Elastic torsional strain in DNA within a fraction of SV40 minichromosomes: relation to transcriptionally active chromatin.

Luchnik, Andrey N.; Bakayev, V.V.; Zbarsky, I.B.; Georgiev, G.P.

doi:10.1002/j.1460-2075.1982.tb01322.x

Cited by 135 publications

(53 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Previously, in the absence of direct data on transcribing mammalian chromatin, the enhanced flexibility of yeast bulk chromatin was proposed to be representative of the mammalian transcribing class (5, 6) and therefore not necessarily anomalous with respect to one particular class of mammalian chromatin. Indeed, it was argued (37) that unconstrained topological tension, one of the properties thought to be characteristic of transcribing eukaryotic chromatin (38) and absent from bulk yeast 2-gm chromatin (5), might be found in the minor fraction of yeast 2-atm chromatin that is transcribed. In contrast, our results indicate that yeast chromatin structure differs not only from the bulk mammalian chromatin but from transcribing mammalian chromatin as well.…”

Section: Discussionmentioning

confidence: 99%

Thermal unwinding of simian virus 40 transcription complex DNA.

Lutter

1989

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Two long-standing questions in the control of eukaryotic gene expression have been how the structure of transcribing chromatin compares with that of nontranscribing chromatin and how chromatin structure differs among various eukaryotic organisms. We have addressed aspects of these two questions by characterizing the rotational flexibility of the DNA of the simian virus 40 (SV40) transcription complex. When transcription complex samples are incubated with topoisomerase at 0C or 37C, the DNA of the 37C sample is unwound by 1.8 turns relative to that of the 0C sample. This amount of unwinding is similar to that observed for bulk, untranscribed SV40 minichromosome DNA, indicating that the chromatin structure of a transcribed gene resembles that of a nontranscribed gene in the degree of constraint that it imposes on its DNA. However, this amount of unwinding differs substantially from the value observed for yeast plasmid chromatin DNA, suggesting that yeast chromatin differs significantly from mammalian chromatin in this fundamental property.Substantial progress has been made in describing structural details of bulk eukaryotic chromatin, but as yet little is known about the structural details of that minor fraction of chromatin that is transcribed (1-3). The work of Weintraub and Groudine (4) demonstrates that some structural difference exists because the enzyme DNase I digests the DNA of transcriptionally active chromatin more rapidly than that of transcriptionally inactive chromatin. This indicates that active chromatin has a more "open" or accessible structure, suggesting that the DNA-histone interactions may perhaps be less stable than those of inactive chromatin.Recent results from studies of yeast plasmid chromatin (5, 6) would seen to support this view. The topology of the DNA of yeast plasmid chromatin was found to change with temperature in an amount that is --70% the value exhibited by bare DNA. This substantial rotational flexibility of the yeast chromatin DNA differs markedly from that of the DNA of the simian virus 40 (SV40) minichromosome (7,8), which has been shown to unwind by only 25% [or =--1.5 turns per 5243 base pairs (bp)] of the value for bare DNA. However, the bulk chromatin of SV40 is predominantly inactive transcriptionally: only ==1% of the SV40 minichromosomes in an infected cell appear to be transcriptionally active (9). Yeast 2-,um plasmid chromatin, on the other hand, is thought for the most part to be transcriptionally active. Noting these functional differences, Saavedra and Huberman (5) have suggested that the relatively flexible structure that they observe in the yeast 2-,um minichromosome may be a fundamental feature of the transcriptionally active subclass of eukaryotic chromatin. By this proposal, the transcribed fraction of mammalian chromatin would be expected to exhibit the enhanced DNA flexibility characteristic of the yeast chromatin.We have carried out experiments here that directly test this proposal by analyzing the topological properties of that fraction of SV40 m...

show abstract

Section: Discussionmentioning

confidence: 99%

Thermal unwinding of simian virus 40 transcription complex DNA.

Lutter

1989

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…However, since only a small fraction of the eukaryotic genome is transcriptionally active at any one time in a given cell, it remains possible that the DNA of this transcribed chromatin, like the DNA of prokaryotes, contains unconstrained supercoiling. Indeed, numerous studies have argued that the transcriptionally active chromatin contains totally unconstrained supercoils (39)(40)(41)56). However, these studies were all correlative, and when direct analyses of the topology of transcribing chromatin were carried out, it was found that transcribed chromatin contains constrained supercoiling in an amount consistent with typical nucleosomal organization (4,10,11,43,52).…”

mentioning

confidence: 99%

Effects of histone acetylation on chromatin topology in vivo.

Lutter¹,

Judis²,

Paretti³

1992

Mol. Cell. Biol.

