scholarly journals RNA and DNA G-quadruplexes bind to human Dicer and inhibit its activity

2020 ◽  
Author(s):  
Natalia Koralewska ◽  
Agnieszka Szczepanska ◽  
Kinga Ciechanowska ◽  
Marta Wojnicka ◽  
Maria Pokornowska ◽  
...  
Keyword(s):  
Genome Instability ◽  
Detailed Knowledge ◽  
Biological Processes ◽  
Biological Functions ◽  
Binding Assays ◽  
Protein Interactome ◽  
G Quadruplex ◽  
Quadruplex Formation ◽  
Rna And Dna

AbstractGuanine (G)-rich single-stranded nucleic acids can adopt G-quadruplex structures. Accumulating evidence indicates that G-quadruplexes serve important regulatory roles in fundamental biological processes such as DNA replication, transcription, and translation, while aberrant G-quadruplex formation is linked to genome instability and cancer. Understanding the biological functions played by G-quadruplexes requires detailed knowledge of their protein interactome. Here, we report that both RNA and DNA G-quadruplexes are bound by human Dicer in vitro. Using in vitro binding assays, mutation studies, and computational modeling we demonstrate that G-quadruplexes can interact with the Platform-PAZ-Connector helix cassette of Dicer, the region responsible for anchoring microRNA precursors (pre-miRNAs). Consequently, we show that G-quadruplexes efficiently and stably inhibit the cleavage of pre-miRNA by Dicer. Our data highlight the potential of human Dicer for binding of G-quadruplexes and allow us to propose a G-quadruplex-driven sequestration mechanism of Dicer regulation.

scholarly journals RNA and DNA G-quadruplexes bind to human dicer and inhibit its activity

2021 ◽  
Vol 78 (7) ◽  
pp. 3709-3724
Author(s):  
Natalia Koralewska ◽  
Agnieszka Szczepanska ◽  
Kinga Ciechanowska ◽  
Marta Wojnicka ◽  
Maria Pokornowska ◽  
...  
Keyword(s):  
Genome Instability ◽  
Detailed Knowledge ◽  
Biological Processes ◽  
Binding Assays ◽  
Vitro Binding ◽  
Protein Interactome ◽  
G Quadruplex ◽  
Quadruplex Formation ◽  
Rna And Dna

AbstractGuanine (G)-rich single-stranded nucleic acids can adopt G-quadruplex structures. Accumulating evidence indicates that G-quadruplexes serve important regulatory roles in fundamental biological processes such as DNA replication, transcription, and translation, while aberrant G-quadruplex formation is linked to genome instability and cancer. Understanding the biological functions played by G-quadruplexes requires detailed knowledge of their protein interactome. Here, we report that both RNA and DNA G-quadruplexes are bound by human Dicer in vitro. Using in vitro binding assays, mutation studies, and computational modeling we demonstrate that G-quadruplexes can interact with the Platform–PAZ–Connector helix cassette of Dicer, the region responsible for anchoring microRNA precursors (pre-miRNAs). Consequently, we show that G-quadruplexes efficiently and stably inhibit the cleavage of pre-miRNA by Dicer. Our data highlight the potential of human Dicer for binding of G-quadruplexes and allow us to propose a G-quadruplex-driven sequestration mechanism of Dicer regulation.

scholarly journals The Functional Consequences of Eukaryotic Topoisomerase 1 Interaction with G-Quadruplex DNA

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 193
Author(s):  
Alexandra Berroyer ◽  
Nayun Kim
Keyword(s):  
Topoisomerase I ◽  
Genome Instability ◽  
Strand Break ◽  
Dna Topology ◽  
Single Strand Break ◽  
Dna Structures ◽  
G4 Dna ◽  
G Quadruplex

