1
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Tao S, Run Y, Monchaud D, Zhang W. i-Motif DNA: identification, formation, and cellular functions. Trends Genet 2024; 40:853-867. [PMID: 38902139 DOI: 10.1016/j.tig.2024.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/22/2024]
Abstract
An i-motif (iM) is a four-stranded (quadruplex) DNA structure that folds from cytosine (C)-rich sequences. iMs can fold under many different conditions in vitro, which paves the way for their formation in living cells. iMs are thought to play key roles in various DNA transactions, notably in the regulation of genome stability, gene transcription, mRNA translation, DNA replication, telomere and centromere functions, and human diseases. We summarize the different techniques used to assess the folding of iMs in vitro and provide an overview of the internal and external factors that affect their formation and stability in vivo. We describe the possible biological relevance of iMs and propose directions towards their use as target in biology.
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Affiliation(s)
- Shentong Tao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production (CIC-MCP), Nanjing Agricultural University, 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Yonghang Run
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production (CIC-MCP), Nanjing Agricultural University, 1 Weigang, Nanjing, Jiangsu 210095, China
| | - David Monchaud
- Institut de Chimie Moleculaire de l'Université de Bourgogne (ICMUB), Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6302, Université Bourgogne Franche Comté (UBFC), Dijon, France
| | - Wenli Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production (CIC-MCP), Nanjing Agricultural University, 1 Weigang, Nanjing, Jiangsu 210095, China.
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2
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De-Paula RB, Bacolla A, Syed A, Tainer JA. Enriched G4 forming repeats in the human genome are associated with robust well-coordinated transcription and reduced cancer transcriptome variation. J Biol Chem 2024:107822. [PMID: 39341500 DOI: 10.1016/j.jbc.2024.107822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 09/01/2024] [Accepted: 09/21/2024] [Indexed: 10/01/2024] Open
Abstract
Non-B DNA G-quadruplex (G4) structures with guanine (G) runs of 2-4 repeats can trigger opposing experimental transcriptional impacts. Here, we employed bioinformatic algorithms to comprehensively assess correlations of steady-state RNA transcript levels with all putative G4 sequence (pG4) locations genome-wide in three mammalian genomes and in normal and tumor human tissues. The human pG4-containing gene set displays higher expression levels than the set without pG4, supporting and extending some prior observations. pG4 enrichment at transcription start sites (TSS) in human, but not chimpanzee and mouse genomes, suggests possible positive selection pressure for pG4 at human TSS, potentially driving genome rewiring and gene expression divergence between human and chimpanzee. Comprehensive bioinformatic analyses revealed lower pG4-containing gene set variability in humans and among different pG4 genes in tumors. As G4 stabilizers are under therapeutic consideration for cancer and pathogens, such distinctions between human normal and tumor G4s along with other species merit attention. Furthermore, in germline and cancer sequences, the most mutagenic pG4 mapped to regions promoting alternative DNA structures. Overall findings establish high pG4 at TSS as a human genome attribute statistically associated with robust well-coordinated transcription and reduced cancer transcriptome variation with implications for biology, model organisms, and medicine.
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Affiliation(s)
- Ruth B De-Paula
- Graduate School of Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Aleem Syed
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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3
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Pipier A, Chetot T, Kalamatianou A, Martin N, Caroff M, Britton S, Chéron N, Trantírek L, Granzhan A, Monchaud D. Structural Optimization of Azacryptands for Targeting Three-Way DNA Junctions. Angew Chem Int Ed Engl 2024; 63:e202409780. [PMID: 38873877 DOI: 10.1002/anie.202409780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 06/15/2024]
Abstract
Transient melting of the duplex-DNA (B-DNA) during DNA transactions allows repeated sequences to fold into non-B-DNA structures, including DNA junctions and G-quadruplexes. These noncanonical structures can act as impediments to DNA polymerase progression along the duplex, thereby triggering DNA damage and ultimately jeopardizing genomic stability. Their stabilization by ad hoc ligands is currently being explored as a putative anticancer strategy since it might represent an efficient way to inflict toxic DNA damage specifically to rapidly dividing cancer cells. The relevance of this strategy is only emerging for three-way DNA junctions (TWJs) and, to date, no molecule has been recognized as a reference TWJ ligand, featuring both high affinity and selectivity. Herein, we characterize such reference ligands through a combination of in vitro techniques comprising affinity and selectivity assays (competitive FRET-melting and TWJ Screen assays), functional tests (qPCR and Taq stop assays) and structural analyses (molecular dynamics and NMR investigations). We identify novel azacryptands TrisNP-amphi and TrisNP-ana as the most promising ligands, interacting with TWJs with high affinity and selectivity. These ligands represent new molecular tools to investigate the cellular roles of TWJs and explore how they can be exploited in innovative anticancer therapies.
