Identification of base-unpairing. region-binding proteins and characterization of their in vivo binding sequences

Methods in Cell Biology

Volumn , Issue 53, 1998, Pages 323-354

  Kohwi Shigematsu, T ^a   DeBelle, I ^a   Dickinson, L A ^a   Galande, S ^a   Kohwi, Y ^a  

^a BURNHAM INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA BINDING PROTEIN;

AFFINITY CHROMATOGRAPHY; ANIMAL; CHEMISTRY; DNA BASE COMPOSITION; FORECASTING; HUMAN; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; REVIEW;

ANIMALS; BASE COMPOSITION; BASE SEQUENCE; CHROMATOGRAPHY, AFFINITY; DNA; DNA-BINDING PROTEINS; FORECASTING; HUMANS; MOLECULAR SEQUENCE DATA;

EID: 0031972490     PISSN: 0091679X     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Article

References (38)

1. Adolph, K. W. (1980). Organization of chromosomes in HeLa cells: Isolation of histone-depleted nuclei and nuclear scaffolds. J. Cell Sei. 42, 291-304.
2. Adolph, K. W., Cheng, S. M. and Laemmli, U. K. (1977). Role of nonhistone proteins in metaphase chromosome structure. Cell (Cambridge, Mass.) 12, 805-816.
3. Altschul, S. F., Gish, W., Miller, W., Meyers, E. W., and Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
4. Alvarez, J. D. et al. (1997). In preparation.
5. Benyajati, C, and Worcel, A. (1976). Isolation, characterization, and structure of the folded interphase genome of Drosophila melanogaster. Cell (Cambridge, Mass.) 9, 393-407.
6. Bode, J., and Maass, K. (1988). Chromatin domain surrounding the human interferon-/3 gene as defined by scaffold-attached regions. Biochemistry 27, 4706-4711.
7. Bode, J., Kohwi, Y., Dickinson, L., Job, T., Klehr, D., Mielke, C, and Kohwi-Shigematsu, T. (1992). Biological significance of unwinding capability of nuclear matrix-associating DNAs. Science 255, 195-197.
8. Cockerill, P. N., and Garrard, W. T. (1986). Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites. Cell (Cambridge, Mass.) 44, 273-282.
9. Cockerill, P. N., Yuen, M.-H., and Garrard, W. T. (1987). The enhancer of the immunoglobulin heavy chain locus is flanked by presumptive chromosomal loop anchorage elements. J. Biol. Cliem. 262, 5394-5397.
10. Cook, P. R., and Brazell, I. A. (1978). Spectrofluorometric measurement of the binding of ethidium to supcrcoiled DNA from cell nuclei. Ear. J. Biochem. 84, 465-477.
11. deBelle, I., Cai, S., and Kohwi-Shigematsu, T. (1997). The genomic sequences bound to SATB1 in vivo in T cells are tightly associated with the nuclear matrix at the bases of the chromatin loops. Submitted for publication.
12. Dickinson, L. A., and Kohwi-Shigematsu, T. (1995). Nucleolin is a matrix attachment region DNAbinding protein that specifically recognizes a region with high base-unpairing potential. Mol. Cell. Biol. 15, 456-465.
13. Dickinson, L. A., Joh, T., Kohwi, Y., and Kohwi-Shigematsu, T. (1992). A tissue-specific MAR/SAR DNA-binding protein with unusual binding site recognition. Cell 70, 631-645.
14. Ekker, S. C, Young, K. E., von Kassier, D. P., and Beachy, P. A. (1991). Optimal DNA sequence recognition by the Ultrabithorax homeodomain of Drosopliila. EMBO J. 10, 1179-1186.
15. Forrester, W. C., van Genderen, C., Jenuwein, T., and Grosschedl, R. (1994). Dependence of enhancer-mediated transcription of the immunoglobulin fj. gene on nuclear matrix attachment regions. Science 265, 1221-1225.
16. Gasser, S. M., and Laemmli, U. K. (1987). A glimpse at chromosomal order. Trends Genet. 3,16-22.
17. Gerdes, M. G., Carter, K. C, Moen, P. T., Jr., and Lawrence, J. B. (1994). Dynamic changes in the higher-level chromatin organization of specific sequences revealed by m Vu hybridization to nuclear halos. J. Cell Biol. 126, 289-304.
