The characterization of ribosomal RNA gene chromatin from Physarum polycephalum.

Amero, Sally Ann; Montoya, Vicky L.; Murdoch, Wendy L.; Ogle, Roy C.; Keating, John L.; Grainger, Robert M.

doi:10.1016/s0021-9258(18)38033-5

Cited by 11 publications

(3 citation statements)

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“…The regions of rDNA free of topoisomerase II cleavage are also free of DNase I, suggesting that they are not in an accessible chromatin conformation. Our DNase I studies are consistent with previous results suggesting that the transcribed region of Physarum rDNA is in an extended, more accessible conformation, compared to the nontranscribed spacer (Amero et al, 1988;Lucchini et al, 1987;Pauli et al, 1988). However, it is noteworthy that a regular pattern of topoisomerase II cleavage sites (every 450 bp) occurs in the 5′ part of the transcription unit, which is not sensitive to DNase I, suggesting that a nucleosomal conformation of chromatin is still present.…”

Section: Discussionsupporting

confidence: 92%

“…The experiments described in this paper constitute the first attempt to map topoisomerase II sites in ViVo in the slime mold P. polycephalum. We focused our work on ribosomal DNA whose chromatin has been the subject of several studies in the past years (Amero et al, 1988;Lucchini et al, 1987;Pauli et al, 1988). The present work addresses several questions concerning the accessibility of rDNA chromatin in diverse situations: active transcription, cell cycle stage, differentiation state, and the role of topoisomerase II in these processes.…”

Section: Discussionmentioning

confidence: 99%

“…We focused our analysis on the extrachromosomal ribosomal DNA, which has been extensively characterized, in regards to both its DNA sequence and its chromatin structure (Amero et al, 1988;Lucchini et al, 1987;Pauli et al, 1988). The replication origins were also recently precisely localized in the minichromosomes carrying the ribosomal genes.…”

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confidence: 99%

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In Vivo Topoisomerase II Cleavage Sites in the Ribosomal DNA of Physarum polycephalum

Borde

Duguet

1996

Biochemistry

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We have analyzed the topoisomerase II cleavage sites in the extrachromosomal ribosomal DNA of the lower eukaryote Physarum polycephalum using the topoisomerase II-specific inhibitor, 6,8-difluoro-7-(4-hydroxyphenyl)-1-cyclopropyl-4-quinolone-3-carboxylic acid. Most of the in vivo topoisomerase II cleavage sites were found either in the transcribed region of ribosomal DNA or in the palindromic region surrounded by the replication origins. Two classes of sites were identified: those which correlate with DNase I hypersensitive sites and corresponding to an open chromatin configuration (transcribed region) and internucleosomal cleavage sites (in the region of replication origins). Topoisomerase II drug-induced cleavage in the ribosomal DNA was considerably reduced upon Physarum differentiation to a dormant stage of life, the spherules. In contrast, the amount of drug-dependent cleavage was found to increase during the metaphase of mitosis, when rDNA transcription is shut off. These findings suggest a role for topoisomerase II in the ribosomal DNA minichromosomes segregation, in addition to its role in transcription. Finally, the similarity between in vivo sites and those observed following drug treatment of isolated nuclei indicates that no profound change occurs in rDNA chromatin conformation during nuclei isolation. By contrast, in vitro cleavage sites with purified topoisomerase II weakly correlate to in vivo, indicating a prominent role for chromatin structure in determining the interaction sites of topoisomerase II with DNA in vivo.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

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In Vivo Topoisomerase II Cleavage Sites in the Ribosomal DNA of Physarum polycephalum

Borde

Duguet

1996

Biochemistry

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Nucleosomes inhibit both transcriptional initiation and elongation by RNA polymerase III in vitro.

Morse

1989

The EMBO Journal

106

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To examine the effect of nucleosomes on in vitro transcription, purified chicken erythrocyte core histones and plasmid DNA bearing the Xenopus 5S RNA gene were assembled into nucleosomes and used as templates for transcription in a Xenopus oocyte nuclear extract. Plasmids having a nucleosome incorporating a specific region of the gene were selected by treating the reconstituted molecules with restriction endonucleases. In this way, it was shown that a nucleosome on or close to the internal control region of the 5S RNA gene inhibits transcription. Furthermore, experiments with 5S maxigenes showed that RNA polymerase III, in contrast to SP6 RNA polymerase, will not transcribe through a nucleosome in vitro.

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Chromatin states at ribosomal DNA loci

Hamperl

Wittner

Babl

et al. 2013

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

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The characterization of ribosomal RNA gene chromatin from Physarum polycephalum.

Cited by 11 publications

References 58 publications

In Vivo Topoisomerase II Cleavage Sites in the Ribosomal DNA of Physarum polycephalum

In Vivo Topoisomerase II Cleavage Sites in the Ribosomal DNA of Physarum polycephalum

Nucleosomes inhibit both transcriptional initiation and elongation by RNA polymerase III in vitro.

Chromatin states at ribosomal DNA loci

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