View full text Add to dashboard Cite

Recently a model for eukaryotic transcriptional activation has been proposed in which histone hyperacetylation causes release of nucleosomal supercoils, and this unconstrained tension in turn stimulates transcription (V. G. Norton, B. S. Imai, P. Yau, and E. M. Bradbury, Cell 57:449-457, 1989; V. G. Norton, K. W. Marvin, P. Yau, and E. M. Bradbury, J. Biol. Chem. 265:19848-19852, 1990). These studies analyzed the effect of histone hyperacetylation on the change in topological linking number which occurs during nucleosome assembly in vitro. We have tested this model by determining the effect of histone hyperacetylation on the linking number change which occurs during assembly in vivo. We find that butyrate treatment of cells infected with simian virus 40 results in hyperacetylation of the histones of the extracted viral minichromosome as expected.However, the change in constrained supercoils of the minichromosome DNA is minimal, a result which is inconsistent with the proposed model. These results indicate that the proposed mechanism of transcriptional activation is unlikely to take place in the cell.

show abstract

“…Similarly, superhelicity of DNA in eucaryotes may be an important parameter of chromatin structure related to the potential for transcription (32,45). When DNA is introduced into frog oocytes, circular templates are transcribed at 500 times the level of linear templates (24).…”

mentioning

confidence: 99%

Localization of specific topoisomerase I interactions within the transcribed region of active heat shock genes by using the inhibitor camptothecin.

Gilmour¹,

Elgin²

1987

Mol. Cell. Biol.

129

View full text Add to dashboard Cite

Camptothecin stabilizes the topoisomerase I-DNA covalent intermediate that forms during the relaxation of torsionally strained DNA. By mapping the position of the resultant DNA nicks, we analyzed the distribution of the covalent intermediates formed on heat shock genes in cultured Drosophila melanogaster cells. Topoisomerase I was found to interact with the transcriptionally active genes hsp22, hsp23, hsp26, and hsp28 after heat shock but not with the inactive genes before heat shock. The interaction occurred predominantly within the transcribed region, with specific sites occurring on both the transcribed and nontranscribed strands of the DNA. Little interaction was seen with nontranscribed flanking sequences. Camptothecin only partially inhibited transcription of the hsp28 gene during heat shock, causing a reduced level of transcripts which were nonetheless full length. Topoisomerase I also interacted with the DNA throughout the transcriptionally active hsp83 gene, including an intron, in both heat-shocked and non-heat-shocked cells. The results point to a dynamic set of interactions at the active locus.In procaryotes, it is clear that the degree of DNA superhelicity can profoundly influence the utilization of specific promoters (reviewed in reference 16). Similarly, superhelicity of DNA in eucaryotes may be an important parameter of chromatin structure related to the potential for transcription (32,45). When DNA is introduced into frog oocytes, circular templates are transcribed at 500 times the level of linear templates (24). Preference for the circular molecules suggests that a topologically constrained structure may be necessary to generate or utilize a suitable template for efficient transcription. Ryoji and Worcel (39) have described the assembly of so-called "dynamic" and "static" chromatin structures in the Xenopus oocyte system. The dynamic structure, which is reported to be that which is transcriptionally active, appears to be torsionally strained, while the transcriptionally inactive static structure is not torsionally strained.It has long been recognized that the advancement of the transcription complex along the DNA would be facilitated by a swivel point which would allow the release of superhelicity generated by the passage of RNA polymerase along the DNA (48). The problem of superhelicity might be particularly severe if components of the transcription process are restrained by attachment to a nuclear matrix (28, 37). A role for a swivel activity in the transient unfolding of the chromatin fiber might also be postulated. A change in the compaction of the chromatin fiber as well as a perturbation of the histone-DNA interactions has been shown to occur at active genes (50, 52). The perturbation of the nucleosome array appears to correlate with the level of transcription; among the heat shock genes of Drosophila melanogaster, those transcribed at higher levels are more sensitive to cleavage by DNase I and methidiumpropyl-ferrous EDTA than are those transcribed at lower levels (6).Two classes of enzy...

show abstract

Elastic torsional strain in DNA within a fraction of SV40 minichromosomes: relation to transcriptionally active chromatin.

Cited by 135 publications

References 39 publications

Thermal unwinding of simian virus 40 transcription complex DNA.

Thermal unwinding of simian virus 40 transcription complex DNA.

Effects of histone acetylation on chromatin topology in vivo.

Localization of specific topoisomerase I interactions within the transcribed region of active heat shock genes by using the inhibitor camptothecin.

Contact Info

Product

Resources

About