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 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 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 G-Quadruplexes at Telomeres: Friend or Foe?

Molecules ◽  
2020 ◽  
Vol 25 (16) ◽  
pp. 3686 ◽  
Author(s):  
Tracy M. Bryan
Keyword(s):  
Tandem Repeats ◽  
Genome Instability ◽  
Protein Complexes ◽  
Telomere Maintenance ◽  
Telomeric Dna ◽  
Positive Role ◽  
Telomere Biology ◽  
Linear Chromosomes

Telomeres are DNA-protein complexes that cap and protect the ends of linear chromosomes. In almost all species, telomeric DNA has a G/C strand bias, and the short tandem repeats of the G-rich strand have the capacity to form into secondary structures in vitro, such as four-stranded G-quadruplexes. This has long prompted speculation that G-quadruplexes play a positive role in telomere biology, resulting in selection for G-rich tandem telomere repeats during evolution. There is some evidence that G-quadruplexes at telomeres may play a protective capping role, at least in yeast, and that they may positively affect telomere maintenance by either the enzyme telomerase or by recombination-based mechanisms. On the other hand, G-quadruplex formation in telomeric DNA, as elsewhere in the genome, can form an impediment to DNA replication and a source of genome instability. This review summarizes recent evidence for the in vivo existence of G-quadruplexes at telomeres, with a focus on human telomeres, and highlights some of the many unanswered questions regarding the location, form, and functions of these structures.

scholarly journals RPA-mediated recruitment of Bre1 couples histone H2B ubiquitination to DNA replication and repair

2021 ◽  
Vol 118 (8) ◽  
pp. e2017497118
Author(s):  
Guangxue Liu ◽  
Jiaqi Yan ◽  
Xuejie Wang ◽  
Junliang Chen ◽  
Xin Wang ◽  
...  
Keyword(s):  
Dna Replication ◽  
Genome Stability ◽  
Genome Instability ◽  
E3 Ligase ◽  
Dna Breaks ◽  
Ubiquitin E3 Ligase ◽  
Dna Replication And Repair ◽  
Local Enrichment

The ubiquitin E3 ligase Bre1-mediated H2B monoubiquitination (H2Bub) is essential for proper DNA replication and repair in eukaryotes. Deficiency in H2Bub causes genome instability and cancer. How the Bre1–H2Bub pathway is evoked in response to DNA replication or repair remains unknown. Here, we identify that the single-stranded DNA (ssDNA) binding factor RPA acts as a key mediator that couples Bre1-mediated H2Bub to DNA replication and repair in yeast. We found that RPA interacts with Bre1 in vitro and in vivo, and this interaction is stimulated by ssDNA. This association ensures the recruitment of Bre1 to replication forks or DNA breaks but does not affect its E3 ligase activity. Disruption of the interaction abolishes the local enrichment of H2Bub, resulting in impaired DNA replication, response to replication stress, and repair by homologous recombination, accompanied by increased genome instability and DNA damage sensitivity. Notably, we found that RNF20, the human homolog of Bre1, interacts with RPA70 in a conserved mode. Thus, RPA functions as a master regulator for the spatial–temporal control of H2Bub chromatin landscape during DNA replication and recombination, extending the versatile roles of RPA in guarding genome stability.

scholarly journals Plasmodium falciparum GBP2 is a telomere-associated protein that binds to G-quadruplex DNA and RNA

2021 ◽  
Author(s):  
James Edwards-Smallbone ◽  
Anders L Jensen ◽  
Lydia E Roberts ◽  
Francis Isidore Garcia Totanes ◽  
Sarah R Hart ◽  
...  
Keyword(s):  
Rna Binding ◽  
Protozoan Parasite ◽  
Telomere Maintenance ◽  
Model Systems ◽  
Quadruplex Dna ◽  
Dna And Rna ◽  
G Quadruplex ◽  
Associated Proteins

