Mapping of the nuclear matrix-bound chromatin hubs by a new M3C experimental procedure

Nucleic Acids Research

Volumn 38, Issue 22, 2010, Pages 8051-8060

  Gavrilov, Alexey A ^a   Zukher, Inna S ^a   Philonenko, Elena S ^a   Razin, Sergey V ^a,b   Iarovaia, Olga V ^a  

^a INSTITUTE OF GENE BIOLOGY   (Russian Federation)

^b MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA GLOBIN;

ANIMAL CELL; ARTICLE; CELL NUCLEUS MATRIX; CELL SPECIFICITY; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONTROLLED STUDY; CPG ISLAND; DNA CLEAVAGE; DNA DETERMINATION; DNA PURIFICATION; ERYTHROID CELL; GENE LOCATION; GENETIC PROCEDURES; HOUSEKEEPING GENE; MATRIX 3C; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROMOTER REGION; PROTEIN ASSEMBLY; RESTRICTION MAPPING; TISSUE SPECIFICITY; TRANSCRIPTION REGULATION;

ANIMALS; CELL FRACTIONATION; CELL LINE; CHICKENS; CHROMATIN; CPG ISLANDS; DNA; DNA RESTRICTION ENZYMES; GLOBINS; NUCLEAR MATRIX;

EID: 78650463917     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq712     Document Type: Article

References (59)

