Interaction of human DNA topoisomerase I with G-quartet structures

Arimondo, Paola B.; Riou, Jean‐François; Mergny, Jean‐Louis; Tazi, Jamal; Sun, Jian‐Sheng; Garestier, Thérèse; Hélène, Claude

doi:10.1093/nar/28.24.4832

Cited by 105 publications

(76 citation statements)

References 35 publications

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“…The association of FISbinding sites with G4 motifs is consistent with several reports indicating that FIS operates by stabilizing local DNA architecture and that supercoiling-responsive promoters harbor FIS-binding sites (Schneider et al 2000). Additionally, it has been demonstrated that topA induces G4 motif formation (Arimondo et al 2000). This is in line with our prediction, as FIS has been observed to induce topA expression during oxidative stress (Weinstein-Fischer et al 2000).…”

Section: Discussionsupporting

confidence: 92%

Genome-wide prediction of G4 DNA as regulatory motifs: Role inEscherichia coliglobal regulation

Rawal¹,

Kummarasetti²,

Ravindran³

et al. 2006

Genome Res.

300

334

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The role of nonlinear DNA in replication, recombination, and transcription has become evident in recent years. Although several studies have predicted and characterized regulatory elements at the sequence level, very few have investigated DNA structure as regulatory motifs. Here, using G-quadruplex or G4 DNA motifs as a model, we have researched the role of DNA structure in transcription on a genome-wide scale. Analyses of >61,000 open reading frames (ORFs) across 18 prokaryotes show enrichment of G4 motifs in regulatory regions and indicate its predominance within promoters of genes pertaining to transcription, secondary metabolite biosynthesis, and signal transduction. Based on this, we predict that G4 DNA may present regulatory signals. This is supported by conserved G4 motifs in promoters of orthologous genes across phylogenetically distant organisms. We hypothesized a regulatory role of G4 DNA during supercoiling stress, when duplex destabilization may result in G4 formation. This is in line with our observations from target site analysis for 55 DNA-binding proteins in Escherichia coli, which reveals significant (P < 0.001) association of G4 motifs with target sites of global regulators FIS and Lrp and the sigma factor RpoD ( 70 ). These factors together control >1000 genes in the early growth phase and are believed to be induced by supercoiled DNA. We also predict G4 motif-induced supercoiling sensitivity for >30 operons in E. coli, and our findings implicate G4 DNA in DNA-topology-mediated global gene regulation in E. coli.

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Section: Discussionsupporting

confidence: 92%

Genome-wide prediction of G4 DNA as regulatory motifs: Role inEscherichia coliglobal regulation

Rawal¹,

Kummarasetti²,

Ravindran³

et al. 2006

Genome Res.

300

334

View full text Add to dashboard Cite

show abstract

“…Furthermore, Top1 promotes the formation of G-quartet structures and binds to non-B forms of DNA, such as cruciform and G-quartet DNA, which can occur in G-rich single-stranded regions (33,34). Non-B form structures may result in irreversible cleavage on either strand of the S region by Top1 because the DNA rotation around the helix may be disturbed after nicking, thus inhibiting the Top1's religation activity (Fig.…”

Section: Discussionmentioning

confidence: 99%

AID-induced decrease in topoisomerase 1 induces DNA structural alteration and DNA cleavage for class switch recombination

Kobayashi

Aida

Nagaoka

et al. 2009

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

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To initiate class switch recombination (CSR) activation-induced cytidine deaminase (AID) induces staggered nick cleavage in the S region, which lies 5 to each Ig constant region gene and is rich in palindromic sequences. Topoisomerase 1 (Top1) controls the supercoiling of DNA by nicking, rotating, and religating one strand of DNA. Curiously, Top1 reduction or AID overexpression causes the genomic instability. Here, we report that the inactivation of Top1 by its specific inhibitor camptothecin drastically blocked both the S region cleavage and CSR, indicating that Top1 is responsible for the S region cleavage in CSR. Surprisingly, AID expression suppressed Top1 mRNA translation and reduced its protein level. In addition, the decrease in the Top1 protein by RNA-mediated knockdown augmented the AID-dependent S region cleavage, as well as CSR. Furthermore, Top1 reduction altered DNA structure of the S region. Taken together, AID-induced Top1 reduction alters S region DNA structure probably to non-B form, on which Top1 can introduce nicks but cannot religate, resulting in S region cleavage.camptothecin ͉ non-B DNA ͉ translation suppression

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“…They are the telomere binding proteins in Oxytricha (b subunit) 8 and in yeast (RAP1), 9 yeast DNA-binding protein Hop1, 10 and human DNA topoisomerase I. 11 (b) Nucleases. The eukaryotic topoisomerase II causes a sequencespecific cleavage on the 5 0 side of parallel G-quadruplexes, 12 while other proteins show a G-quadruplex-dependent nuclease activity.…”

Section: Introductionmentioning

confidence: 99%

Measured and calculated CD spectra of G‐quartets stacked with the same or opposite polarities

et al. 2007

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Circular dichroism (CD) spectroscopy is widely used to characterize the structures of DNA G-quadruplexes. CD bands at 200-300 nm have been empirically related to G-quadruplexes having parallel or antiparallel sugar-phosphate backbones. We propose that a more fundamental interpretation of the origin of the CD bands is in the stacking interactions of neighboring G-quartets, which can have the same or opposing polarities of hydrogen bond acceptors and donors. From an empirical summation of CD spectra of the d(G)5 G-quadruplex and of the thrombin binding aptamer that have neighboring G-quartets with the same and opposite polarities, respectively, the spectra of aptamers selected by the Ff gene 5 protein (g5p) appear to arise from a combination of the two types of polarities of neighboring G-quartets. The aptamer CD spectra resemble the spectrum of d(G3T4G3), in which two adjacent quartets have the same and two have opposite polarities. Quantum-chemical spectral calculations were performed using a matrix method, based on guanine chromophores oriented as in d(G3T4G3). The calculations show that the two types of G-quartet stacks have CD spectra with features resembling experimental spectra of the corresponding types of G-quadruplexes.

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Interaction of human DNA topoisomerase I with G-quartet structures

Cited by 105 publications

References 35 publications

Genome-wide prediction of G4 DNA as regulatory motifs: Role inEscherichia coliglobal regulation

Genome-wide prediction of G4 DNA as regulatory motifs: Role inEscherichia coliglobal regulation

AID-induced decrease in topoisomerase 1 induces DNA structural alteration and DNA cleavage for class switch recombination

Measured and calculated CD spectra of G‐quartets stacked with the same or opposite polarities

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