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Affiliation(s)
- Angélique Pipier
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, 9, Avenue Alain Savary, 21078, Dijon, France
| | - Titouan Chetot
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, 91405, Orsay, France
| | - Apollonia Kalamatianou
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, 91405, Orsay, France
| | - Nicolas Martin
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, 91405, Orsay, France
| | - Maëlle Caroff
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Sébastien Britton
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Nicolas Chéron
- PASTEUR, Département de chimie, École Normale Supérieure (ENS), PSL University, Sorbonne Université, CNRS UMR8640, 75005, Paris, France
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Anton Granzhan
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, 91405, Orsay, France
| | - David Monchaud
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, 9, Avenue Alain Savary, 21078, Dijon, France
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4
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Hardikar S, Ren R, Ying Z, Zhou J, Horton JR, Bramble MD, Liu B, Lu Y, Liu B, Coletta LD, Shen J, Dan J, Zhang X, Cheng X, Chen T. The ICF syndrome protein CDCA7 harbors a unique DNA binding domain that recognizes a CpG dyad in the context of a non-B DNA. SCIENCE ADVANCES 2024; 10:eadr0036. [PMID: 39178265 PMCID: PMC11343032 DOI: 10.1126/sciadv.adr0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 07/18/2024] [Indexed: 08/25/2024]
Abstract
CDCA7, encoding a protein with a carboxyl-terminal cysteine-rich domain (CRD), is mutated in immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome, a disease related to hypomethylation of juxtacentromeric satellite DNA. How CDCA7 directs DNA methylation to juxtacentromeric regions is unknown. Here, we show that the CDCA7 CRD adopts a unique zinc-binding structure that recognizes a CpG dyad in a non-B DNA formed by two sequence motifs. CDCA7, but not ICF mutants, preferentially binds the non-B DNA with strand-specific CpG hemi-methylation. The unmethylated sequence motif is highly enriched at centromeres of human chromosomes, whereas the methylated motif is distributed throughout the genome. At S phase, CDCA7, but not ICF mutants, is concentrated in constitutive heterochromatin foci, and the formation of such foci can be inhibited by exogenous hemi-methylated non-B DNA bound by the CRD. Binding of the non-B DNA formed in juxtacentromeric regions during DNA replication provides a mechanism by which CDCA7 controls the specificity of DNA methylation.
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Affiliation(s)
- Swanand Hardikar
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhengzhou Ying
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jujun Zhou
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R. Horton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew D. Bramble
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bigang Liu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Luis Della Coletta
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jiameng Dan
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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5
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Neidle S. A Phenotypic Approach to the Discovery of Potent G-Quadruplex Targeted Drugs. Molecules 2024; 29:3653. [PMID: 39125057 PMCID: PMC11314571 DOI: 10.3390/molecules29153653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 08/12/2024] Open
Abstract
G-quadruplex (G4) sequences, which can fold into higher-order G4 structures, are abundant in the human genome and are over-represented in the promoter regions of many genes involved in human cancer initiation, progression, and metastasis. They are plausible targets for G4-binding small molecules, which would, in the case of promoter G4s, result in the transcriptional downregulation of these genes. However, structural information is currently available on only a very small number of G4s and their ligand complexes. This limitation, coupled with the currently restricted information on the G4-containing genes involved in most complex human cancers, has led to the development of a phenotypic-led approach to G4 ligand drug discovery. This approach was illustrated by the discovery of several generations of tri- and tetra-substituted naphthalene diimide (ND) ligands that were found to show potent growth inhibition in pancreatic cancer cell lines and are active in in vivo models for this hard-to-treat disease. The cycles of discovery have culminated in a highly potent tetra-substituted ND derivative, QN-302, which is currently being evaluated in a Phase 1 clinical trial. The major genes whose expression has been down-regulated by QN-302 are presented here: all contain G4 propensity and have been found to be up-regulated in human pancreatic cancer. Some of these genes are also upregulated in other human cancers, supporting the hypothesis that QN-302 is a pan-G4 drug of potential utility beyond pancreatic cancer.