Topoisomerase I in eukaryotic cells is an important regulator of DNA topology. Its catalytic function is to remove positive or negative superhelical tension by binding to duplex DNA, creating a reversible single-strand break, and finally religating the broken strand. Proper maintenance of DNA topological homeostasis, in turn, is critically important in the regulation of replication, transcription, DNA repair, and other processes of DNA metabolism. One of the cellular processes regulated by the DNA topology and thus by Topoisomerase I is the formation of non-canonical DNA structures. Non-canonical or non-B DNA structures, including the four-stranded G-quadruplex or G4 DNA, are potentially pathological in that they interfere with replication or transcription, forming hotspots of genome instability. In this review, we first describe the role of Topoisomerase I in reducing the formation of non-canonical nucleic acid structures in the genome. We further discuss the interesting recent discovery that Top1 and Top1 mutants bind to G4 DNA structures in vivo and in vitro and speculate on the possible consequences of these interactions.

scholarly journals Overview of RNA G-quadruplex structures

2017 ◽  
Vol 63 (4) ◽  
Author(s):  
Magdalena Małgowska
Keyword(s):  
Three Dimensional ◽  
Telomere Maintenance ◽  
Structural Studies ◽  
Biological Functions ◽  
Cellular Processes ◽  
Novel Drugs ◽  
G Quadruplex ◽  
Conformational Diversity

G-quadruplexes are non-canonical secondary structures which may be formed by guanine rich sequences, both in vitro and in living cells. The number of biological functions assigned to these structural motifs has grown rapidly since the discovery of their involvement in the telomere maintenance. Knowledge of the three-dimensional structures of G-quadruplexes plays an important role in understanding their conformational diversity, physiological functions, and in the design of novel drugs targeting G-quadruplexes. For the last decades, structural studies have been mainly focused on the DNA G-quadruplexes. Their RNA counterparts gained an increased interest along with still-emerging recognition of the central role of RNA in multiple cellular processes. In this review we focus on structural properties of RNA G-quadruplexes, based on high-resolution structures, available in RCSB PDB data base and on structural models. In addition, we point out to the current challenges in this field of research.

scholarly journals MicroRNAs in Female Malignancies

2019 ◽  
Vol 18 ◽  
pp. 117693511982874 ◽  
Author(s):  
Themis Liolios ◽  
Stavroula Lila Kastora ◽  
Giorgia Colombo
Keyword(s):  
Gene Expression ◽  
Computational Analysis ◽  
Target Genes ◽  
Vulvar Cancer ◽  
Chemotherapeutic Agents ◽  
In Vitro Assays ◽  
Biological Processes ◽  
Potential Mechanism ◽  
Biological Functions

MicroRNAs (miRNAs) are endogenous 22-nucleotide RNAs that can play a fundamental regulatory role in the gene expression of various organisms. Current research suggests that miRNAs can assume pivotal roles in carcinogenesis. In this article, through bioinformatics mining and computational analysis, we determine a single miRNA commonly involved in the development of breast, cervical, endometrial, ovarian, and vulvar cancer, whereas we underline the existence of 7 more miRNAs common in all examined malignancies with the exception of vulvar cancer. Furthermore, we identify their target genes and encoded biological functions. We also analyze common biological processes on which all of the identified miRNAs act and we suggest a potential mechanism of action. In addition, we analyze exclusive miRNAs among the examined malignancies and bioinformatically explore their functionality. Collectively, our data can be employed in in vitro assays as a stepping stone in the identification of a universal machinery that is derailed in female malignancies, whereas exclusive miRNAs may be employed as putative targets for future chemotherapeutic agents or cancer-specific biomarkers.

scholarly journals Thermodynamically stable and genetically unstable G-quadruplexes are depleted in genomes across species

2019 ◽  
Vol 47 (12) ◽  
pp. 6098-6113 ◽  
Author(s):  
Emilia Puig Lombardi ◽  
Allyson Holmes ◽  
Daniela Verga ◽  
Marie-Paule Teulade-Fichou ◽  
Alain Nicolas ◽  
...  
Keyword(s):  
Negative Selection ◽  
Genome Stability ◽  
Genome Instability ◽  
Regulation Of Gene Expression ◽  
Biological Processes ◽  
Single Nucleotide ◽  
Folding Potential ◽  
Species Specific

