Faculty Opinions recommendation of DNA topology and global architecture of point centromeres.

2016 ◽  
Author(s):  
Yamini Dalal ◽  
Daniël Melters
Keyword(s):  
Dna Topology

Curaxin-Induced DNA Topology Alterations Trigger the Distinct Binding Response of CTCF and FACT at the Single-Molecule Level

Biochemistry ◽  
2021 ◽  
Vol 60 (7) ◽  
pp. 494-499
Author(s):  
Ke Lu ◽  
Cuifang Liu ◽  
Yinuo Liu ◽  
Anfeng Luo ◽  
Jun Chen ◽  
...  
Keyword(s):  
Single Molecule ◽  
Dna Topology ◽  
Single Molecule Level

Effect of DNA topology on plasmid DNA repair in vivo

FEBS Letters ◽  
2000 ◽  
Vol 476 (3) ◽  
pp. 174-178 ◽  
Author(s):  
Jik-Young Park ◽  
Byungchan Ahn
Keyword(s):  
Dna Repair ◽  
Plasmid Dna ◽  
Dna Topology

scholarly journals Endogenous Fluctuations of DNA Topology in the Chloroplast of Chlamydomonas reinhardtii

1998 ◽  
Vol 18 (12) ◽  
pp. 7235-7242 ◽  
Author(s):  
Maria L. Salvador ◽  
Uwe Klein ◽  
Lawrence Bogorad
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Chloroplast Genome ◽  
Continuous Light ◽  
Dna Supercoiling ◽  
Dna Topology ◽  
Chloroplast Gene ◽  
Chloroplast Gene Expression ◽  
Endogenous Fluctuations ◽  
Unicellular Green Alga ◽  
In Cells

ABSTRACT DNA supercoiling in the chloroplast of the unicellular green algaChlamydomonas reinhardtii was found to change with a diurnal rhythm in cells growing in alternating 12-h dark–12-h light periods. Highest and lowest DNA superhelicities occurred at the beginning and towards the end of the 12-h light periods, respectively. The fluctuations in DNA supercoiling occurred concurrently and in the same direction in two separate parts of the chloroplast genome, one containing the genes psaB, rbcL, andatpA and the other containing the atpB gene. Fluctuations were not confined to transcribed DNA regions, indicating simultaneous changes in DNA conformation all over the chloroplast genome. Because the diurnal fluctuations persisted in cells kept in continuous light, DNA supercoiling is judged to be under endogenous control. The endogenous fluctuations in chloroplast DNA topology correlated tightly with the endogenous fluctuations of overall chloroplast gene transcription and with those of the pool sizes of most chloroplast transcripts analyzed. This result suggests that DNA superhelical changes have a role in the regulation of chloroplast gene expression in Chlamydomonas.

scholarly journals Topoisomerase activity is linked to altered nucleosome positioning and transcriptional regulation in the fission yeast fbp1 gene

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242348
Author(s):  
Ryuta Asada ◽  
Satoshi Senmatsu ◽  
Ben Montpetit ◽  
Kouji Hirota
Keyword(s):  
Transcriptional Regulation ◽  
Fission Yeast ◽  
Chromatin Structure ◽  
Promoter Region ◽  
Nucleosome Positioning ◽  
Dna Topology ◽  
Upstream Region ◽  
Inactive Form ◽  
Topological State ◽  
Transcriptional Output

Chromatin structure, including nucleosome positioning, has a fundamental role in transcriptional regulation through influencing protein-DNA interactions. DNA topology is known to influence chromatin structure, and in doing so, can also alter transcription. However, detailed mechanism(s) linking transcriptional regulation events to chromatin structure that is regulated by changes in DNA topology remain to be well defined. Here we demonstrate that nucleosome positioning and transcriptional output from the fission yeast fbp1 and prp3 genes are altered by excess topoisomerase activity. Given that lncRNAs (long noncoding RNAs) are transcribed from the fbp1 upstream region and are important for fbp1 gene expression, we hypothesized that local changes in DNA topological state caused by topoisomerase activity could alter lncRNA and fbp1 transcription. In support of this, we found that topoisomerase overexpression caused destabilization of positioned nucleosomes within the fbp1 promoter region, which was accompanied by aberrant fbp1 transcription. Similarly, the direct recruitment of topoisomerase, but not a catalytically inactive form, to the promoter region of fbp1 caused local changes in nucleosome positioning that was also accompanied by altered fbp1 transcription. These data indicate that changes in DNA topological state induced by topoisomerase activity could lead to altered fbp1 transcription through modulating nucleosome positioning.

Hormonal induction of transfected genes depends on DNA topology

1990 ◽  
Vol 10 (2) ◽  
pp. 625-633
Author(s):  
B Piña ◽  
R J Haché ◽  
J Arnemann ◽  
G Chalepakis ◽  
E P Slater ◽  
...  
Keyword(s):  
Cell Line ◽  
Mammary Tumor ◽  
Binding Sites ◽  
Glucocorticoid Receptors ◽  
Hormone Receptors ◽  
Regulatory Element ◽  
Tumor Cell Line ◽  
Dna Topology ◽  
Mammary Tumor Cell ◽  
Mammary Tumor Cell Line

Plasmids containing the hormone regulatory element of mouse mammary tumor virus linked to the thymidine kinase promoter of herpes simplex virus and the reporter gene chloramphenicol acetyltransferase of Escherichia coli respond to glucocorticoids and progestins when transfected into appropriate cells. In the human mammary tumor cell line T47D, the response to progestins, but not to glucocorticoids, is highly dependent on the topology of the transfected DNA. Although negatively supercoiled plasmids respond optimally to the synthetic progestin R5020, their linearized counterparts exhibit markedly reduced progestin inducibility. This is not due to changes in the efficiency of DNA transfection, since the amount of DNA incorporated into the cell nucleus is not significantly dependent on the initial topology of the plasmids. In contrast, cotransfection experiments with glucocorticoid receptor cDNA in the same cell line show no significant influence of DNA topology on induction by dexamethasone. A similar result was obtained with fibroblasts that contain endogenous glucocorticoid receptors. When the distance between receptor-binding sites or between the binding sites and the promoter was increased, the dependence of progestin induction on DNA topology was more pronounced. In contrast to the original plasmid, these constructs also revealed a similar topological dependence for induction by glucocorticoids. The differential influence of DNA topology is not due to differences in the affinity of the two hormone receptors for DNA of various topologies, but probably reflects an influence of DNA topology on the interaction between different DNA-bound receptor molecules and between receptors and other transcription factors.

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