In the early-diverging protozoan parasite Plasmodium, few telomere-binding proteins have been identified and several are unique. Plasmodium telomeres, like those of most eukaryotes, contain guanine-rich repeats that can form G-quadruplex structures. In model systems, quadruplex-binding drugs can disrupt telomere maintenance and some quadruplex-binding drugs are potent anti-plasmodial agents. Therefore, telomere-interacting and quadruplex-interacting proteins may offer new targets for anti-malarial therapy. Here, we report that P. falciparum GBP2 is such a protein. It was identified via Proteomics of Isolated Chromatin fragments, applied here for the first time in Plasmodium. In vitro, PfGBP2 binds specifically to G-rich telomere repeats in quadruplex form and it can also bind to G-rich RNA. In vivo, PfGBP2 partially colocalises with the known telomeric protein HP1 but is also found in the cytoplasm, probably due to its affinity for RNA. Consistently, its interactome includes numerous RNA-associated proteins. PfGBP2 is evidently a multifunctional DNA/RNA-binding factor in Plasmodium.

scholarly journals Berberine Inhibits FoxM1 Dependent Transcriptional Regulation of POLE2 and Interferes with the Survival of Lung Adenocarcinoma

2021 ◽  
Author(s):  
Lulu Ni ◽  
Ping Sun ◽  
Xiaochun Fan ◽  
Zhongjie Li ◽  
Hongli Ren ◽  
...  
Keyword(s):  
Dna Replication ◽  
Lung Adenocarcinoma ◽  
Molecular Mechanisms ◽  
Cellular Functions ◽  
In Vivo Experiments ◽  
Elevated Expression ◽  
Tcga Dataset ◽  
Plasmid Transfection

Abstract Background：Berberine is one of the most interesting and promising natural anticancer drugs. POLE2 is involved in many cellular functions such as DNA replication and is highly expressed in a variety of cancers. However, the specific molecular mechanism of berberine interfering with POLE2 expression in lung adenocarcinoma (LUAD) is still unknown to a great extent.Method:The KEGG database (Release 91.0) and Gene Ontology (GO) category database were used for functional annotation of differentially expressed genes after berberine treatment. Reproducibility assessment using TCGA dataset. The biological functions of berberine in LUAD were investigated by a series of in vitro and in vivo experiments: MTT, colony formation, mouse xenograft and plasmid transfection. The molecular mechanisms of berberine were demonstrated by plasmid transfection, quantitative RT-PCR and Western blotting.Result:The elevated expression of FoxM1 and the high enrichment of DNA replication pathway were confirmed in LUAD by microarray and TCGA analysis, and were positively correlated with poor prognosis. Functionally, berberine inhibited the proliferation and survival of LUAD cell lines in vitro and in vivo. Mechanistically, berberine treatment down regulated the expression of FoxM1which closely related to survival, survival related genes in cell cycle and DNA replication pathway, and significantly down regulated the expression of survival related POLE2. Interestingly, we found that the transcription factor FoxM1 could act as a bridge between berberine and POLE2.Conclusion: Berberine significantly inhibited LUAD progression via the FoxM1/POLE2, and FoxM1/POLE2 may act as a clinical prognostic factor and a therapeutic target for LUAD. Berberine may be used as a promising therapeutic candidate for LUAD patients.

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 Changes in the topology of DNA replication intermediates: Important discrepancies between in vitro and in vivo

BioEssays ◽  
2021 ◽  
Vol 43 (5) ◽  
pp. 2000309
Author(s):  
Jorge B. Schvartzman ◽  
Víctor Martínez ◽  
Pablo Hernández ◽  
Dora B. Krimer ◽  
María‐José Fernández‐Nestosa
Keyword(s):  
Dna Replication ◽  
Replication Intermediates

scholarly journals Role of Papillomavirus E1 Initiator Dimerization in DNA Replication

2005 ◽  
Vol 79 (13) ◽  
pp. 8661-8664 ◽  
Author(s):  
Stephen Schuck ◽  
Arne Stenlund
Keyword(s):  
Dna Replication ◽  
Dna Binding ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Severe Effect ◽  
Origin Of Dna Replication ◽  
Initiation Of Dna Replication

ABSTRACT Viral initiator proteins are polypeptides that form oligomeric complexes on the origin of DNA replication (ori). These complexes carry out a multitude of functions related to initiation of DNA replication, and although many of these functions have been characterized biochemically, little is understood about how the complexes are assembled. Here we demonstrate that loss of one particular interaction, the dimerization between E1 DNA binding domains, has a severe effect on DNA replication in vivo but has surprisingly modest effects on most individual biochemical activities in vitro. We conclude that the dimer interaction is primarily required for initial recognition of ori.

Sign in / Sign up

Export Citation Format

Share Document