Abstract
In the nucleus of eukaryotic cells, DNA is packaged into a nucleoprotein complex known as chromatin (1). This complex provides the compaction and structural organization of the DNA for processes such as replication, transcription, recombination, and repair. The highly compact structure of chromatin does not only restrict the access of DNA to enzymes and regulating factors, it can even act as an activating principle bringing distant DNA-protein binding sites into close proximity.
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References
Wolffe, A. (1992) In Chromatin: Structure and Function. Academic Press, London and New York.
Kladde, M. P., Xu, M., and Simpson, R. T. (1997) Direct study of DNA-protein interactions in repressed and active chromatin in living cells. EMBO J. 15, 6290–6300.
Thoma, F. and Sogo, J. M. (1988) In Chromosomes and Chromatin. CRC Press, Boca Raton, FL, pp. 85–107.
Sogo, J. M. and Thoma, F. (1989) In Methods in Enzymology (Wassermann, P. M. and Kornberg, R. D., eds.), 170, pp. 142–165.
Lucchini, R. and Sogo, J. M. (1998) Transcription of ribosomal RNA genes by eukaryotic RNA polymerase I (Paule, M. R., ed.) Landes Bioscience, pp. 255–276.
Hanson, C., Shen, C., and Hearst, J. (1976) Cross-linking of DNA in situ as a probe for chromatin structure. Science 193, 62–64.
Conconi, A., Losa, R., Koller, T., and Sogo, J. (1984) Psoralen-crosslinking of soluble and of H1-depleted soluble rat liver chromatin. J. Mol. Biol. 178, 920–928.
Sogo, J., Stahl, H., Koller, T., and Knippers, R. (1986) Structure of replicating simian virus 40 minichromosomes. The replication fork, core histone segregation and terminal structures. J. Mol. Biol. 189, 189–204.
Widmer, R. M., Koller, T., and Sogo, J. M. (1988) Analysis of the psoralen-crosslinking pattern in chromatin DNA by exonuclease digestion. Nucleic Acids Res. 16, 7013–7024.
Gasser, R., Koller, T., and Sogo, J. M. (1996) The stability of nucleosomes at the replication fork. J. Mol. Biol., 258, 224–239.
Sogo, J. M. and Lasky, R. A. (1995) In Chromatin Structure and Gene Expression (Elgin, S., ed.), Oxford University Press, pp. 49–70.
Conconi, A., Widmer, R., Koller, T., and Sogo, J. (1989) Two different chromatin structures coexist in ribosomal RNA genes throughout the cell cycle. Cell 57, 753–761.
Sargan, D. and Butterworth, P. (1982) Eukaryotic ternary transcription complexes. II. An approach to the determination of chromatin conformation at the site of transcription. Nucleic Acids Res. 10, 4655–4669.
De Bernardin, W., Koller, T., and Sogo, J. (1986) Structure of in-vivo transcribing chromatin as studied in simian virus 40 minichromosomes. J. Mol. Biol. 191, 469–482.
Gruss, C., Wu, J., Koller, T., and Sogo, J. M. (1993) Disruption of the nucleosomes at the replication fork. EMBO J. 12, 4533–4545.
Zhen, W.-P., Buchardt, O., Nielsen, H., and Nielsen, P. E. (1986) Site-specificity of psoralen-DNA interstrand cross-linking determined by nuclease Bal31 digestion. Biochemistry 25, 6598–6603.
Ostrander, E. A., Karty, R. A., and Hallick, L. M. (1988) High resolution psoralen mapping reveals an altered DNA helical structure in the SV 40 regulatory region. Nucleic Acids Res. 16, 212–227.
Kochel, T. J. and Sinden, R. R. (1989) Hyperreactivity of B-Z junctions to 4,5′,8-trimethylpsoralen photobinding assayed by an exonuclease III/photoreversal mapping procedure. J. Mol. Biol. 205, 91–102.
Thoma, F. (1986) Protein-DNA interactions and NSRs determine nucleosome positions on yeast plasmid chromatin. J. Mol. Biol. 190, 177–190.
Tanaka, S., Livingstone, M., and Thoma, F. (1996) Chromatin structure of the yeast URA3 gene at high resolution provides insight into structure and positioning of nucleosomes in the chromosomal context. J. Mol. Biol. 257, 919–934.
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© 1999 Humana Press Inc.
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Wellinger, R.E., Lucchini, R., Dammann, R., Sogo, J.M. (1999). In Vivo Mapping of Nucleosomes Using Psoralen-DNA Crosslinking and Primer Extension. In: Becker, P.B. (eds) Chromatin Protocols. Methods in Molecular Biology™, vol 119. Humana Press. https://doi.org/10.1385/1-59259-681-9:161
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DOI: https://doi.org/10.1385/1-59259-681-9:161
Publisher Name: Humana Press
Print ISBN: 978-0-89603-665-9
Online ISBN: 978-1-59259-681-2
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