Abstract G-quadruplexes play various roles in multiple biological processes, which can be positive when a G4 is involved in the regulation of gene expression or detrimental when the folding of a stable G4 impairs DNA replication promoting genome instability. This duality interrogates the significance of their presence within genomes. To address the potential biased evolution of G4 motifs, we analyzed their occurrence, features and polymorphisms in a large spectrum of species. We found extreme bias of the short-looped G4 motifs, which are the most thermodynamically stable in vitro and thus carry the highest folding potential in vivo. In the human genome, there is an over-representation of single-nucleotide-loop G4 motifs (G4-L1), which are highly conserved among humans and show a striking excess of the thermodynamically least stable G4-L1A (G3AG3AG3AG3) sequences. Functional assays in yeast showed that G4-L1A caused the lowest levels of both spontaneous and G4-ligand-induced instability. Analyses across 600 species revealed the depletion of the most stable G4-L1C/T quadruplexes in most genomes in favor of G4-L1A in vertebrates or G4-L1G in other eukaryotes. We discuss how these trends might be the result of species-specific mutagenic processes associated to a negative selection against the most stable motifs, thus neutralizing their detrimental effects on genome stability while preserving positive G4-associated biological roles.

A multi-functional guanine derivative for studying the DNA G-quadruplex structure

The Analyst ◽  
2017 ◽  
Vol 142 (21) ◽  
pp. 4083-4088 ◽  
Author(s):  
Takumi Ishizuka ◽  
Pei-Yan Zhao ◽  
Hong-Liang Bao ◽  
Yan Xu
Keyword(s):  
Fluorescent Probe ◽  
Living Cells ◽  
Quadruplex Structure ◽  
G Quadruplex ◽  
Quadruplex Formation

A multi-functional guanine derivative, 8FG, as a G-quadruplex stabilizer, a fluorescent probe for the detection of G-quadruplex formation, and a 19F sensor for the observation of the G-quadruplex in vitro and in living cells.

G-quadruplex unwinding helicases and their function in vivo

2017 ◽  
Vol 45 (5) ◽  
pp. 1173-1182 ◽  
Author(s):  
Markus Sauer ◽  
Katrin Paeschke
Keyword(s):  
Dna Replication ◽  
Genome Instability ◽  
Evolutionary Conservation ◽  
Telomere Maintenance ◽  
Cellular Functions ◽  
G Quadruplex

The concept that G-quadruplex (G4) structures can form within DNA or RNA in vitro has been long known and extensively discussed. In recent years, accumulating evidences imply that G-quadruplex structures form in vivo. Initially, inefficient regulation of G-quadruplex structures was mainly associated with genome instability. However, due to the location of G-quadruplex motifs and their evolutionary conservation, different cellular functions of these structures have been postulated (e.g. in telomere maintenance, DNA replication, transcription, and translation). Regardless of their function, efficient and controlled formation and unwinding are very important, because ‘mis’-regulated G-quadruplex structures are detrimental for a given process, causing genome instability and diseases. Several helicases have been shown to target and regulate specific G-quadruplex structures. This mini-review focuses on the biological consequences of G4 disruption by different helicases in vivo.

scholarly journals G-quadruplexes in H1N1 influenza genomes

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Václav Brázda ◽  
Otília Porubiaková ◽  
Alessio Cantara ◽  
Natália Bohálová ◽  
Jan Coufal ◽  
...  
Keyword(s):  
H1n1 Virus ◽  
Antiviral Treatment ◽  
H1n1 Influenza ◽  
Influenza Viruses ◽  
Close Relative ◽  
Spectroscopic Methods ◽  
Genotype 4 ◽  
G Quadruplex ◽  
Quadruplex Formation

