1
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Cui X, Zhang C, Fu C, Hu J, Li T, Li L. YY1 is involved in homologous recombination inhibition at guanine quadruplex sites in human cells. Nucleic Acids Res 2024:gkae502. [PMID: 38869071 DOI: 10.1093/nar/gkae502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024] Open
Abstract
Homologous recombination (HR) is a key process for repairing DNA double strand breaks and for promoting genetic diversity. However, HR occurs unevenly across the genome, and certain genomic features can influence its activity. One such feature is the presence of guanine quadruplexes (G4s), stable secondary structures widely distributed throughout the genome. These G4s play essential roles in gene transcription and genome stability regulation. Especially, elevated G4 levels in cells deficient in the Bloom syndrome helicase (BLM) significantly enhance HR at G4 sites, potentially threatening genome stability. Here, we investigated the role of G4-binding protein Yin Yang-1 (YY1) in modulating HR at G4 sites in human cells. Our results show that YY1's binding to G4 structures suppresses sister chromatid exchange after BLM knockdown, and YY1's chromatin occupancy negatively correlates with the overall HR rate observed across the genome. By limiting RAD51 homolog 1 (RAD51) access, YY1 preferentially binds to essential genomic regions, shielding them from excessive HR. Our findings unveil a novel role of YY1-G4 interaction, revealing novel insights into cellular mechanisms involved in HR regulation.
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Affiliation(s)
- Xinyu Cui
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chengwen Zhang
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunqing Fu
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinglei Hu
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tengjiao Li
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin Li
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
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2
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Yang L, Ruan Y, Chen B, Zhu Y, Xu H. Circ_0001671 regulates prostate cancer progression through miR-27b-3p/BLM axis. Sci Rep 2024; 14:12181. [PMID: 38806577 PMCID: PMC11133351 DOI: 10.1038/s41598-024-63068-x] [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: 01/13/2024] [Accepted: 05/24/2024] [Indexed: 05/30/2024] Open
Abstract
Prostate cancer (PCa) ranks as the second most prevalent cancer among males globally. However, the exact mechanisms underlying its progression remain inadequately elucidated. The present study sought to investigate the role and underlying molecular mechanism of hsa_circ_0001671 (circ_0001671) in the pathogenic behavior of PCa cells. Guided by the ceRNA theory, miR-27b-3p was employed to identify circRNAs that could potentially regulate Bloom Syndrome Protein (BLM). A series of experimental approaches including bioinformatics, luciferase assays, Fluorescent In Situ Hybridization (FISH), RNA-pulldown, and RNA Immunoprecipitation (RIP) were utilized to validate the miRNA sponge function of circ_0001671. Divergent primer PCR, RNase R treatments, and Sanger sequencing were conducted for the identification of circ_0001671. Quantitative RT-PCR and Western blot analyses were performed to validate gene expression levels. Both in vitro and in vivo experiments were conducted to assess the functional role of circ_0001671 in PCa cells.It was observed that the expression levels of circ_0001671 and BLM were significantly elevated in PCa tissues and cell lines, whereas miR-27b-3p showed decreased expression. Circ_0001671 was found to promote cellular proliferation, migration, and invasion, while inhibiting apoptosis. In vivo assays confirmed that circ_0001671 facilitated tumor growth. Further mechanistic studies revealed that circ_0001671 acted as a competing endogenous RNA (ceRNA) for BLM by sponging miR-27b-3p. The oncogenic role of circ_0001671 in PCa was shown to be modulated through the miR-27b-3p/BLM axis. In conclusion, circ_0001671 exerts an oncogenic effect in prostate cancer through the regulation of BLM by sponging miR-27b-3p, thus suggesting a novel molecular target for the treatment of PCa.
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Affiliation(s)
- Lihong Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Yong Ruan
- College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Bin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Yuhang Zhu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Houqiang Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Life Sciences, Guizhou University, Guiyang, 550025, China.
- College of Animal Science, Guizhou University, Guiyang, 550025, China.
