Scaffold/matrix attachment regions and intrinsic DNA curvature

Biochemistry (Moscow)

Volumn 71, Issue 5, 2006, Pages 481-488

  Fiorini, A ^a   Gouveia, F De S ^a   Fernandez, M A ^a  

^a STATE UNIVERSITY OF MARINGÁ   (Brazil)

Author keywords

In silico prediction; Intrinsically bent DNA; Nuclear matrix; Nuclear scaffold; S MARs

Indexed keywords

CARBOXYLIC ACIDS; CHROMOSOMES; PROTEINS;

IN SILICO PREDICTION; INTRINSICALLY BENT DNA; NUCLEAR MATRIX; NUCLEAR SCAFFOLD; S/MARS;

DNA;

DNA; HETERODUPLEX;

ANIMAL; CHEMISTRY; CHROMATIN; CONFORMATION; GENETICS; HUMAN; MATRIX ATTACHMENT REGION; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN BINDING; REVIEW;

ANIMALS; BASE SEQUENCE; CHROMATIN; DNA; HUMANS; MATRIX ATTACHMENT REGIONS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HETERODUPLEXES; PROTEIN BINDING;

EID: 33744530331     PISSN: 00062979     EISSN: 16083040     Source Type: Journal    
DOI: 10.1134/S0006297906050038     Document Type: Article

References (118)

