CX (2004) BRCA1 histone H2AX phosphorylation, and male meiotic sex chromosome inactivation. Curr Biol 14: 2135-2142.

189. Valerie К & Povirk LF (2003) Regulation and mechanisms of mammalian double-strand break repair. Oncogene, 22, 5792-5812.

190. Van Dyck E, Hajibagheri NM, Stasiak A, West SC (1998) Visualisation of human rad52 protein and its complexes with hRad51 and DNA. J Mol Biol. 284(4): 1027-38.

191. Van Dyck E, Stasiak AZ, Stasiak A, West SC (1999) Binding of double-strand breaks in DNA by human Rad52 protein. Nature 398: 728-731.

192. Van Holde KE (1989) "Chromatin". Springer Verlag, New York.213. van Leeuwen F, van Steensel В (2005) Histone modifications: from genome-wide maps to functional insights. Genome Biol. 6(6): 113-8.

193. Verheijen R, Kuijpers H, Vooijs P, van Venrooij W, Ramaekers F (1986) Protein composition of nuclear matrix preparations from HeLa cells: an immunochemical approach. J Cell Sci. 80: 103-22.

194. Verheijen R, van Venrooij W, Ramaekers F (1988) The nuclear matrix: structure and composition. J Cell Sci. 90:11 -36.

195. Verschure PJ, van Der Kraan I, Manders EM, van Driel R (1999) Spatial relationship between transcription sites and chromosome territories. J Cell Biol. 147(1): 13-24.

196. Walker JR, Софта RA, Goldberg J (2001) Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. Nature 412:607-14.

197. Walter J., Schermelieh L., Cremer M., Tashiro S., Cremer T. (2003) Chromosome order in HeLa cells changes during mitosis and early Gl, but is stably maintained during subsequent interphase stages. J Cell Biol. 160(5):685-97.

198. Wang J. (2002). Cellular roles of DNA topoisomerases: a molecular perspective. Nat. Rev. Mol Cell Biol, 3(6): 430-40.

199. Wiegant J, Kalle W, Mullenders L, Brookes S, Hoovers JM, Dauwerse JG, van Ommen GJ, Raap AK (1992) High-resolution in situ hybridization using DNA halo preparations. Hum Mol Genet. 1(8):587-91

200. Wolffe AP & Dimitrov S (1993) Histone-modulated gene activity: developmental implications. Crit Rev Eukaryot Gene Expr 3: 167-191.

201. Woodcock CL & Dimitrov S (2001) Higher-order structure of chromatin and chromosomes. Curr. Opin. Genet. Dev. 11: 130-135.

202. Woodcock CL, McEwen BF, Frank J (1991) Ultrastructure of chromatin. II. Three-dimensional reconstruction of isolated fibers. J. Cell Sci. 99: 107-114.

203. Wyman C, Ristic D, Kanaar R (2004) Homologous recombination-mediated double-strand break repair. DNA Repair (Amst). 3(8-9):827-33.

204. Xu M, Hammer RE, Blasquez VC, Jones SL, Garrard WT (1989) Immunoglobulin kappa gene expression after stable integration. II. Role of the intronic MAR and enhancer in transgenic mice. J Biol Chem. 264(35):21190-5.

205. Yanagida M (2005) Basic mechanism of eukaryotic chromosome segregation. Philos Trans R Soc Lond В Biol Sci. 360:609-21.

206. Yaneva M, Kowalewski T, Lieber MR (1997) Interaction of DNA-dependent protein kinase with DNA and with Ku: biochemical and atomicforce microscopy studies. EMBO J. 16(16):5098-5112.

207. Yoshino N, Kojima T, Asami S, Motohashi S, Yoshida Y, Chin M, Shichino H, Yoshida Y, Nemoto N, Kaneko M, Mugishima H, Suzuki T (2003) Diagnostic significance and clinical applications of chimeric genes in Ewing's sarcoma. Biol PharmBull 26:585-588.

208. Yu J Bock JH, Slightom JL, Villeponteau В (1994) A 5' beta-globin matrix-attachment region and the polyoma enhancer together confer position-independent transcription. Gene 139(2): 139-45.

209. Zhang Z, Zhu L, Lin D, Chen F, Chen DJ, Chen Y (2001) The three-dimensional structure of the C-terminal DNA-binding domain of human Ku70. J Biol Chem. 276(41):38231-6.

210. Разин С., Ржешовска-Вольны Й., Моро Ж., Шеррер К. (1985) Локализация участков прикрепления ДНК к ядерному скелету в генах альфа-глобина цыпленка в функционально активных и функционально неактивных ядрах. Мол. Биол. 19: 456-66.

211. Чернов И., Акопов С., Николаев Л. (2004) Структура и функции участков прикрепления ДНК к ядерному матриксу (S/MARs). Биооргапическая химия 30(1):3-14.1. Благодарности

212. Автор выражает искреннюю благодарность своим научным руководителям и всем коллегам по лаборатории структурно-функциональной организации хромосом ИБГ РАН.