Abstract
The structure of transcribing chromatin was studied by DNA-DNA and DNA-RNA photocrosslinking with psoralen. In the hyperactive ribosomal genes of Dictyostelium discoideum and Physarum polycephalum, no nucleosomes could be detected within the coding region. Two distinct types of ribosomal chromatin co-exist in Friend cells, one that contains nucleosomes which represent the inactive gene copies, and the other one which is free of nucleosomes and corresponds to the actively transcribed genes. In contrast, transcribing SV40 minichromosomes appeared quite similar to the bulk of minichromosomes. Nucleosomes or nucleosome-like structures appeared close to the sites of RNA synthesis. We propose that the association of histones with DNA does not prevent transcription elongation by RNA polymerase II on SV40 minichromosomes.
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References
Allegra, P., Steiner, R., Clayton, D.F. and Allfrey, V.G.: ‘Affinity chromatographic purification of nucleosomes containing transcriptionally active DNA sequences’. J.Mol.Biol., 196, 379–388 (1987).
Barsoum, J. and Varshavsky, A.: ‘Preferential localization of variant nucleosomes near the 5`end of the mouse dihydroflate reductase gene’. J.Biol. Chem. 260s, 7688–7697.
Björkroth, B., Ericsson, C., Lamb, M.M. and Daneholt, B.: ‘Structure of the chromatin axis during transcription’. Chromosoma (Berl.) 96, 333–340 (1988).
Butler, P.J.B.: ‘The folding of chromatin’. CRC Critical Reviews in Biochemistry 15, 57–91 (1983).
Carlson, J.O., Pfenninger, O., Sinden, R.R., Lehman, J.M. and Pettijohn, D.E.: ‘New procedure using a psoralen derivate for analysis of nucleosome associated DNA sequences in chromatin of living cells’. Nucl.Acids Res. 10, 2043–2063 (1982).
Cech, T.R. and Karrer, K.M.: ‘Chromatin structure of the ribosomal RNA genes of Tetrahymena thermophila as analyzed by trimethylpsoralen crosslinking “in vivo”’. J.Mol.Biol. 136, 395–416 (1980).
Chen, T.A., and Allfrey, V.G.: ‘Rapid and reversible changes in nucleosome structure accompany the activation, repression and superinduction of murine fib roblast protonco genes c-fos and c-myc’. Proc. Natl.Acad.Sci.USA 84, 5252–5256 (1987).
Conconi, A., Losa, R., Koller, Th. and Sogo, J.M.: ‘Psoralen- crosslinking of soluble and HI-depleted soluble rat liver chromatin’. J.Mol.Biol. 178, 920–928 (1984).
Culotta, V. and Sollner-Webb, B.: ‘Sites of topoisomerase I action on X. laevis ribosomal chromatin: Transcriptionally active rDNA has an 200 bp repeating structure’. Cell 52, 585–597 (1988).
Davis, A.M., Rendelhuber, T.L. and Garrard, W.T.: ‘Variegated chromatin structures of mouse ribosomal RNA genes’. J.Mol.Biol. 167, 133–155 (1983).
De Bernardin, W., Koller Th. and Sogo, J.M.: ‘Structure of “in vivo” transcribing chromatin as studied in SV40 minichromosomes’. J.Mol.Biol. 191, 469–482 (1986).
Ferris, P.J.: ‘Nucleotide sequence of the central non-transcribed spacer region of Physarum polycephalum rDNA’. Gene 39, 203–211.
Gariglio, P., Llopis, R., Oudet, P. and Chambon, P.: ‘The template of the isolated native simian virus 40 transcriptional complexes in a minichromosome’. J.Mol.Biol. 131, 75–105 (1979).
Homberger, H. and Koller, Th.: ‘The integrity of the histone-DNA complex in chromatin fibres is not necessary for the maintenance of the shape of mitotic chromosomes’. Chromosoma (Berl.) 96, 197–204 (1988).
Hanson, C.V., Shen, C.J. and Hearst, J.E.: ‘Cross-linking of DNA “in situ” as a probe for chromatin structure’. Science 193, 62–64 (1976).
Johnson, E.M., Sterner, R. and Allfrey, V.G.: ‘Altered nucleosomes of active nucleolar chromatin contain accessible histone H3 in its hyperacetylated forms’. J.Biol.Chem. 262, 6943–6946 (1987).
Judelson, H.S. and Vogt, V.M.: ‘Accessibility of ribosomal genes to trimethyl psoralen in nuclei of Physarum polycephalum’. Mol.Cell.Biol. 2, 211–220 (1982).
Kim, S.-H., Peckler, S., Graves, B., Kanne, D., Rapoport, H. and Hearst, J.E.: ‘Sharp kink of DNA at psoralen-crosslink site deduced from crystal structure of psoralen-thymine monoadduct’. Cold Spring Harbor Symp.Quant.Biol. 47, 361–365 (1982).
Labhart, P. and Koller, Th.: ‘Structure of the active nucleolar chromatin of Xenopus laevis oocytes’. Cell 28, 279–292 (1982).
Levi, A. and Noll, M.: ‘Chromatin fine structure of active and repressed genes’. Nature 289, 198–203 (1981).
Lucchini, R., Pauli, U., Braun, R. and Koller, Th.: ‘Structure of the extrachromosomal ribosomal RNA chromatin of Physarum polycephalum’. J.Mol.Biol. 196, 829–843 (1987).
Llopis, R., Perrin, F., Bellard, F. and Gariglio, P.: ‘Quantitation of transcribing native SV40 minichromsomes extracted from CV1 cells late in infection’ J.Virol. 38, 82–90 (19821).