1. Bode, J., Goetze, S., Heng, H., Krawetz, S. A., and Benham, C. (2003) Chromosome Res., 11, 435-445.
2. Gasser, S. M., and Laemmli, U. K. (1986) Cell, 46, 521-530.
3. Berezney, R. (1991) J. Cell. Biochem., 47, 109-123.
4. Hozak, P., Sasseville, A. M., Raymond, Y., and Cook, P. R. (1995) J. Cell. Sci., 108, 635-644.
5. Cockerill, P. N., and Garrard, W. T. (1986) FEBS Lett., 204, 5-7.
6. Paulson, J. R., and Laemmli, U. K. (1977) Cell, 12, 817-828.
7. Mirkovitch, J., Mirault, M. E., and Laemmli, U. K. (1984) Cell, 39, 223-232.
8. Bode, J., Schlake, T., Rios-Ramirez, M., Mielke, C., Stengert, M., Kay, V., and Klehr-Wirth, D. (1995) Int. Rev. Cytol., 162A, 389-454.
9. Razin, S. V., Gromova, I. I., and Iarovaia, O. V. (1995) Int. Rev. Cytol., 162B, 405-448.
10. Farache, G., Razin, S. V., Rzeszowska-Wolny, J., Moreau, J., Targa, F. R., and Scherrer, K. (1990) Mol Cell. Biol., 10, 5349-5358.
11. Iarovaia, O. V., Akopov, S. B., Nikolaev, L. G., Sverdlov, E. D., and Razin, S. V. (2005) Nucleic Acids Res., 33, 4157-4163.
12. Adachi, Y., Kas, E., and Laemmli, U. K. (1989) EMBO J., 8, 3997-4006.
13. Berrios, M., Osheroff, N., and Fisher, P. A. (1985) Proc. Natl. Acad. Sci. USA, 82, 4142-4146.
14. Earnshaw, W. C., Halligan, B., Cooke, C. A., Heck, M. M., and Liu, L. F. (1985) J. Cell Biol., 100, 1706-1715.
15. Iarovaia, O., Hancock, R., Lagarkova, M., Miassod, R., and Razin, S. V. (1996) Mol. Cell. Biol., 16, 302-308.
16. Razin, S. V. (2001) Cell. Mol. Biol. Lett., 6, 59-69.
17. Lewis, C. D., and Laemmli, U. K. (1982) Cell, 29, 171-181.
18. Izaurralde, E., Mirkovitch, J., and Laemmli, U. K. (1988) J. Mol. Biol., 200, 111-125.
19. Kramer, J. A., and Krawetz, S. A. (1996) J. Biol. Chem., 271, 11619-11622.
20. Maya-Mendoza, A., and Aranda-Anzaldo, A. (2003) Analyt. Biochem., 313, 196-207.
21. Ostermeier, G. C., Liu, Z., Martins, R. P., Bharadwaj, R. R., Ellis, J., Draghici, S., and Krawetz, S. A. (2003) Nucleic Acids Res., 31, 3257-3266.
22. Gerdes, M. G., Carter, K. C., Moen, P. T., Jr., and Lawrence, J. B. (1994) J. Cell Biol., 126, 289-304.
23. Heng, H. H., Goetze, S., Ye, C. J., Liu, G., Stevens, J. B., Bremer, S. W., Wykes, S. M., Bode, J., and Krawetz, S. A. (2004) J. Cell Sci., 117, 999-1008.
24. Iarovaia, O. V., Shkumatov, P., and Razin, S. V. (2004) J. Cell Sci., 117, 4583-4590.
25. Ioudinkova, E., Petrov, A., Razin, S. V., and Vassetzky, Y. S. (2005) Genomics, 85, 143-151.
26. http://www.ncbi.nlm.nih.gov
27. www.ebi.ac.uk/embl/
28. http://www.ddbj.nig.ac.jp
29. Chinn, A. M., and Comai, L. (1996) Plant. Mol. Biol., 32, 959-968.
30. Whitelaw, C. B., Grolli, S., Accornero, P., Donofrio, G., Farini, E., and Webster, J. (2000) Gene, 244, 73-80.
31. Loc, P. V., and Stratling, W. H. (1988) EMBO J., 7, 655-664.
32. Jarman, A. P., and Higgs, D. R. (1989) Progr. Clin. Biol. Res., 316B, 33-45.
33. Borunova, V., Iarovaia, O. V., Vassetzky, Y. S., and Razin, S. V. (2005) FEBS Lett., 579, 4746-4750.
34. Deppert, W (1996) J. Cell. Biochem., 62, 172-180.
35. Kramer, J. A., and Krawetz, S. A. (1996) J. Biol. Chem., 271, 11619-11622.
36. Fernandez, M. A., Baron, B., Prigent, M., Toledo, F., Buttin, G., and Debatisse, M. (1997) J. Cell. Biochem., 67, 541-551.
37. Fukuda, Y., and Nishikawa, S. (2003) Plant Mol. Biol., 51, 665-675.
38. Boulikas, T. (1996) J. Cell. Biochem., 60, 297-316.
39. Hornberger, H. P. (1989) Chromosoma (Berl.), 98, 99-104.
40. Razin, S. V., Kekelidze, M. G., Lukanidin, E. M., Scherrer, K., and Georgiev, G. P. (1986) Nucleic Acids Res., 14, 8189-8207.
41. Dijkwel, P. A., and Hamlin, J. L. (1988) Mol. Cell. Biol., 8, 5398-5409.
42. Gasser, S. M., Amati, B. B., Cardenas, M. E., and Hofmann, J. F. (1989) Int. Rev. Cytol., 119, 57-96.
