Parallel intramolecular DNA triple helix with G and T bases in the third strand stabilized by Zn2+ ions

Khomyakova, Elena

doi:10.1093/nar/28.18.3511

Cited by 25 publications

(15 citation statements)

References 39 publications

(42 reference statements)

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“…Interestingly, by using the ChIRP technique, similar GA-enriched motifs were identified among the binding sites of the chromatin-modulating RNAs roX2 and HOTAIR , indicating that GA-enriched motifs may play an important role in the targeting of lncRNAs across the genome 19 . Previously, several studies using different techniques have shown that GA-rich homopurine sequences can form triplex structures 38 39 40 . Overrepresentation of GA-rich sequences among the genomic binding sites of the lncRNAs analysed ( MEG3 , HOTAIR and roX ) raises the possibility that the lncRNAs may be recruited to their target genes via RNA–DNA triplex formation.…”

Section: Resultsmentioning

confidence: 99%

MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures

et al. 2015

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Long noncoding RNAs (lncRNAs) regulate gene expression by association with chromatin, but how they target chromatin remains poorly understood. We have used chromatin RNA immunoprecipitation-coupled high-throughput sequencing to identify 276 lncRNAs enriched in repressive chromatin from breast cancer cells. Using one of the chromatin-interacting lncRNAs, MEG3, we explore the mechanisms by which lncRNAs target chromatin. Here we show that MEG3 and EZH2 share common target genes, including the TGF-β pathway genes. Genome-wide mapping of MEG3 binding sites reveals that MEG3 modulates the activity of TGF-β genes by binding to distal regulatory elements. MEG3 binding sites have GA-rich sequences, which guide MEG3 to the chromatin through RNA–DNA triplex formation. We have found that RNA–DNA triplex structures are widespread and are present over the MEG3 binding sites associated with the TGF-β pathway genes. Our findings suggest that RNA–DNA triplex formation could be a general characteristic of target gene recognition by the chromatin-interacting lncRNAs.

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Section: Resultsmentioning

confidence: 99%

MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures

et al. 2015

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“…Characteristic CD spectra of DNA triplex structures differ with the sequence of the oligonucleotide ( 64 ). However, most of the intramolecular triplex DNA show a minimum around 240 nm, a maximum around 257 nm and a second minimum at ∼280 nm ( 39 , 65 ). These peaks were also observed in the CD spectra of the TM ECO oligonucleotides.…”

Section: Resultsmentioning

confidence: 99%

Intrastrand triplex DNA repeats in bacteria: a source of genomic instability

et al. 2015

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Repetitive nucleic acid sequences are often prone to form secondary structures distinct from B-DNA. Prominent examples of such structures are DNA triplexes. We observed that certain intrastrand triplex motifs are highly conserved and abundant in prokaryotic genomes. A systematic search of 5246 different prokaryotic plasmids and genomes for intrastrand triplex motifs was conducted and the results summarized in the ITxF database available online at http://bioinformatics.uni-konstanz.de/utils/ITxF/. Next we investigated biophysical and biochemical properties of a particular G/C-rich triplex motif (TM) that occurs in many copies in more than 260 bacterial genomes by CD and nuclear magnetic resonance spectroscopy as well as in vivo footprinting techniques. A characterization of putative properties and functions of these unusually frequent nucleic acid motifs demonstrated that the occurrence of the TM is associated with a high degree of genomic instability. TM-containing genomic loci are significantly more rearranged among closely related Escherichia coli strains compared to control sites. In addition, we found very high frequencies of TM motifs in certain Enterobacteria and Cyanobacteria that were previously described as genetically highly diverse. In conclusion we link intrastrand triplex motifs with the induction of genomic instability. We speculate that the observed instability might be an adaptive feature of these genomes that creates variation for natural selection to act upon.

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“…] a different triple helical structure is formed, both with Zn 2+ and Mg 2+ [3]. Besides, specific interactions with Zn 2+ ions in low water activity conditions were found to be necessary to stabilize the parallel intramolecular DNA triple helix with G and T bases in the third strand [13].…”

Section: Introductionmentioning

confidence: 98%

“…Particularly, several different effects of zinc(II) ions on the DNA structure have been presented [1,3,4,[9][10][11]13,28,33,34].…”

Section: Introductionmentioning

confidence: 99%

Zn²⁺–DNA interactions in aqueous systems: A Raman spectroscopic study

et al. 2009

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The influence of Zn2+ions on the structure of natural calf thymus DNA was studied by Raman spectroscopy. Measurements were done at room temperature and pH 6.2±0.1, in the presence of 10 mM Na+, and of Zn2+in a concentration range varying between 0 and 250 mM, respectively. No condensation of DNA was observed.As judging from the marker bands near 681 cm−1(dG), 729 cm−1(dA), 752 cm−1(dT), and 787 cm−1(dC, dT) altered nucleoside conformations in these residues are supposed to occur, in different intervals of Zn2+ions concentration. Changes in the conformational marker centered around 835 cm−1, upon Zn2+binding to DNA, were detected. Binding of zinc(II) ions to the charged phosphate groups of DNA, stabilizing the double helical structure, is indicated in the spectra. We have found that binding of metal ions at N3 of cytosine takes place at zinc(II) concentrations between 150–250 mM and interaction of Zn2+ions with adenine is observed in a concentration range from 10 to 250 mM. Binding of zinc(II) ions to N7 of guanine and, possibly, in a lesser extent to adenine was also observed as indicated by the Raman marker bands near 1490 and 1581 cm−1. There is no intensity change of the band at 1668 cm−1, suggesting no change in their base pairing and no change induced in the structure of water by Zn2+cations. No evidence for DNA melting was identified.

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Parallel intramolecular DNA triple helix with G and T bases in the third strand stabilized by Zn2+ ions

Abstract: ABSTRACT

Cited by 25 publications

References 39 publications

MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures

MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures

Intrastrand triplex DNA repeats in bacteria: a source of genomic instability

Zn²⁺–DNA interactions in aqueous systems: A Raman spectroscopic study

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Parallel intramolecular DNA triple helix with G and T bases in the third strand stabilized by Zn2+ ions

Abstract: ABSTRACT

Cited by 25 publications

References 39 publications

MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures

MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures

Intrastrand triplex DNA repeats in bacteria: a source of genomic instability

Zn2+–DNA interactions in aqueous systems: A Raman spectroscopic study

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Zn²⁺–DNA interactions in aqueous systems: A Raman spectroscopic study