1. Dekker, J., Rippe, K., Dekker, M. and Kleckner, N. (2002) Capturing chromosome conformation. Science, 295, 1306-1311.
2. Splinter, E., Grosveld, F. and de Laat, W. (2004) 3C technology: analyzing the spatial organization of genomic loci in vivo. Methods Enzymol., 375, 493-507.
3. Palstra, R.J., Tolhuis, B., Splinter, E., Nijmeijer, R., Grosveld, F. and de Laat, W. (2003) The beta-globin nuclear compartment in development and erythroid differentiation. Nat. Genet., 35, 190-194.
4. De Laat, W. and Grosveld, F. (2003) Spatial organization of gene expression: the active chromatin hub. Chromosome Res., 11, 447-459.
5. De Laat, W., Klous, P., Kooren, J., Noordermeer, D., Palstra, R.J., Simonis, M., Splinter, E. and Grosveld, F. (2008) Three-dimensional organization of gene expression in erythroid cells. Curr. Top. Dev. Biol., 82, 117-139.
6. Gavrilov, A.A. and Razin, S.V. (2008) Spatial configuration of the chicken a-globin gene domain: immature and active chromatin hubs. Nucleic Acids Res., 36, 4629-4640.
7. Lanzuolo, C., Roure, V., Dekker, J., Bantignies, F. and Orlando, V. (2007) Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex. Nat. Cell. Biol., 9, 1167-1174.
8. Ling, J.Q., Li, T., Hu, J.F., Vu, T.H., Chen, H.L., Qiu, X.W., Cherry, A.M. and Hoffman, A.R. (2006) CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/ Nf1. Science, 312, 269-272.
9. Zhou, G.L., Xin, L., Song, W., Di, L.J., Liu, G., Wu, X.S., Liu, D.P. and Liang, C.C. (2006) Active chromatin hub of the mouse alpha-globin locus forms in a transcription factory of clustered housekeeping genes. Mol. Cell. Biol., 26, 5096-5105.
10. Berezney, R. and Coffey, D.S. (1977) Nuclear matrix: isolation and characterization of a framework structure from rat liver nuclei. J. Cell. Biol., 73, 616-637. (Pubitemid 8115197)
11. Pederson, T. (2000) Half a century of "the nuclear matrix". Mol. Biol. Cell., 11, 799-805.
12. Misteli, T. (2007) Beyond the sequence: cellular organization of genome function. Cell, 128, 787-800.
13. Hancock, R. (2000) A new look at the nuclear matrix. Chromosoma, 109, 219-225.
14. Brown, K. (1999) Nuclear structure, gene expression and development. Crit. Rev. Eukaryot. Gene. Expr., 9, 203-212.
15. Barboro, P., D'Arrigo, C., Mormino, M., Coradeghini, R., Parodi, S., Patrone, E. and Balbi, C. (2003) An intranuclear frame for chromatin compartmentalization and higher-order folding. J. Cell. Biochem., 88, 113-120.
16. Cai, S., Han, H.J. and Kohwi-Shigematsu, T. (2003) Tissue-specific nuclear architecture and gene expression regulated by SATB1. Nat. Genet., 34, 42-51.
17. Malyavantham, K.S., Bhattacharya, S. and Berezney, R. (2010) The architecture of functional neighborhoods within the mammalian cell nucleus. Adv. Enzyme Regul., 50, 126-134.
18. Razin, S.V., Mantieva, V.L. and Georgiev, G.P. (1979) The similarity of DNA sequences remaining bound to scaffold upon nuclease treatment of interphase nuclei and metaphase chromosomes. Nucleic Acids Res., 7, 1713-1735.
19. Dorman, E.R., Bushey, A.M. and Corces, V.G. (2007) The role of insulator elements in large-scale chromatin structure in interphase. Semin. Cell. Dev. Biol., 18, 682-690.
20. Stein, G.S., Lian, J.B., Van Wijnen, A.J., Stein, J.L., Javed, A., Montecino, M., Zaidi, S.K., Young, D., Choi, J.Y., Gutierrez, S. et al. (2004) Nuclear microenvironments support assembly and organization of the transcriptional regulatory machinery for cell proliferation and differentiation. J. Cell. Biochem., 91, 287-302.
21. Jackson, D.A. (1997) Chromatin domains and nuclear compartments: establishing sites of gene expression in eukaryotic nuclei. Mol. Biol. Rep., 24, 209-220.
22. Razin, S.V., Gromova, II and Iarovaia, O.V. (1995) Specificity and functional significance of DNA interaction with the nuclear matrix: new approaches to clarify the old questions. Int. Rev. Cytol., 162B, 405-448.
23. Cook, P.R., Brazell, I.A. and Jost, E. (1976) Characterization of nuclear structures containing superhelical DNA. J. Cell. Sci., 22, 303-324.
24. Cook, P.R. and Brazell, I.A. (1980) Mapping sequences in loops of nuclear DNA by their progressive detachment from the nuclear cage. Nucleic Acids Res., 8, 2895-2907.
25. Beug, H., Von Kirchbach, A., Doderlin, J., Conscience, J.F. and Graf, T. (1979) Chicken hematopoietic cells transformed by seven strains of defective avian leukemia viruses display three distinct phenotypes of differentiation. Cell, 18, 375-390.
26. Beug, H., Doederlein, G., Freudenstrein, C. and Graf, T. (1979) Erythroblast cell lines transformed by a temperature sensitive mutant of avian erythroblastosis virus. A model system to study erythroid differentiation in vitro. J. Cell. Physiol., 1, 195-207.
27. Ioudinkova, E., Razin, S.V., Borunova, V., de Conto, F., Rynditch, A. and Scherrer, K. (2005) RNA-dependent nuclear matrix contains a 33kb globin full domain transcript as well as prosomes but no 26S proteasomes. J. Cell. Biochem., 94, 529-539.
28. Gavrilov, A., Eivazova, E., Priozhkova, I., Lipinski, M., Razin, S. and Vassetzky, Y. (2009) Chromosome conformation capture (from 3C to 5C) and its ChIP-based modification. Methods Mol. Biol., 567, 171-188.
29. Flint, J., Tufarelli, C., Peden, J., Clark, K., Daniels, R.J., Hardison, R., Miller, W., Philipsen, S., Tan-Un, K.C., McMorrow, T. et al. (2001) Comparative genome analysis delimits a chromosomal domain and identifies key regulatory elements in the alpha globin cluster. Hum. Mol. Genet., 10, 371-382.