43. Phi-Van, L., von Kries, J. P., Ostertag, W., and Stratling, W. H. (1990) Mol. Cell. Biol., 10, 2302-2307.
44. Razin, S. V., Vassetzky, Y. S., and Hancock, R. (1991) Biochem. Biophys. Res. Commun., 177, 265-270.
45. Roberge, M., and Gasser, S. M. (1992) Mol. Microbiol., 6, 419-423.
46. Mesner, L. D., Hamlin, J. L., and Dijkwel, P. A. (2003) Proc. Natl. Acad. Sci. USA, 100, 3281-3286.
47. Brun, C., Dang, Q., and Miassod, R. (1990) Mol. Cell. Biol., 10, 5455-5463.
48. Lim, H. S., Kim, M. S., Park, J. Y., Choi, K. E., Hwang, J. Y., Kim, D. S., and Lee, H. H. (2002) Mol. Cells, 13, 185-193.
49. Sykes, R. C., Lin, D., Hwang, S. J., Framson, P. E., and Chinault, A. C. (1988) Mol. Gen. Genet., 212, 301-309.
50. Chen, Y., Zhao, M., Li, Z. P., and He, M. L. (2002) Biochem. Biophys. Res. Commun., 299, 723-729.
51. Nepveu, A. (2001) Gene, 270, 1-15.
52. Townson, S. M., Sullivan, T., Zhang, Q., Clark, G. M., Osborne, C. K., Lee, A. V., and Oesterreich, S. (2000) Clin. Cancer Res., 6, 3788-3796.
53. Yamamura, J., and Nomura, K. (2001) FEBS Lett., 489, 166-170.
54. Kramer, J. A., and Krawetz, S. A. (1995) Mamm. Genome, 6, 677-679.
55. Walter, W. R., Singh, G. B., and Krawetz, S. A. (1998) Biochem. Biophys. Res. Commun., 242, 419-422.
56. Gale, K. C., and Osheroff, N. (1992) J. Biol. Chem., 267, 12090-12097.
57. Nobile, C., Toffolatti, L., Rizzi, F., Simionati, B., Nigro, V., Cardazzo, B., Patarnello, T., Valle, G., and Danieli, G. A. (2002) Hum. Genet., 110, 418-421.
58. Iarovaia, O. V., Bystritskiy, A., Ravcheev, D., Hancock, R., and Razin, S. V. (2004) Nucleic Acids Res., 32, 2079-2086.
59. McNaughton, J. C., Cockburn, D. J., Hughes, G., Jones, W. A., Laing, N. G., Ray, P. N., Stockwell, R A., and Petersen, G. B. (1998) Gene, 222, 41-51.
60. Berezney, R., and Coffey, D. S. (1974) Biochem. Biophys. Res. Commun., 60, 1410-1417.
61. Kas, E., Izaurralde, E., and Laemmli, U. K. (1989) J. Mol. Biol., 210, 587-599.
62. Singh, G. B., Kramer, J. A., and Krawetz, S. A. (1997) Nucleic Acids Res., 25, 1419-1425.
63. Glazko, G. V., Rogozin, I. B., and Glazkov, M. V. (2001) Biochim. Biophys. Acta, 1517, 351-364.
64. Frisch, M., Frech, K., Klingenhoff, A., Cartharius, K., Liebich, I., and Werner, T. (2002) Genome Res., 12, 349-354.
65. Krawetz, S. A., Draghici, S., Goodrich, R., Liu, Z., and Charles Ostermeier, G. (2004) Meth. Mol. Med., 108, 439-458.
66. Bates, A. D., and Maxwell, A. (2005) DNA Topology, Oxford University Press, Oxford.
67. Anderson, J. N. (1986) Nucleic Acids Res., 14, 8513-8533.
68. Eckdahl, T. T., and Anderson, J. N. (1987) Nucleic Acids Res., 15, 8531-8545.
69. Laundon, C. H., and Griffith, J. D. (1987) Biochemistry, 26, 3759-3762.
70. Lindemose, S., Nielsen, P. E., and Mollegaard, N. E. (2005) Nucleic Acids Res., 33, 1790-1803.
71. Trifonov, E. N., and Sussman, J. L. (1980) Proc. Natl. Acad. Sci. USA, 77, 3816-3820.
72. Levene, S. D., and Crothers, D. M. (1983) J. Biomol. Struct. Dyn., 1, 429-435.
73. Young, M. A., and Beveridge, D. L. (1998) J. Mol. Biol., 281, 675-687.
74. Bolshoy, A., McNamara, P., Harrington, R. E., and Trifonov, E. N. (1991) Proc. Natl. Acad. Sci. USA, 88, 2312-2316.
75. Marini, J. C., Levene, S. D., Crothers, D. M., and Englund, P. T. (1982) Proc. Natl. Acad. Sci. USA, 79, 7664-7668.
76. Stellwagen, E., Lu, Y., and Stellwagen, N. C. (2005) Nucleic Acids Res., 33, 4425-4432.
77. Stellwagen, N. C. (1983) Biochemistry, 22, 6186-6193.
78. Calladine, C. R., Collis, C. M., Drew, H. R., and Mott, M. R. (1991) J. Mol. Biol., 221, 981-1005.
79. Wu, H. M., and Crothers, D. M. (1984) Nature, 308, 509-513.