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Affiliation(s)
- Stephen Neidle
- The School of Pharmacy, University College London, London WC1N 1AX, UK
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6
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Pham P, Wood EA, Dunbar EL, Cox M, Goodman M. Controlling genome topology with sequences that trigger post-replication gap formation during replisome passage: the E. coli RRS elements. Nucleic Acids Res 2024; 52:6392-6405. [PMID: 38676944 PMCID: PMC11194060 DOI: 10.1093/nar/gkae320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
We report that the Escherichia coli chromosome includes novel GC-rich genomic structural elements that trigger formation of post-replication gaps upon replisome passage. The two nearly perfect 222 bp repeats, designated Replication Risk Sequences or RRS, are each 650 kb from the terminus sequence dif and flank the Ter macrodomain. RRS sequence and positioning is highly conserved in enterobacteria. At least one RRS appears to be essential unless a 200 kb region encompassing one of them is amplified. The RRS contain a G-quadruplex on the lagging strand which impedes DNA polymerase extension producing lagging strand ssDNA gaps, $ \le$2000 bp long, upon replisome passage. Deletion of both RRS elements has substantial effects on global genome structure and topology. We hypothesize that RRS elements serve as topological relief valves during chromosome replication and segregation. There have been no screens for genomic sequences that trigger transient gap formation. Functional analogs of RRS could be widespread, possibly including some enigmatic G-quadruplexes in eukaryotes.
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Affiliation(s)
- Phuong Pham
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089-2910, USA
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Emma L Dunbar
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Myron F Goodman
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089-2910, USA
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7
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Herr LM, Schaffer ED, Fuchs KF, Datta A, Brosh RM. Replication stress as a driver of cellular senescence and aging. Commun Biol 2024; 7:616. [PMID: 38777831 PMCID: PMC11111458 DOI: 10.1038/s42003-024-06263-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Replication stress refers to slowing or stalling of replication fork progression during DNA synthesis that disrupts faithful copying of the genome. While long considered a nexus for DNA damage, the role of replication stress in aging is under-appreciated. The consequential role of replication stress in promotion of organismal aging phenotypes is evidenced by an extensive list of hereditary accelerated aging disorders marked by molecular defects in factors that promote replication fork progression and operate uniquely in the replication stress response. Additionally, recent studies have revealed cellular pathways and phenotypes elicited by replication stress that align with designated hallmarks of aging. Here we review recent advances demonstrating the role of replication stress as an ultimate driver of cellular senescence and aging. We discuss clinical implications of the intriguing links between cellular senescence and aging including application of senotherapeutic approaches in the context of replication stress.
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Affiliation(s)
- Lauren M Herr
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Ethan D Schaffer
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Kathleen F Fuchs
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Arindam Datta
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Robert M Brosh
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
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8
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Bartas M, Brázda V, Pečinka P. Special Issue "Bioinformatics of Unusual DNA and RNA Structures". Int J Mol Sci 2024; 25:5226. [PMID: 38791265 PMCID: PMC11121459 DOI: 10.3390/ijms25105226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 04/29/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Nucleic acids are not only static carriers of genetic information but also play vital roles in controlling cellular lifecycles through their fascinating structural diversity [...].
