scholarly journals Mgs1 function at G-quadruplex structures during DNA replication

2020 ◽  
Author(s):  
Katrin Paeschke ◽  
Peter Burkovics
Keyword(s):  
Dna Replication ◽  
Genome Stability ◽  
Mechanistic Model ◽  
Regulation Of Gene Expression ◽  
Telomere Maintenance ◽  
Dna Structures ◽  
Genomic Deletions ◽  
G Quadruplex

AbstractThe coordinated action of DNA polymerases and DNA helicases is essential at genomic sites that are hard to replicate. Among these are sites that harbour G-quadruplex DNA structures (G4). G4s are stable alternative DNA structures, which have been implicated to be involved in important cellular processes like the regulation of gene expression or telomere maintenance. G4 structures were shown to hinder replication fork progression and cause genomic deletions, mutations and recombination events. Many helicases unwind G4 structures and preserve genome stability, but a detailed understanding of G4 replication and the re-start of stalled replication forks around formed G4 structures is not clear, yet. In our recent study, we identified that Mgs1 preferentially binds to G4 DNA structures in vitro and is associated with putative G4-forming chromosomal regions in vivo. Mgs1 binding to G4 motifs in vivo is partially dependent on the helicase Pif1. Pif1 is the major G4-unwinding helicase in S. cerevisiae. In the absence of Mgs1, we determined elevated gross chromosomal rearrangement (GCR) rates in yeast, similar to Pif1 deletion. Here, we highlight the recent findings and set these into context with a new mechanistic model. We propose that Mgs1's functions support DNA replication at G4-forming regions.

scholarly journals Helicases FANCJ, RTEL1 and BLM Act on Guanine Quadruplex DNA in Vivo

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 870 ◽  
Author(s):  
Peter Lansdorp ◽  
Niek van Wietmarschen
Keyword(s):  
Gene Expression ◽  
Genome Stability ◽  
Cell Function ◽  
Historical Context ◽  
Telomere Maintenance ◽  
Dna Structures ◽  
G4 Dna ◽  
Guanine Quadruplex

Guanine quadruplex (G4) structures are among the most stable secondary DNA structures that can form in vitro, and evidence for their existence in vivo has been steadily accumulating. Originally described mainly for their deleterious effects on genome stability, more recent research has focused on (potential) functions of G4 structures in telomere maintenance, gene expression, and other cellular processes. The combined research on G4 structures has revealed that properly regulating G4 DNA structures in cells is important to prevent genome instability and disruption of normal cell function. In this short review we provide some background and historical context of our work resulting in the identification of FANCJ, RTEL1 and BLM as helicases that act on G4 structures in vivo. Taken together these studies highlight important roles of different G4 DNA structures and specific G4 helicases at selected genomic locations and telomeres in regulating gene expression and maintaining genome stability.

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-quadruplex RNA motifs influence gene expression in the malaria parasite Plasmodium falciparum

2021 ◽  
Author(s):  
Franck Dumetz ◽  
Eugene Yui-Ching Chow ◽  
Lynne M. Harris ◽  
Mubarak I. Umar ◽  
Anders Jensen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plasmodium Falciparum ◽  
Malaria Parasite ◽  
Regulation Of Gene Expression ◽  
Low Complexity ◽  
Telomere Maintenance ◽  
Translation Efficiency ◽  
G Quadruplex

ABSTRACTG-quadruplexes are non-helical secondary structures that can fold in vivo in both DNA and RNA. In human cells, they can influence replication, transcription and telomere maintenance in DNA, or translation, transcript processing and stability of RNA. We have previously showed that G-quadruplexes are detectable in the DNA of the malaria parasite Plasmodium falciparum, despite a very highly A/T-biased genome with unusually few guanine-rich sequences. Here, we show that RNA G-quadruplexes can also form in P. falciparum RNA, using rG4-seq for transcriptome-wide structure-specific RNA probing. Many of the motifs, detected here via the rG4seeker pipeline, have non-canonical forms and would not be predicted by standard in silico algorithms. However, in vitro biophysical assays verified the formation of non-canonical motifs. The G-quadruplexes in the P. falciparum transcriptome are frequently clustered in certain genes and associated with regions encoding low-complexity peptide repeats. They are overrepresented in particular classes of genes, notably those that encode PfEMP1 virulence factors, stress response genes and DNA binding proteins. In vitro translation experiments and in vivo measures of translation efficiency showed that G-quadruplexes can influence the translation of P. falciparum mRNAs. Thus, the G-quadruplex is a novel player in post-transcriptional regulation of gene expression in this major human pathogen.