80. Fiorini, A., Basso, L. R., Jr., Paco-Larson, M. L., and Fernandez, M. A. (2001) J. Cell. Biochem., 83, 1-13.
81. Calladine, C. R., Drew, H. R., and McCall, M. J. (1988) J. Mol. Biol., 201, 127-137.
82. Diekmann, S., and Lilley, D. M. (1987) Nucleic Acids Res., 15, 5765-5774.
83. Barbic, A., Zimmer, D. P., and Crothers, D. M. (2003) Proc. Natl. Acad. Sci. USA, 100, 2369-2373.
84. Ohyama, T., and Kusakabe, T. (1993) Analyt. Biochem., 212, 287-289.
85. Bode, J., Stengert-Iber, M., Kay, V., Schlake, T., and Dietz-Pfeilstetter, A. (1996) Crit. Rev. Eukaryot. Gene Expr., 6, 115-138.
86. Snyder, M., Buchman, A. R., and Davis, R. W. (1986) Nature, 324, 87-89.
87. Von Kries, J. P., Phi-Van, L., Diekmann, S., and Stratling, W. H. (1990) Nucleic Acids Res., 18, 3881-3885.
88. Razin, S. (1992) FEMS Microbiol. Lett., 79, 423-431.
89. Boulikas, T. (1993) J. Cell. Biochem., 52, 14-22.
90. Du, C., Sanzgiri, R. P., Shaiu, W.-L., Choi, J.-K., Hou, Z., Benbow, R. M., and Dobbs, D. L. (1995) Nucleic Acids Res., 23, 1766-1774.
91. Fukuda, Y (1999) Plant Mol. Biol., 39, 1051-1062.
92. Fukuda, Y. (2000) Plant Mol. Biol., 44, 91-98.
93. Avramova, Z., Tikhonov, A., Chen, M., and Bennetzen, J. L. (1998) Nucleic Acids Res., 26, 761-767.
94. Linial, M., and Shlomai, J. (1988) Nucleic Acids Res., 16, 6477-6492.
95. Welter, C., Dooley, S., Zang, K. D., and Biln, N. (1989) Nucleic Acids Res., 17, 6077-6086.
96. Hagerman, P. J. (1990) Annu. Rev. Biochem., 59, 755-781.
97. Milot, E., Belmaaza, A., Wallenburg, J. C., Gusew, N., Bradley, W. E., and Chartrand, P. (1992) EMBO J., 11, 5063-5070.
98. Kim, Y., Geiger, J. H., Hahn, S., and Sigler, P. B. (1993) Nature, 365, 512-520.
99. Perez-Martin, J., Rojo, F., and de Lorenzo, V. (1994) Microbiol. Rev., 58, 268-290.
100. Perez-Martin, J., and de Lorenzo, V. (1997) Annu. Rev. Microbiol., 51, 593-628.
101. De Souza, O. N., and Ornstein, R. L. (1998) Biopolymers, 46, 403-415.
102. Altman, A. L., and Fanning, E. (2004) Mol. Cell. Biol., 24, 4138-4150.
103. Izaurralde, E., Kas, E., and Laemmli, U. K. (1989) J. Mol. Biol., 210, 573-585.
104. Dickinson, L. A., Joh, T., Kohwi, Y., and Kohwi-Shigematsu, T. (1992) Cell, 70, 631-645.
105. Romig, H., Fackelmayer, F. O., Renz, A., Ramsperger, U., and Richter, A. (1992) EMBO J., 11, 3431-3440.
106. Lobov, I. B., Tsutsui, K., Mitchell, A. R., and Podgornaya, O. I. (2001) J. Cell. Biochem., 83, 218-229.
107. Camilloni, G., Caserta, M., Amadei, A., and Di Mauro, E. (1991) Biochim. Biophys. Acta, 1129, 73-82.
108. Howard, M. T., Lee, M. P., Hsieh, T. S., and Griffith, J. D. (1991) J. Mol. Biol., 217, 53-62.
109. Hibino, Y., Nakamura, K., Tsukada, S., and Sugano, N. (1993) Biochim. Biophys. Acta, 1174, 162-170.
110. Churchill, M. E., Jones, D. N., Glaser, T., Hefner, H., Searles, M. A., and Travers, A. A. (1995) EMBO J., 14, 1264-1275.
111. Atlung, T., and Ingmer, H. (1997) Mol. Microbiol., 24, 7-17.
112. Bechert, T., Diekmann, S., and Arndt-Jovin, D. J. (1994) J. Biomol. Struct. Dyn., 12, 605-623.
113. Buzas, Z., and Boldogkoi, Z. (1999) Electrophoresis, 20, 2838-2840.
114. Griess, E. A., Rensing, S. A., Grasser, K. D., Maier, U. G., and Feix, G. (1993) J. Mol. Evol., 37, 204-210.
115. Kneidl, C., Dinkl, E., and Grummt, F. (1995) Plant Mol. Biol., 27, 705-713.
116. Pemov, A., Bavykin, S., and Hamlin, J. L. (1998) Proc. Natl. Acad. Sci. USA, 95, 14757-14762.
117. Brylawski, B. P., Cohen, S. M., Cordeiro-Stone, M., Schell, M. J., and Kaufman, D. G. (2000) Crit. Rev. Eukaryot. Gene Expr., 10, 91-99.
118. Fiorini, A., Gouveia, F. de S., Soares, M. A. de M., Stocker, A. J., Ciferri, R. R., and Fernandez, M. A. (2006) Mol. Biol. Rep., in press.