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Affiliation(s)
- Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
| | - Václav Brázda
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic;
| | - Petr Pečinka
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
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9
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Pham P, Wood EA, Dunbar EL, Cox MM, Goodman MF. Controlling Genome Topology with Sequences that Trigger Post-replication Gap Formation During Replisome Passage: The E. coli RRS Elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.01.560376. [PMID: 37873128 PMCID: PMC10592627 DOI: 10.1101/2023.10.01.560376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
We report that the Escherichia coli chromosome includes novel GC-rich genomic structural elements that trigger formation of post-replication gaps upon replisome passage. The two nearly perfect 222 bp repeats, designated Replication Risk Sequences or RRS, are each 650 kb from the terminus sequence dif and flank the Ter macrodomain. RRS sequence and positioning is highly conserved in enterobacteria. At least one RRS appears to be essential unless a 200 kb region encompassing one of them is amplified. The RRS contain a G-quadruplex on the lagging strand which impedes DNA polymerase extension producing lagging strand ssDNA gaps, ≤2000 bp long, upon replisome passage. Deletion of both RRS elements has substantial effects on global genome structure and topology. We hypothesize that RRS elements serve as topological relief valves during chromosome replication and segregation. There have been no screens for genomic sequences that trigger transient gap formation. Functional analogs of RRS could be widespread, possibly including some enigmatic G-quadruplexes in eukaryotes.
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Affiliation(s)
- Phuong Pham
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089-2910
| | - Elizabeth A. Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544
| | - Emma L. Dunbar
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544
| | - Myron F. Goodman
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089-2910
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10
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Guo L, Bao Y, Zhao Y, Ren Z, Bi L, Zhang X, Liu C, Hou X, Wang MD, Sun B. Joint Efforts of Replicative Helicase and SSB Ensure Inherent Replicative Tolerance of G-Quadruplex. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307696. [PMID: 38126671 PMCID: PMC10916570 DOI: 10.1002/advs.202307696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/28/2023] [Indexed: 12/23/2023]
Abstract
G-quadruplex (G4) is a four-stranded noncanonical DNA structure that has long been recognized as a potential hindrance to DNA replication. However, how replisomes effectively deal with G4s to avoid replication failure is still obscure. Here, using single-molecule and ensemble approaches, the consequence of the collision between bacteriophage T7 replisome and an intramolecular G4 located on either the leading or lagging strand is examined. It is found that the adjacent fork junctions induced by G4 formation incur the binding of T7 DNA polymerase (DNAP). In addition to G4, these inactive DNAPs present insuperable obstacles, impeding the progression of DNA synthesis. Nevertheless, T7 helicase can dismantle them and resolve lagging-strand G4s, paving the way for the advancement of the replication fork. Moreover, with the assistance of the single-stranded DNA binding protein (SSB) gp2.5, T7 helicase is also capable of maintaining a leading-strand G4 structure in an unfolded state, allowing for a fraction of T7 DNAPs to synthesize through without collapse. These findings broaden the functional repertoire of a replicative helicase and underscore the inherent G4 tolerance of a replisome.
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Affiliation(s)
- Lijuan Guo
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Yanling Bao
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Yilin Zhao
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Zhiyun Ren
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghai200031China
- University of Chinese Academy of SciencesBeijing100049China
| | - Lulu Bi
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Xia Zhang
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic ChemistryChinese Academy of SciencesShanghai201210China
| | - Xi‐Miao Hou
- College of Life SciencesNorthwest A&F UniversityYanglingShaanxi712100China
| | - Michelle D. Wang
- Department of Physics, Laboratory of Atomic and Solid State PhysicsCornell UniversityIthacaNY14853USA
- Howard Hughes Medical InstituteCornell UniversityIthacaNY14853USA
| | - Bo Sun
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
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11
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Mitteaux J, Raevens S, Wang Z, Pirrotta M, Valverde IE, Hudson RHE, Monchaud D. PhpC modulates G-quadruplex-RNA landscapes in human cells. Chem Commun (Camb) 2024; 60:424-427. [PMID: 38086624 DOI: 10.1039/d3cc05155b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Stabilizing DNA/RNA G-quadruplexes (G4s) using small molecules (ligands) has proven an efficient strategy to decipher G4 biology. Quite paradoxically, this search has also highlighted the need for finding molecules able to disrupt G4s to tackle G4-associated cellular dysfunctions. We report here on both qualitative and quantitative investigations that validate the G4-RNA-destabilizing properties of the leading compound PhpC in human cells.