Marzluff, W. and Huang, R.C.C, R.C.C.: ‘Transcription of RNA in isolated nuclei. Transcription and translation. A practical approach’. Ed. by B.D. Hames and S.J. Higgins. IRL Press. 89–129 (1984).
McKnight, S.L., Bustin, M. and Miller, O.L., Jr.: ‘Electron microscopic analysis of chromosome metabolism in the Drosophila melanogaster embryo’. Cold Spring Harbor Symp.Quant.Biol. 42, 741–754 (1978).
Ness, P.J., Labhart, P., Banz, E., Koller, Th. and Parish, R.W.: ‘Chromatin structure along the ribosomal DNA in Dictyostelium’. J.Mol.Biol. 166, 361–381 (1983).
Ness, P.J., Koller, Th. and Thoma, F.: ‘Topoisomerase I cleavage sites identified and mapped in the chromatin of Dictyostelium ribosomal RNA genes’. J.Mol.Biol. 200, 127–139 (1988).
Ohlenbusch, H.H., Olivera, B.M., Tuan, D. and Davidson, N.: ‘Selective dissociation of histones from calf thymus nucleoprotein’. J.Mol.Biol. 25, 299–315 (1967).
Pederson, D.S., Thoma, F. and Simpson, R.: ‘Core particle, fiber and transcriptionally active chromatin structure’. Ann.Rev. of Cell Biol. 2, 117–147 (1986).
Petryaniak, B. and Lutter, L.C.: ‘Topological characterization of the simian virus 40 transcription complex’. J.Mol.Biol. 48, 289–295 (1987).
Sargan, D.R. and Butterworth, P.H.W.: ‘Eukaryotic ternary transcription complexes: Transcription complexes of RNA polymerase II are associated with histone-containing, nucleosome-like particles “in vivo”’. Nucl.Acids Res. 13, 3805–3822 (1985).
Scheer, U.: ‘Changes of nucleosome frequency in nucleolar and non-nucleolar chromatin as a function of transcription: An electron microscope study’. Cell 13, 535–549 (1978).
Shen, C.-K.J. and Hearst, J.E.: ‘Photochemical crosslinking of transcription complexes with psoralen. I. Covalent attachment of in vitro SV40 nascent RNA to its double-stranded DNA template’. Nucl.Acids Res. 5, 1429–1441 (1978).
Sinden, R.R. and Hagemann, P.J.: ‘Interstrand psoralen crosslinks do not introduce appreciable bends in DNA’. Biochem. 23, 6299–6303 (1984).
Sogo, J.M., Ness, P.J., Widmer, R.M., Parish, R.W. and Koller, Th.: ‘Psoralen crosslinking of DNA as a probe for the structure of active nucleolar chromatin’. J.Mol.Biol. 178, 897–928 (1984).
Sogo, J.M., Stahl, H., Koller, Th. and Knippers, R.: ‘Structure of replicating simian virus 40 minichromosomes. The replication fork, core histone segregation and terminal structures’. J.Mol.Biol. 189, 189–204 (1986).
Solomon, M.J., Larsen, P.L. and Varshavsky, A.: ‘Mapping protein-DNA interactions “in vivo” with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene’. Cell 53, 937–947 (1988).
Sterner, R., Boffa, L.C., Chen, T.A. and Allfrey, V.G.: ‘Cell cycle-dependent changes in conformation of nucleosomes containing human histone genes sequences’. Nucl.Acids Res. 15, 4375–4391 (1987).
Thoma, F. and Sogo, J.M, J.M.: ‘Structures of bulk and transcriptionally active chromatin revealed by electron microscopy’. Chromosomes and Chromatin Vol I, ed. by K.W. Adolph. CRL Press, 85–107 (1988).
Wasilik, B., Thevenin, G., Oudet, P. and Chambon, P.: ‘Transcription of “in vitro” assembled chromatin by Escherichi coli RIVA polymerase’. J.Mol.BViol. 128, 409–438 (1979).
Weisehahn, G.P., Hyde, J. E. and Hearst, J.E.: ‘The photoaddiction of trimethylpsoralen to Drosophila melanogaster nuclei: A probe for chromatin structure’. Biochem. 16, 925–932 (1977).
Widmer, R.M., Lucchini, R., Lezzi, M., Meyer, B., Sogo, J.M., Edström, J.-E. and Koller, Th.: ‘Chromatin structure of a hyperactive secretory protein gene (in Balbiani ring 2) of Chironomus’. EMBO J. 3, 1635–1641 (1984).
Widmer, R.M., Koller, Th. and Sogo, J.M.: ‘Analysis of the psoralen-crosslinking pattern in chromatin DNA by exonuclease digestion’. Nucl.Acids Res. 16, 7013–7024 (1988).
Wu, C., Wong, Y.-C. and Elgin, S.C.R.: ‘The chromatin structure of specific genes. II. Disruption of chromatin during gene activity’. Cell 16, 807–814 (1979).
Wurtz, T. and Fakan, S.: ‘Isolation and characterization of a transcribing polynucleosomal chromatin fraction’. Biol.Cell. 48, 109–120 (1983).
Zhang, H., Wang, J.C. and Liu, L.F.: ‘Involvement of DNA topoisomerase I in transcription of human ribosomal RNA genes’. Proc.Nat. Acad.Sci.USA 85, 1060–1064 (1988).
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Sogo, J.M., Conconi, A., Widmer, R.M. (1989). The use of Psoralen-Photocrosslinking for the Analysis of the Chromatin Structure during Transcription. In: Nielsen, P.E. (eds) Photochemical Probes in Biochemistry. NATO ASI Series, vol 272. Springer, Dordrecht. https://doi.org/10.1007/978-94-009-0925-0_13
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DOI: https://doi.org/10.1007/978-94-009-0925-0_13
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