G Quadruplex in Plants: A Ubiquitous Regulatory Element and Its Biological Relevance

Yadav, Vikas; Hemansi,; Kim, Nayun; Tuteja, Narendra; Yadav, P. S.

doi:10.3389/fpls.2017.01163

Cited by 42 publications

(37 citation statements)

References 71 publications

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“…Those helicases include, but are not limited to, RecQ family helicases, Pif1 family helicases, and Fe-S helicases (10). Even G4 is thought to play an important regulatory role in plants (47). However, to the best of our knowledge, no plant G4 unwinding helicases have been identified.…”

Section: Ptg4 Can Be Unwound By Atrecq2 But Not Atrecq3mentioning

confidence: 99%

A comprehensive evaluation of a typical plant telomeric G-quadruplex (G4) DNA reveals the dynamics of G4 formation, rearrangement, and unfolding

Wu¹,

Zhang²,

Song

2020

Journal of Biological Chemistry

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Telomeres are specific nucleoprotein structures that are located at the ends of linear eukaryotic chromosomes and play crucial roles in genomic stability. Telomere DNA consists of simple repeats of a short G-rich sequence: TTAGGG in mammals and TTTAGGG in most plants. In recent years, the mammalian telomeric G-rich repeats have been shown to form G-quadruplex (G4) structures, which are crucial for modulating telomere functions. Surprisingly, even though plant telomeres are essential for plant growth, development, and environmental adaptions, only few reports exist on plant telomeric G4 DNA (pTG4). Here, using bulk and single-molecule assays, including CD spectroscopy, and single-molecule FRET approaches, we comprehensively characterized the structure and dynamics of a typical plant telomeric sequence, d[GGG(TTTAGGG)3]. We found that this sequence can fold into mixed G4s in potassium, including parallel and antiparallel structures. We also directly detected intermediate dynamic transitions, including G-hairpin, parallel G-triplex, and antiparallel G-triplex structures. Moreover, we observed that pTG4 is unfolded by the AtRecQ2 helicase but not by AtRecQ3. The results of our work shed light on our understanding about the existence, topological structures, stability, intermediates, unwinding, and functions of pTG4.

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Section: Ptg4 Can Be Unwound By Atrecq2 But Not Atrecq3mentioning

confidence: 99%

A comprehensive evaluation of a typical plant telomeric G-quadruplex (G4) DNA reveals the dynamics of G4 formation, rearrangement, and unfolding

Wu¹,

Zhang²,

Song

2020

Journal of Biological Chemistry

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“…Notably, helicases that resolve G-quadruplex structures, such as RecQ [170,171] and Pif1 [142] families, were found in both nonhuman and human systems. Most recently, the presence of G-quadruplexes in plant genomes has also emerged [172].…”