scholarly journals G-quadruplex–R-loop interactions and the mechanism of anticancer G-quadruplex binders

2020 ◽  
Vol 48 (21) ◽  
pp. 11942-11957
Author(s):  
Giulia Miglietta ◽  
Marco Russo ◽  
Giovanni Capranico
Keyword(s):  
Selective Inhibition ◽  
Telomere Maintenance ◽  
Published Data ◽  
Gene Promoters ◽  
Untranslated Exon ◽  
G Quadruplex ◽  
Functional Consequences ◽  
Hoogsteen Hydrogen Bonds

Abstract Genomic DNA and cellular RNAs can form a variety of non-B secondary structures, including G-quadruplex (G4) and R-loops. G4s are constituted by stacked guanine tetrads held together by Hoogsteen hydrogen bonds and can form at key regulatory sites of eukaryote genomes and transcripts, including gene promoters, untranslated exon regions and telomeres. R-loops are 3-stranded structures wherein the two strands of a DNA duplex are melted and one of them is annealed to an RNA. Specific G4 binders are intensively investigated to discover new effective anticancer drugs based on a common rationale, i.e.: the selective inhibition of oncogene expression or specific impairment of telomere maintenance. However, despite the high number of known G4 binders, such a selective molecular activity has not been fully established and several published data point to a different mode of action. We will review published data that address the close structural interplay between G4s and R-loops in vitro and in vivo, and how these interactions can have functional consequences in relation to G4 binder activity. We propose that R-loops can play a previously-underestimated role in G4 binder action, in relation to DNA damage induction, telomere maintenance, genome and epigenome instability and alterations of gene expression programs.

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 The Relevance of G-Quadruplexes for DNA Repair

2021 ◽  
Vol 22 (22) ◽  
pp. 12599
Author(s):  
Rebecca Linke ◽  
Michaela Limmer ◽  
Stefan Juranek ◽  
Annkristin Heine ◽  
Katrin Paeschke
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Genome Stability ◽  
Genome Instability ◽  
Genetic Disorders ◽  
Telomere Maintenance ◽  
Dna Structures ◽  
G4 Dna ◽  
G Quadruplex ◽  
Repair Pathways

DNA molecules can adopt a variety of alternative structures. Among these structures are G-quadruplex DNA structures (G4s), which support cellular function by affecting transcription, translation, and telomere maintenance. These structures can also induce genome instability by stalling replication, increasing DNA damage, and recombination events. G-quadruplex-driven genome instability is connected to tumorigenesis and other genetic disorders. In recent years, the connection between genome stability, DNA repair and G4 formation was further underlined by the identification of multiple DNA repair proteins and ligands which bind and stabilize said G4 structures to block specific DNA repair pathways. The relevance of G4s for different DNA repair pathways is complex and depends on the repair pathway itself. G4 structures can induce DNA damage and block efficient DNA repair, but they can also support the activity and function of certain repair pathways. In this review, we highlight the roles and consequences of G4 DNA structures for DNA repair initiation, processing, and the efficiency of various DNA repair pathways.

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.

scholarly journals Multistep mechanism of DNA replication-coupled G-quadruplex resolution

2020 ◽  
Author(s):  
Koichi Sato ◽  
Nerea Martin-Pintado ◽  
Harm Post ◽  
Maarten Altelaar ◽  
Puck Knipscheer
Keyword(s):  
Dna Replication ◽  
Genome Stability ◽  
Genome Instability ◽  
Genome Maintenance ◽  
Replicative Helicase ◽  
Dna Structures ◽  
G Quadruplex ◽  
Egg Extracts ◽  
Leading Strand ◽  
Lagging Strand

