Differential Effect of DNA Supercoiling on Transcription of Adenovirus Genes in vitro

Banerjee, Subhasis; Spector, David J.

doi:10.1099/0022-1317-73-10-2631

Cited by 8 publications

(8 citation statements)

References 42 publications

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“…We found that most partially hybridized RNAs were associated with CCC mtDNA (structure e ); given that highly supercoiled DNA plasmids are better transcriptional templates in bacteria (47) and adenovirus (56), our results are consistent with CCC mtDNA being a major template for transcription in vivo . This idea is supported by observations of promoter-specific transcription on supercoiled templates using yeast mitochondrial RNA polymerase (POLRMT) in vitro (57), although mammalian POLRMT does not show promoter specificity (58).…”

Section: Discussionsupporting

confidence: 78%

Two-dimensional intact mitochondrial DNA agarose electrophoresis reveals the structural complexity of the mammalian mitochondrial genome

Kolesar

Wang

Taguchi

et al. 2012

Nucleic Acids Research

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The mitochondrial genome exists in numerous structural conformations, complicating the study of mitochondrial DNA (mtDNA) metabolism. Here, we describe the development of 2D intact mtDNA agarose gel electrophoresis (2D-IMAGE) for the separation and detection of approximately two-dozen distinct topoisomers. Although the major topoisomers were well conserved across many cell and tissue types, unique differences in certain cells and tissues were also observed. RNase treatment revealed that partially hybridized RNAs associated primarily with covalently closed circular DNA, consistent with this structure being the template for transcription. Circular structures composed of RNA:DNA hybrids contained only heavy-strand DNA sequences, implicating them as lagging-strand replication intermediates. During recovery from replicative arrest, 2D-IMAGE showed changes in both template selection and replication products. These studies suggest that discrete topoisomers are associated with specific mtDNA-directed processes. Because of the increased resolution, 2D-IMAGE has the potential to identify novel mtDNA intermediates involved in replication or transcription, or pathology including oxidative linearization, deletions or depletion.

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Section: Discussionsupporting

confidence: 78%

Two-dimensional intact mitochondrial DNA agarose electrophoresis reveals the structural complexity of the mammalian mitochondrial genome

Kolesar

Wang

Taguchi

et al. 2012

Nucleic Acids Research

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“…Topoisomerase I1 has been proposed to have both catalytic (chromatin loop fastener) and structural (scaffold) roles in chromosome condensation (Adachi et al, 1989). We observed that topoisomerase 11-mediated DNA catenation (Cantor et al, 1988;Banerjee and Spector, 1992) and RNA pol 11-dependent transcription (S. Banerjee, unpublished data) in HIE dialysed in the presence of 10-12 mM Mg++ were much higher than that seen in Mg++-free extracts described in this work. Preincubation of HIE in the absence of Mg++ might have further inhibited these activities.…”

Section: Discussionmentioning

confidence: 49%

Sperm nuclear chromatin transformations in somatic cell‐free extracts

Banerjee

Hultén

1994

Molecular Reproduction Devel

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HeLa cell extracts induced decondensation of lysolecithin permeabilized Xenopus, pig, and human sperm chromatin; decondensation began almost immediately on incubation in the extract and was completed within 10-20 min. The average enlargements of human and pig sperm nuclei were 15-fold and 3-fold, respectively. The structural organization of pig and human sperm chromatin was significantly different. Decondensation was differentially inhibited by Mg++ and polyamines; inhibition was least for Xenopus and most for pig sperm nuclei. The nuclear membrane was disintegrated on chromatin dispersion, whereas the nuclei which failed to decondense exhibited distinct nuclear envelopes. The decondensing factors were stable at 65 degrees C for 15 min. The dispersed chromatin was remodelled to somatic nucleosomal structures within 60 min. The remodelled chromatin could be recondensed to chromosome-like structures, when incubated further in extracts from mitosis arrested HeLa cells.

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“…In the case of adenoviruses, the superhelicity was suggested to facilitate unwinding of DNA during transcription (25). Similarly, the negative superhelicity of the linear replicons in Streptomyces may also be important for transcription, or alternatively replication, packaging or other DNA transaction activities.…”

Section: Discussionmentioning

confidence: 99%

“…The TP–TP interactions allow these linear replicons to assume more compact superhelical structures. The superhelicity increases transcription of adenoviral genes in a promoter-specific manner (25). …”

Section: Introductionmentioning

confidence: 99%

Linear Streptomyces plasmids form superhelical circles through interactions between their terminal proteins

Tsai

Huang

Teßmer

et al. 2010

Nucleic Acids Research

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Linear chromosomes and linear plasmids of Streptomyces possess covalently bound terminal proteins (TPs) at the 5′ ends of their telomeres. These TPs are proposed to act as primers for DNA synthesis that patches the single-stranded gaps at the 3′ ends during replication. Most (‘archetypal’) Streptomyces TPs (designated Tpg) are highly conserved in size and sequence. In addition, there are a number of atypical TPs with heterologous sequences and sizes, one of which is Tpc that caps SCP1 plasmid of Streptomyces coelicolor. Interactions between the TPs on the linear Streptomyces replicons have been suggested by electrophoretic behaviors of TP-capped DNA and circular genetic maps of Streptomyces chromosomes. Using chemical cross-linking, we demonstrated intramolecular and intermolecular interactions in vivo between Tpgs, between Tpcs and between Tpg and Tpc. Interactions between the chromosomal and plasmid telomeres were also detected in vivo. The intramolecular telomere interactions produced negative superhelicity in the linear DNA, which was relaxed by topoisomerase I. Such intramolecular association between the TPs poses a post-replicational complication in the formation of a pseudo-dimeric structure that requires resolution by exchanging TPs or DNA.

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Differential Effect of DNA Supercoiling on Transcription of Adenovirus Genes in vitro

Cited by 8 publications

References 42 publications

Two-dimensional intact mitochondrial DNA agarose electrophoresis reveals the structural complexity of the mammalian mitochondrial genome

Two-dimensional intact mitochondrial DNA agarose electrophoresis reveals the structural complexity of the mammalian mitochondrial genome

Sperm nuclear chromatin transformations in somatic cell‐free extracts

Linear Streptomyces plasmids form superhelical circles through interactions between their terminal proteins

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