Abstract Background Influenza viruses are dangerous pathogens. Seventy-Seven genomes of recently emerged genotype 4 reassortant Eurasian avian-like H1N1 virus (G4-EA-H1N1) are currently available. We investigated the presence and variation of potential G-quadruplex forming sequences (PQS), which can serve as targets for antiviral treatment. Results PQS were identified in all 77 genomes. The total number of PQS in G4-EA-H1N1 genomes was 571. Interestingly, the number of PQS per genome in individual close relative viruses varied from 4 to 12. PQS were not randomly distributed in the 8 segments of the G4-EA-H1N1 genome, the highest frequency of PQS being found in the NP segment (1.39 per 1000 nt), which is considered a potential target for antiviral therapy. In contrast, no PQS was found in the NS segment. Analyses of variability pointed the importance of some PQS; even if genome variation of influenza virus is extreme, the PQS with the highest G4Hunter score is the most conserved in all tested genomes. G-quadruplex formation in vitro was experimentally confirmed using spectroscopic methods. Conclusions The results presented here hint several G-quadruplex-forming sequences in G4-EA-H1N1 genomes, that could provide good therapeutic targets.

scholarly journals Engineering yellow fluorescent protein probe for visualization of parallel DNA G-quadruplex

2018 ◽  
Vol 21 (3) ◽  
pp. 84-89 ◽  
Author(s):  
Tuom TT Truong ◽  
Trang PT Phan ◽  
Linh TT Le ◽  
Dung H Nguyen ◽  
Hoang D Nguyen ◽  
...  
Keyword(s):  
Small Molecules ◽  
Fluorescent Protein ◽  
Yellow Fluorescent Protein ◽  
Biological Processes ◽  
Naked Eye ◽  
High Affinity ◽  
Quadruplex Structure ◽  
G Quadruplex

Introduction: The formation of G-quadruplex plays a key role in many biological processes. Therefore, visualization of G-quadruplex is highly essential for design of G-quadruplex-targeted small molecules (drugs). Herein, we report on an engineered fluorescent protein probe which was able to distinguish G-quadruplex topologies. Methods: The fluorescent protein probe was generated by genetically incorporating yellow fluorescent protein (YFP) to RNA helicase associated with AU-rich element (RHAU) peptide motif. Results: This probe could selectively bind and visualize parallel G-quadruplex structure (T95-2T) at high affinity (Kd~130 nM). Visualization of the parallel G-quadruplex by RHAU-YFP could be easily observed in vitro by using normal Gel Doc or the naked eye. Conclusion: The YFP probe could be encoded in cells to provide a powerful tool for detection of parallel G-quadruplexes both in vitro and in vivo.  

scholarly journals Human mitochondrial degradosome prevents harmful mitochondrial R loops and mitochondrial genome instability

2018 ◽  
Vol 115 (43) ◽  
pp. 11024-11029 ◽  
Author(s):  
Sonia Silva ◽  
Lola P. Camino ◽  
Andrés Aguilera
Keyword(s):  
Mitochondrial Dna ◽  
Molecular Mechanisms ◽  
Genome Instability ◽  
Dna Helicase ◽  
Genome Integrity ◽  
Mitochondrial Rna ◽  
Biological Functions ◽  
Rna Surveillance ◽  
Nucleic Acid Structures ◽  
Rna And Dna

R loops are nucleic acid structures comprising an DNA–RNA hybrid and a displaced single-stranded DNA. These structures may occur transiently during transcription, playing essential biological functions. However, persistent R loops may become pathological as they are important drivers of genome instability and have been associated with human diseases. The mitochondrial degradosome is a functionally conserved complex from bacteria to human mitochondria. It is composed of the ATP-dependent RNA and DNA helicase SUV3 and the PNPase ribonuclease, playing a central role in mitochondrial RNA surveillance and degradation. Here we describe a new role for the mitochondrial degradosome in preventing the accumulation of pathological R loops in the mitochondrial DNA, in addition to preventing dsRNA accumulation. Our data indicate that, similar to the molecular mechanisms acting in the nucleus, RNA surveillance mechanisms in the mitochondria are crucial to maintain its genome integrity by counteracting pathological R-loop accumulation.

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