SummaryG-quadruplex (or G4) structures are non-canonical DNA structures that form in guanine-rich sequences and threaten genome stability when not properly resolved. G4 unwinding occurs during S phase via an unknown mechanism. Using Xenopus egg extracts, we define a three-step G4 unwinding mechanism that is coupled to DNA replication. First, the replicative helicase (CMG) stalls at a leading strand G4 structure. Second, the DHX36 helicase mediates the bypass of the CMG past the intact G4 structure, which allows approach of the leading strand to the G4. Third, G4 structure unwinding by the FANCJ helicase enables the DNA polymerase to synthesize past the G4 motif. A G4 on the lagging strand template does not stall CMG, but still requires DNA replication for unwinding. DHX36 and FANCJ have partially redundant roles, conferring robustness to this pathway. Our data reveal a novel genome maintenance pathway that promotes faithful G4 replication thereby avoiding genome instability.

scholarly journals E. coli Rep helicase and RecA recombinase unwind G4 DNA and are important for resistance to G4-stabilizing ligands

2020 ◽  
Vol 48 (12) ◽  
pp. 6640-6653 ◽  
Author(s):  
Tapas Paul ◽  
Andrew F Voter ◽  
Rachel R Cueny ◽  
Momčilo Gavrilov ◽  
Taekjip Ha ◽  
...  
Keyword(s):  
Atp Hydrolysis ◽  
Cellular Toxicity ◽  
Dna Structures ◽  
E Coli ◽  
G4 Dna ◽  
G Quadruplex ◽  
Physical Barriers ◽  
Stabilizing Ligands

Abstract G-quadruplex (G4) DNA structures can form physical barriers within the genome that must be unwound to ensure cellular genomic integrity. Here, we report unanticipated roles for the Escherichia coli Rep helicase and RecA recombinase in tolerating toxicity induced by G4-stabilizing ligands in vivo. We demonstrate that Rep and Rep-X (an enhanced version of Rep) display G4 unwinding activities in vitro that are significantly higher than the closely related UvrD helicase. G4 unwinding mediated by Rep involves repetitive cycles of G4 unfolding and refolding fueled by ATP hydrolysis. Rep-X and Rep also dislodge G4-stabilizing ligands, in agreement with our in vivo G4-ligand sensitivity result. We further demonstrate that RecA filaments disrupt G4 structures and remove G4 ligands in vitro, consistent with its role in countering cellular toxicity of G4-stabilizing ligands. Together, our study reveals novel genome caretaking functions for Rep and RecA in resolving deleterious G4 structures.

scholarly journals Mitochondrial genetic variation is enriched in G-quadruplex regions that stall DNA synthesis in vitro

2020 ◽  
Vol 29 (8) ◽  
pp. 1292-1309 ◽  
Author(s):  
Thomas J Butler ◽  
Katrina N Estep ◽  
Joshua A Sommers ◽  
Robert W Maul ◽  
Ann Zenobia Moore ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Variation ◽  
Dna Replication ◽  
Dna Synthesis ◽  
Dna Sequences ◽  
Computational Analysis ◽  
Italian Population ◽  
Dna Structures ◽  
G Quadruplex

Abstract As the powerhouses of the eukaryotic cell, mitochondria must maintain their genomes which encode proteins essential for energy production. Mitochondria are characterized by guanine-rich DNA sequences that spontaneously form unusual three-dimensional structures known as G-quadruplexes (G4). G4 structures can be problematic for the essential processes of DNA replication and transcription because they deter normal progression of the enzymatic-driven processes. In this study, we addressed the hypothesis that mitochondrial G4 is a source of mutagenesis leading to base-pair substitutions. Our computational analysis of 2757 individual genomes from two Italian population cohorts (SardiNIA and InCHIANTI) revealed a statistically significant enrichment of mitochondrial mutations within sequences corresponding to stable G4 DNA structures. Guided by the computational analysis results, we designed biochemical reconstitution experiments and demonstrated that DNA synthesis by two known mitochondrial DNA polymerases (Pol γ, PrimPol) in vitro was strongly blocked by representative stable G4 mitochondrial DNA structures, which could be overcome in a specific manner by the ATP-dependent G4-resolving helicase Pif1. However, error-prone DNA synthesis by PrimPol using the G4 template sequence persisted even in the presence of Pif1. Altogether, our results suggest that genetic variation is enriched in G-quadruplex regions that impede mitochondrial DNA replication.

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