Section: G-quadruplexes In Nonhuman Genomesmentioning

confidence: 99%

G-Quadruplex DNA and RNA

Yang

2019

Methods in Molecular Biology

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G-quadruplexes (G4s) have become one of the most exciting nucleic acid secondary structures. A noncanonical, four-stranded structure formed in guanine-rich DNA and RNA sequences, G-quadruplexes can readily form under physiologically relevant conditions and are globularly folded structures. DNA is widely recognized as a double-helical structure essential in genetic information storage. However, only~3% of the human genome is expressed in protein; RNA and DNA may form noncanonical secondary structures that are functionally important. G-quadruplexes are one such example which have gained considerable attention for their formation and regulatory roles in biologically significant regions, such as human telomeres, oncogene-promoter regions, replication initiation sites, and 5 0 -and 3 0 -untranslated region (UTR) of mRNA. They are shown to be a regulatory motif in a number of critical cellular processes including gene transcription, translation, replication, and genomic stability. G-quadruplexes are also found in nonhuman genomes, particularly those of human pathogens. Therefore, G-quadruplexes have emerged as a new class of molecular targets for drug development. In addition, there is considerable interest in the use of G-quadruplexes for biomaterials, biosensors, and biocatalysts. The First International Meeting on Quadruplex DNA was held in 2007, and the G-quadruplex field has been growing dramatically over the last decade. The methods used to study G-quadruplexes have been essential to the rapid progress in our understanding of this exciting nucleic acid secondary structure. G-quadruplexes have been found to form in specific human guanine-rich sequences with functional significance, such as telomeres, oncogene-promoter regions, and 5 0 -and 3 0 -untranslated region (UTR) of mRNA, as well as in nonhuman genomes. G-Quadruplexes in TelomeresThe first biologically relevant G-quadruplex was observed in telomeric DNA. Telomeres are specific DNA-protein complexes at the ends of linear chromosomes, providing protection against gene erosion from cell divisions, chromosomal nonhomologous end-joinings, and nuclease attacks [19][20][21]. Telomeric G-quadruplexes were first reported as novel intramolecular structures containing guanine-guanine base-pairs in single-stranded telomeric sequences of several organisms [22], and as guaninetetrads between hairpin loops of the Tetrahymena telomeric DNA [23]. The importance of monovalent cations in the stabilization of G-quadruplex structures was revealed by Williamson, Cech in their monovalent cation-induced square-planar G-quartet model using the Oxytricha and Tetrahymena telomeric DNA [14]. Human telomeres consist of tandem repeats of the hexanucleotide d (TTAGGG) n 5-10 kb in length, which terminate in a singlestranded 3 0 -overhang of 35-600 bases [24]. Telomeres of cancer cells do not shorten upon replication, mainly due to the activation of a reverse transcriptase, telomerase, that extends the telomeric sequence at the chromosome ends [25]. Telomerase is activated in 80-85% of hu...

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“…DNA and RNA sequences are not confined to the human genome but also observed in a host of other organisms including plants, [60] bacteria, [61] viruses [62][63][64] and parasites. [65][66][67] This provides many potential opportunities to exploit G4 for the development of new therapeutic strategies.…”

Section: G4 As Nanodevicesmentioning

confidence: 99%

“…The significant level of interest in G4 partly stems from its potential as a therapeutic target , , . Indeed, G4‐forming DNA and RNA sequences are not confined to the human genome but also observed in a host of other organisms including plants, bacteria, viruses and parasites . This provides many potential opportunities to exploit G4 for the development of new therapeutic strategies.…”

Section: Introductionmentioning

confidence: 99%

Binding and Beyond: What Else Can G‐Quadruplex Ligands Do?

2019

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G‐quadruplexes (G4) are four‐stranded structures formed from guanine‐rich oligonucleotides. Their defined 3D structures and polymorphic nature set them apart from classical nucleic acid morphology and suggest a range of potential applications in the development of functional materials. Meanwhile, the occurrence of G4 across the genomes of animals, plants and pathogens suggests roles for these structures in biology that may be exploited for therapeutic effect. Hundreds of G4 ligands are reported to bind these sequences with high specificity and affinity, but such ligands can also be engineered to do more than simply associate with G4 in a straightforward host‐guest fashion. Ligands have been developed that can switch G4 topology, direct the selective covalent modification of nucleic acid structures, or respond to external stimuli to permit spatiotemporal control of their activity. Herein we survey the main themes of such “value‐added” G4 ligands and consider the opportunities and challenges of their potential applications.

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G Quadruplex in Plants: A Ubiquitous Regulatory Element and Its Biological Relevance

Cited by 42 publications

References 71 publications

A comprehensive evaluation of a typical plant telomeric G-quadruplex (G4) DNA reveals the dynamics of G4 formation, rearrangement, and unfolding

A comprehensive evaluation of a typical plant telomeric G-quadruplex (G4) DNA reveals the dynamics of G4 formation, rearrangement, and unfolding

G-Quadruplex DNA and RNA

Binding and Beyond: What Else Can G‐Quadruplex Ligands Do?

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