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Affiliation(s)
- Jérémie Mitteaux
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), CNRS UMR 6302, 9, avenue Alain Savary, Dijon 21078, France.
| | - Sandy Raevens
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), CNRS UMR 6302, 9, avenue Alain Savary, Dijon 21078, France.
| | - Zi Wang
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Marc Pirrotta
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), CNRS UMR 6302, 9, avenue Alain Savary, Dijon 21078, France.
| | - Ibai E Valverde
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), CNRS UMR 6302, 9, avenue Alain Savary, Dijon 21078, France.
| | - Robert H E Hudson
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), CNRS UMR 6302, 9, avenue Alain Savary, Dijon 21078, France.
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12
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Kumar C, Remus D. Looping out of control: R-loops in transcription-replication conflict. Chromosoma 2024; 133:37-56. [PMID: 37419963 PMCID: PMC10771546 DOI: 10.1007/s00412-023-00804-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/09/2023]
Abstract
Transcription-replication conflict is a major cause of replication stress that arises when replication forks collide with the transcription machinery. Replication fork stalling at sites of transcription compromises chromosome replication fidelity and can induce DNA damage with potentially deleterious consequences for genome stability and organismal health. The block to DNA replication by the transcription machinery is complex and can involve stalled or elongating RNA polymerases, promoter-bound transcription factor complexes, or DNA topology constraints. In addition, studies over the past two decades have identified co-transcriptional R-loops as a major source for impairment of DNA replication forks at active genes. However, how R-loops impede DNA replication at the molecular level is incompletely understood. Current evidence suggests that RNA:DNA hybrids, DNA secondary structures, stalled RNA polymerases, and condensed chromatin states associated with R-loops contribute to the of fork progression. Moreover, since both R-loops and replication forks are intrinsically asymmetric structures, the outcome of R-loop-replisome collisions is influenced by collision orientation. Collectively, the data suggest that the impact of R-loops on DNA replication is highly dependent on their specific structural composition. Here, we will summarize our current understanding of the molecular basis for R-loop-induced replication fork progression defects.
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Affiliation(s)
- Charanya Kumar
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, USA
| | - Dirk Remus
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, USA.
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Hardikar S, Ren R, Ying Z, Horton JR, Bramble MD, Liu B, Lu Y, Liu B, Dan J, Zhang X, Cheng X, Chen T. The ICF syndrome protein CDCA7 harbors a unique DNA-binding domain that recognizes a CpG dyad in the context of a non-B DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571946. [PMID: 38168392 PMCID: PMC10760177 DOI: 10.1101/2023.12.15.571946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
CDCA7 , encoding a protein with a C-terminal cysteine-rich domain (CRD), is mutated in immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome, a disease related to hypomethylation of juxtacentromeric satellite DNA. How CDCA7 directs DNA methylation to juxtacentromeric regions is unknown. Here, we show that the CDCA7 CRD adopts a unique zinc-binding structure that recognizes a CpG dyad in a non-B DNA formed by two sequence motifs. CDCA7, but not ICF mutants, preferentially binds the non-B DNA with strand-specific CpG hemi-methylation. The unmethylated sequence motif is highly enriched at centromeres of human chromosomes, whereas the methylated motif is distributed throughout the genome. At S phase, CDCA7, but not ICF mutants, is concentrated in constitutive heterochromatin foci, and the formation of such foci can be inhibited by exogenous hemi-methylated non-B DNA bound by the CRD. Binding of the non-B DNA formed in juxtacentromeric regions during DNA replication provides a mechanism by which CDCA7 controls the specificity of DNA methylation.
