Genomewide identification of nuclear matrix attachment regions: An analysis of methods

Biochemical Society Transactions

Volumn 35, Issue 3, 2007, Pages 612-617

  Linnemann, A K ^a   Platts, A E ^a   Doggett, N ^b   Gluch, A ^c   Bode, J ^c   Krawetz, S A ^a  

^a WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

Author keywords

Chromosome 16; Genomic analysis; Lithium di iodosalicylic acid (LIS); Matrix attachment region; Nuclear matrix

Indexed keywords

OLIGONUCLEOTIDE; SODIUM CHLORIDE;

CHROMOSOME 16; CONFERENCE PAPER; COSMID; HUMAN CHROMOSOME; MATRIX ATTACHMENT REGION; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

BINDING SITES; CHROMOSOMES, HUMAN, PAIR 16; GENOME, HUMAN; HUMANS; NUCLEAR MATRIX; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 34250806035     PISSN: 03005127     EISSN: None     Source Type: Journal    
DOI: 10.1042/BST0350612     Document Type: Conference Paper

References (47)

1. Zbarskii, I.B. and Debov, S.S. (1951) Biokhimiia 16, 390-395
2. Berezney, R. and Coffey, D.S. (1974) Biochem. Biophys. Res. Commun. 60, 1410-1417
3. Berezney, R. and Coffey, D.S. (1976) Adv. Enzyme Regul. 14, 63-100
4. Bode, J., Goetze, S., Heng, H.H., Krawetz, S.A. and Benham, C. (2003) Chromosome Res. 11, 435-445
5. Bode, J., Benham, C., Knopp, A. and Mielke, C. (2000) Crit. Rev. Eukaryotic Gene Expression 10, 73-90
6. Martins, R.P., Ostermeier, G.C. and Krawetz, S.A. (2004) J. Biol. Chem. 279, 51862-51868
7. Farrell, C.M., West, A.G. and Felsenfeld, G. (2002) Mol. Cell. Biol. 22, 3820-3831
8. Goetze, S., Baer, A., Winkelmann, S., Nehlsen, K., Seibler, J., Maass, K. and Bode, J. (2005) Mol. Cell. Biol. 25, 2260-2272
9. Yusufzai, T.M. and Felsenfeld, G (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 8620-8624
10. Kramer, J.A., Zhang, S., Yaron, Y., Zhao, Y. and Krawetz, S.A. (1997) Genet. Test. 1, 125-129
11. Petrov, A., Pirozhkova, I., Carnac, G., Laoudj, D., Lipinski, M. and Vassetzky, Y.S. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 6982-6987
12. Yanagisawa, J., Ado, J., Nakayama, J., Kohwi, Y. and Kohwi-Shigematsu, T. (1996) Cancer Res. 56, 457-462
13. Spencer, V.A., Samuel, S.K. and Davie, J.R. (2001) Cancer Res. 61, 1362-1366
14. Schoenlein, P.V., Barrett, J.T. and Welter, D. (1999) Chromosoma 108, 121-131
15. Bode, J., Benham, C., Ernst, E., Knopp, A., Marschalek, R., Strick, R. and Strissel, P. (2000) J. Cell. Biochem. 35 (Suppl.), 3-22
16. Deppert, W. (1996) J. Cell. Biochem. 62, 172-180
17. Britanova, O., Akopov, S., Lukyanov, S., Gruss, P. and Tarabykin, V. (2005) Eur. J. Neurosci. 21, 658-668
18. Koina, E. and Piper, A. (2005) J. Cell. Biochem. 95, 391-402
19. Yaron, Y., Kramer, J.A., Gyi, K., Ebrahim, S.A.D., Evans, M.I., Johnson, M.P. and Krawetz, S.A. (1998) Int. J. Androl. 21, 13-18