30. Klochkov, D., Rincon-Arano, H., Ioudinkova, E.S., Valadez-Graham, V., Gavrilov, A., Recillas-Targa, F. and Razin, S.V. (2006) A CTCF-dependent silencer located in the differentially methylated area may regulate expression of a housekeeping gene overlapping a tissue-specific gene domain. Mol. Cell. Biol., 26, 1589-1597.
31. Nunez, E., Fu, X.D. and Rosenfeld, M.G. (2009) Nuclear organization in the 3D space of the nucleus - cause or consequence? Curr. Opin. Genet. Dev., 19, 424-436.
32. Noordermeer, D. and de Laat, W. (2008) Joining the loops: beta-globin gene regulation. IUBMB Life, 60, 824-833.
33. Mishiro, T., Ishihara, K., Hino, S., Tsutsumi, S., Aburatani, H., Shirahige, K., Kinoshita, Y. and Nakao, M. (2009) Architectural roles of multiple chromatin insulators at the human apolipoprotein gene cluster. EMBO J., 28, 1234-1245.
34. Zlatanova, J. and Caiafa, P. (2009) CCCTC-binding factor: to loop or to bridge. Cell. Mol. Life Sci., 66, 1647-1660.
35. Splinter, E., Heath, H., Kooren, J., Palstra, R.J., Klous, P., Grosveld, F., Galjart, N. and de Laat, W. (2006) CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. Genes Dev., 20, 2349-2354.
36. Savitskaya, E., Melnikova, L., Kostuchenko, M., Kravchenko, E., Pomerantseva, E., Boikova, T., Chetverina, D., Parshikov, A., Zobacheva, P., Gracheva, E. et al. (2006) Study of long-distance functional interactions between Su(Hw) insulators that can regulate enhancer-promoter communication in Drosophila melanogaster. Mol. Cell. Biol., 26, 754-761.
37. Muravyova, E., Golovnin, A., Gracheva, E., Parshikov, A., Belenkaya, T., Pirrotta, V. and Georgiev, P. (2001) Loss of insulator activity by paired Su(Hw) chromatin insulators. Science, 291, 495-498.
38. Byrd, K. and Corces, G. (2003) Visualisation of chromatin domains created by the gypsy insulator of Drosophila. J. Cell. Biol., 162, 565-574.
39. Dunn, K.L., Zhao, H. and Davie, J.R. (2003) The insulator binding protein CTCF associates with the nuclear matrix. Exp. Cell. Res., 288, 218-223.
40. 0-HS4 chicken beta-globin insulator is a CTCF-dependent nuclear matrix-associated element. Proc. Natl Acad. Sci. USA, 101, 8620-8624.
41. Mika, S. and Rost, B. (2005) NMPdb: Database of Nuclear Matrix Proteins. Nucleic Acids Res., 33, D160-D163.
42. Ishii, K., Hirano, Y., Araki, N., Oda, T., Kumeta, M., Takeyasu, K., Furukawa, K. and Horigome, T. (2008) Nuclear matrix contains novel WD-repeat and disordered-region-rich proteins. FEBS Lett., 582, 3515-3519.
43. Albrethsen, J., Knol, J.C. and Jimenez, C.R. (2009) Unravelling the nuclear matrix proteome. J. Proteomics, 72, 71-81.
44. Barboro, P., D'Arrigo, C., Repaci, E., Patrone, E. and Balbi, C. (2010) Organization of the lamin scaffold in the internal nuclear matrix of normal and transformed hepatocytes. Exp. Cell Res., 316, 992-1001.
45. Berezney, R. (2002) Regulating the mammalian genome: the role of nuclear architecture. Adv. Enzyme Regul., 42, 39-52.
46. Elcock, L.S. and Bridger, J.M. (2008) Exploring the effects of a dysfunctional nuclear matrix. Biochem. Soc. Trans., 36, 1378-1383.
47. Razin, S.V., Gromova, I.I. and Iarovaia, O.V. (1995) Specificity and functional significance of DNA interaction with the nuclear matrix: new approaches to clarify the old questions. Int. Rev. Cytol., 162B, 405-448.
48. Cockerill, P.N. and Garrard, W.T. (1986) Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the nenhancer in a region containing topoisomerase II sites. Cell, 44, 273-282.
49. Mirkovitch, J., Mirault, M.-E. and Laemmli, U.K. (1984) Organization of the higher-order chromatin loop: specific DNA attachment sites on nuclear scaffold. Cell, 39, 223-232.
50. Bode, J., Schlake, T., Rios-Ramirez, M., Mielke, C., Stengert, M., Kay, V. and Klehr-Wirth, D. (1995) Scaffold/matrix-attached regions: structural properties creating transcriptionally active loci. Int. Rev. Cytol., 162A, 389-454.
51. Hempel, K. and Stratling, W.H. (1996) The chicken lysozyme gene 5' MAR and the Drosophila histone SAR are electroelutable from encapsulated and digested nuclei. J. Cell. Sci., 109, 1459-1469.
52. Razin, S.V., Hancock, R., Iarovaia, O., Westergaard, O., Gromova, I. and Georgiev, G.P. (1993) Structural-functional organization of chromosomal DNA domains. Cold Spring Harbor Symp. Quant. Biol., 58, 25-35.
53. Gromova, II, Thomsen, B. and Razin, S.V. (1995) Different topoisomerase II antitumor 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.
54. Iarovaia, O.V., Bystritskiy, A., Ravcheev, D., Hancock, R. and Razin, S.V. (2004) Visualization of individual DNA loops and a map of loop-domains in the human dystrophin gene. Nucleic Acids Res., 32, 2079-2086. (Pubitemid 38854763)
55. Razin, S.V., Petrov, P. and Hancock, R. (1991) Precise localization of the a-globin gene cluster within one of the 20- to 300-Kilobase DNA fragment released by cleavage of chicken chromosomal DNA at topoisomerase II site in vivo: evidence that the fragment are DNA loops or domains. Proc. Natl Acad. Sci. USA, 88, 8515-8519.
56. Philonenko, E.S., Klochkov, D.B., Borunova, V.V., Gavrilov, A.A., Razin, S.V. and Iarovaia, O.V. (2009) TMEM8 - a non-globin gene entrapped in the globin web. Nucleic Acids Res., 37, 7394-7406.
57. Sutherland, H. and Bickmore, W.A. (2009) Transcription factories: gene expression in unions? Nat. Rev. Genet., 10, 457-466.
58. Faro-Trindade, I. and Cook, P.R. (2006) Transcription factories: structures conserved during differentiation and evolution. Biochem. Soc. Trans., 34, 1133-1137.
59. Motohashi, T., Miyoshi, S., Osawa, M., Eyre, H.J., Sutherland, G.R., Matsuda, Y., Nakamura, Y., Shibuya, A., Iwama, A. and Nakauchi, H. (2000) Molecular cloning and chromosomal mapping of a novel five-span transmembrane protein gene, M83. Biochem. Biophys. Res. Commun., 276, 244-250.