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De Magis A, Limmer M, Mudiyam V, Monchaud D, Juranek S, Paeschke K. UV-induced G4 DNA structures recruit ZRF1 which prevents UV-induced senescence. Nat Commun 2023; 14:6705. [PMID: 37872164 PMCID: PMC10593929 DOI: 10.1038/s41467-023-42494-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
Senescence has two roles in oncology: it is known as a potent tumor-suppressive mechanism, which also supports tissue regeneration and repair, it is also known to contribute to reduced patient resilience, which might lead to cancer recurrence and resistance after therapy. Senescence can be activated in a DNA damage-dependent and -independent manner. It is not clear which type of genomic lesions induces senescence, but it is known that UV irradiation can activate cellular senescence in photoaged skin. Proteins that support the repair of DNA damage are linked to senescence but how they contribute to senescence after UV irradiation is still unknown. Here, we unraveled a mechanism showing that upon UV irradiation multiple G-quadruplex (G4) DNA structures accumulate in cell nuclei, which leads to the recruitment of ZRF1 to these G4 sites. ZRF1 binding to G4s ensures genome stability. The absence of ZRF1 triggers an accumulation of G4 structures, improper UV lesion repair, and entry into senescence. On the molecular level loss of ZRF1 as well as high G4 levels lead to the upregulation of DDB2, a protein associated with the UV-damage repair pathway, which drives cells into senescence.
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Affiliation(s)
- Alessio De Magis
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Michaela Limmer
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Venkat Mudiyam
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), CNRS UMR 6302, Université de Bourgogne, Dijon, France
| | - Stefan Juranek
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Katrin Paeschke
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany.
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany.
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Matos-Rodrigues G, Hisey JA, Nussenzweig A, Mirkin SM. Detection of alternative DNA structures and its implications for human disease. Mol Cell 2023; 83:3622-3641. [PMID: 37863029 DOI: 10.1016/j.molcel.2023.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 10/22/2023]
Abstract
Around 3% of the genome consists of simple DNA repeats that are prone to forming alternative (non-B) DNA structures, such as hairpins, cruciforms, triplexes (H-DNA), four-stranded guanine quadruplexes (G4-DNA), and others, as well as composite RNA:DNA structures (e.g., R-loops, G-loops, and H-loops). These DNA structures are dynamic and favored by the unwinding of duplex DNA. For many years, the association of alternative DNA structures with genome function was limited by the lack of methods to detect them in vivo. Here, we review the recent advancements in the field and present state-of-the-art technologies and methods to study alternative DNA structures. We discuss the limitations of these methods as well as how they are beginning to provide insights into causal relationships between alternative DNA structures, genome function and stability, and human disease.
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Affiliation(s)
| | - Julia A Hisey
- Department of Biology, Tufts University, Medford, MA, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
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Han ZQ, Wen LN. Application of G-quadruplex targets in gastrointestinal cancers: Advancements, challenges and prospects. World J Gastrointest Oncol 2023; 15:1149-1173. [PMID: 37546556 PMCID: PMC10401460 DOI: 10.4251/wjgo.v15.i7.1149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/11/2023] [Accepted: 05/08/2023] [Indexed: 07/12/2023] Open
Abstract
Genomic instability and inflammation are considered to be two enabling characteristics that support cancer development and progression. G-quadruplex structure is a key element that contributes to genomic instability and inflammation. G-quadruplexes were once regarded as simply an obstacle that can block the transcription of oncogenes. A ligand targeting G-quadruplexes was found to have anticancer activity, making G-quadruplexes potential anticancer targets. However, further investigation has revealed that G-quadruplexes are widely distributed throughout the human genome and have many functions, such as regulating DNA replication, DNA repair, transcription, translation, epigenetics, and inflammatory response. G-quadruplexes play double regulatory roles in transcription and translation. In this review, we focus on G-quadruplexes as novel targets for the treatment of gastrointestinal cancers. We summarize the application basis of G-quadruplexes in gastrointestinal cancers, including their distribution sites, structural characteristics, and physiological functions. We describe the current status of applications for the treatment of esophageal cancer, pancreatic cancer, hepatocellular carcinoma, gastric cancer, colorectal cancer, and gastrointestinal stromal tumors, as well as the associated challenges. Finally, we review the prospective clinical applications of G-quadruplex targets, providing references for targeted treatment strategies in gastrointestinal cancers.
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Affiliation(s)
- Zong-Qiang Han
- Department of Laboratory Medicine, Beijing Xiaotangshan Hospital, Beijing 102211, China
| | - Li-Na Wen
- Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
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