20. Heng, H.H.Q., Krawetz, S.K., Lu, W., Bremer, S., Liu, G. and Ye, C.J. (2001) Cytogenet. Cell. Genet. 93, 155-161
21. Jackson, D.A., Dickinson, P. and Cook, P.R. (1990) EMBO J. 9, 567-571
22. Jackson, D.A., McCready, S.J. and Cook, P.R. (1984) J. Cell. Sci. 1 (Suppl.), 59-79
23. Berezney, R., Dubey, D.D. and Huberman, J.A. (2000) Chromosoma 108, 471-484
24. Kramer, J.A., Adams, M.D., Singh, G.B., Doggett, N.A. and Krawetz, S.A. (1998) Somat. Cell Mol. Genet. 24, 131-133
25. Liebich, I., Bode, J., Frisch, M. and Wingender, E. (2002) Nucleic Acids Res. 30, 372-374
26. Luderus, M.E., van Steensel, B., Chong, L., Sibon, O.C., Cremers, F.F. and de Lange, T. (1996) J. Cell. Biol. 135, 867-881
27. Purbowasito, W., Suda, C., Yokomine, T., Zubair, M., Sado, T., Tsutsui, K. and Sasaki, H. (2004) DNA Res. 11, 391-407
28. Kramer, J.A., Adams, M., Singh, G., Dogget, N. and Krawetz, S.A. (1998) J. Exp. Zool. 282, 245-253
29. Glazko, G.V., Koonin, E.V., Rogozin, I.B. and Shabalina, S.A. (2003) Trends Genet. 19, 119-124
30. Rudd, S., Frisch, M., Grote, K., Meyers, B.C., Mayer, K. and Werner, T. (2004) Plant Physiol. 135, 715-722
31. Platts, A.E., Quayle, A.K. and Krawetz, S.A. (2006) Cell. Mol. Biol. Lett. 11, 191-213
32. Das, A.T., Luderus, M.E. and Lamers, W.H. (1993) Eur. J. Biochem. 215, 777-785
33. Bode, J., Winkelmann, S., Gotze, S., Spiker, S., Tsutsui, K., Bi, C., Prasanth, A.K. and Benham, C. (2006) J. Mol. Biol. 358, 597-613
34. Yamamura, J. and Nomura, K. (2001) FEBS Lett. 489, 166-170
35. Fukuda, Y. (2000) Plant Mol. Biol. 44, 91-98
36. Bode, J., Schlake, T., Rios-Ramirez, M., Mielke, C., Stengert, M., Kay, V. and Klehr-Wirth, D. (1995) Int. Rev. Cytol. 162A, 389-454
37. Ma, H., Siegel, A.J. and Berezney, R. (1999) J. Cell Biol. 146, 531-542
38. Donev, R.M. (2000) Mol. Cell. Biochem. 214, 103-110
39. Sabo, P.J., Hawrylycz, M., Wallace, J.C., Humbert, R., Yu, M., Shafer, A., Kawamoto, J., Hall, R., Mack, J., Dorschner, M.O. et al. (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 16837-16842
40. Doggett, N.A., Goodwin, L.A., Tesmer, J.G., Meincke, L.J., Bruce, D.C., Clark, L.M., Altherr, M.R., Ford, A.A., Chi, H.C., Marrone, B.L. et al. (1995) Nature 377, 335-365
41. Sumer, H., Craig, J.M., Sibson, M. and Choo, K.H. (2003) Genome Res. 13, 1737-1743
42. Ioudinkova, E., Petrov, A., Razin, S.V. and Vassetzky, Y.S. (2005) Genomics 85, 143-151
43. Krawetz, S.A., Draghici, S., Goodrich, R., Liu, Z. and Ostermeier, G.C. (2005) Methods Mol. Med. 108, 439-458
44. Kay, V. and Bode, J. (1995) Methods Mol. Cell. Biol. 5, 186-194
45. 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
46. Krawetz, S.A. and Womble, D.D. (eds) (2003) Introduction to Bioinformatics: A Theoretical and Practical Approach, Humana Press Inc., Totowa
47. Strissel, P.L., Espinosa, III, R., Rowley, J.D. and Swift, H. (1996) Chromosoma 105, 122-133