18. Herrscher, R. F., Kaplan, M. H., Lelsz, D. L., Das, C, Scheurmann, R., and Tucker, P. W. (1995). The immunoglobulin heavy-chain matrix-associating regions are bound by Bright: A B cell-specific /ram-activator that describes a new DNA-binding protein family. Genes Dev. 9, 3067-3082.
19. Igo-Kemenes, T., and Zachau, H. R. (1978). Domains in chromatin structure. Cold Spring Harbor Symp. Quant. Biol. 42, 109-118
20. Jordan, G. (1987). At the heart of the nucloelus. Nature (London) 329, 489-490.
21. Kadonaga, J. T., and Tjian, R. (1986). Affinity purification of sequence-specific DNA binding proteins. Proc. Natl. Acad. Sei. U.S.A. 83, 5889-5893.
22. Kohwi-Shigematsu, T., and Kohwi, Y. (1990). Torsional stress stabilizes extended base unpairing in suppressor sites flanking immunoglobulin heavy chain enhancer. Biochemistry 29, 9551-9560.
23. Kohwi-Shigematsu, T., and Kohwi, Y. (1992). Detection of non-B DNA structures at specific sites in supercoiled plasmid DNA and chromatin with haloacetaldehyde and diethylpyrocarbonate. In "Methods in Enzymology" (D. M. Lilley and J. E. Dahlberg, eds.), vol. 212, pp. 155-180. Academic Press, San Diego, CA.
24. Lebkowski, J. S., and Laemmli, U. K. (1982a). Evidence for two levels of DNA folding in histonedepleted HeLa interphase nuclei. J. Mol. Biol. 156, 309-324.
25. Lebkowski, J. S., and Laemmli, U. K. (1982b). Nonhistone proteins and long range organization of HeLa interphase DNA. J. Mol. Biol. 156, 325-344.
26. Leonard, N. J. (1992). Etheno-bridged nucleotides in structural diagnosis and carcinogenesis. Chemtracts-Biochem. Molec. Biol. 3, 273-297.
27. 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 (Cambridge, Mass.) 9, 23-232.
28. Nakagomi, K., Kohwi, Y., Dickinson, L. A., and Kohwi-Shigematsu, T. (1994). A novel DNAbinding motif in the nuclear matrix attachment DNA-binding protein SATB1. Mol. Cell. Biol. 14, 1852-1860.
29. Nelson, W. G., Pienta, K. J., Barrack, E. R., and Coffey, D. S. (1986). The role of the nuclear matrix in the organization and function of DNA. Annit. Rev. Biophys. Chem. 15, 457-475.
30. Orlando, V., and Paro, R. (1993). Mapping polycomb-repressed domains in the bithorax complex using in vivo formaldehyde cross-linked chromatin. Cell (Cambridge, Mass.) 75,1187-1198.
31. Paulson, J. R., and Laemmli, U. K. (1977). The structure of histone-depleted metaphase chromosomes. Cell (Cambridge, Mass.) 12, 817-828
32. Penman, S. (1995). Rethinking cell structure. Proc. Nail. Acad. Sei. U.S.A. 92, 5251-5257.
33. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989). "Molecular Cloning: A Laboratory Manual," 2nd ed. Cold Spring Harbor Lab. Press, Cold Spring Harbor, NY.
34. Singh, H., Lebowitz, J. H., Baldwin, A. S., Jr., and Sharp, P. A. (1988). Molecular cloning of an enhancer binding protein: Isolation by screening of an expression library with a recognition site DNA. Cell (Cambridge, Mass.) 52, 415-423.
35. Solomon, M. J., and Varshavsky, A. (1985). Formaldehyde-mediated DNA-protein crosslinking: A probe for in vivo chromatin structures. Proc. Natl. Acad. Sei. U.S.A. 82, 6470-6474.
36. Vogelstein, B., Pardoll, D. M., and Coffey, D. S. (1980). Supercoiled loops and eucaryotic DNA replication. Cell 22, 79-85.
37. Wang, B., Dickinson, L. A., Koivunen, E., Ruoslahti, E., and Kohwi-Shigematsu, T. (1.995). A novel matrix attachment region DNA binding motif identified using a random phage peptide library. J. Biol. Chem. 270, 23239-23242.
38. Yanagisawa, J., Ando, J., Nakayama, J., Kohwi, Y. and Kohwi-Shigematsu, T. (1996). A matrix attachment region (MAR)-binding activity due to a pi 14 kilodalton protein is found only in human breast carcinomas and not in normal and benign breast disease tissues. Cancer Res. 56, 457-462.