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3
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Fu L, Wu Q, Fu J. Exploring the biological roles of DHX36, a DNA/RNA G-quadruplex helicase, highlights functions in male infertility: A comprehensive review. Int J Biol Macromol 2024; 268:131811. [PMID: 38677694 DOI: 10.1016/j.ijbiomac.2024.131811] [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: 01/04/2024] [Revised: 03/20/2024] [Accepted: 03/23/2024] [Indexed: 04/29/2024]
Abstract
It is estimated that 15 % of couples at reproductive age worldwide suffer from infertility, approximately 50 % of cases are caused by male factors. Significant progress has been made in the diagnosis and treatment of male infertility through assisted reproductive technology and molecular genetics methods. However, there is still inadequate research on the underlying mechanisms of gene regulation in the process of spermatogenesis. Guanine-quadruplexes (G4s) are a class of non-canonical secondary structures of nucleic acid commonly found in genomes and RNAs that play important roles in various biological processes. Interestingly, the DEAH-box helicase 36 (DHX36) displays high specificity for the G4s which can unwind both DNA G4s and RNA G4s enzymatically and is highly expressed in testis, thereby regulating multiple cellular functions including transcription, pre-mRNA splicing, translation, telomere maintenance, genomic stability, and RNA metabolism in development and male infertility. This review provides an overview of the roles of G4s and DHX36 in reproduction and development. We mainly focus on the potential role of DHX36 in male infertility. We also discuss possible future research directions regarding the mechanism of spermatogenesis mediated by DHX36 through G4s in spermatogenesis-related genes and provide new targets for gene therapy of male infertility.
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Affiliation(s)
- Li Fu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China; Department of Reproductive Medicine, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, China; Faculty of Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Qiang Wu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
| | - Junjiang Fu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China.
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4
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Kligfeld H, Han I, Abraham A, Shukla V. Alternative DNA structures in hematopoiesis and adaptive immunity. Adv Immunol 2024; 161:109-126. [PMID: 38763699 DOI: 10.1016/bs.ai.2024.03.002] [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] [Indexed: 05/21/2024]
Abstract
Besides the canonical B-form, DNA also adopts alternative non-B form conformations which are highly conserved in all domains of life. While extensive research over decades has centered on the genomic functions of B-form DNA, understanding how non-B-form conformations influence functional genomic states remains a fundamental and open question. Recent studies have ascribed alternative DNA conformations such as G-quadruplexes and R-loops as important functional features in eukaryotic genomes. This review delves into the biological importance of alternative DNA structures, with a specific focus on hematopoiesis and adaptive immunity. We discuss the emerging roles of G-quadruplex and R-loop structures, the two most well-studied alternative DNA conformations, in the hematopoietic compartment and present evidence for their functional roles in normal cellular physiology and associated pathologies.
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Affiliation(s)
- Heather Kligfeld
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, United States; Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, United States
| | - Isabella Han
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, United States
| | - Ajay Abraham
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, United States; Center for Human Immunobiology, Northwestern University, Chicago, IL, United States
| | - Vipul Shukla
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, United States; Center for Human Immunobiology, Northwestern University, Chicago, IL, United States; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, United States.
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5
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Barela Hudgell MA, Momtaz F, Jafri A, Alekseyev MA, Smith LC. Local Genomic Instability of the SpTransformer Gene Family in the Purple Sea Urchin Inferred from BAC Insert Deletions. Genes (Basel) 2024; 15:222. [PMID: 38397211 PMCID: PMC10887614 DOI: 10.3390/genes15020222] [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: 01/09/2024] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
The SpTransformer (SpTrf) gene family in the purple sea urchin, Strongylocentrotus purpuratus, encodes immune response proteins. The genes are clustered, surrounded by short tandem repeats, and some are present in genomic segmental duplications. The genes share regions of sequence and include repeats in the coding exon. This complex structure is consistent with putative local genomic instability. Instability of the SpTrf gene cluster was tested by 10 days of growth of Escherichia coli harboring bacterial artificial chromosome (BAC) clones of sea urchin genomic DNA with inserts containing SpTrf genes. After the growth period, the BAC DNA inserts were analyzed for size and SpTrf gene content. Clones with multiple SpTrf genes showed a variety of deletions, including loss of one, most, or all genes from the cluster. Alternatively, a BAC insert with a single SpTrf gene was stable. BAC insert instability is consistent with variations in the gene family composition among sea urchins, the types of SpTrf genes in the family, and a reduction in the gene copy number in single coelomocytes. Based on the sequence variability among SpTrf genes within and among sea urchins, local genomic instability of the family may be important for driving sequence diversity in this gene family that would be of benefit to sea urchins in their arms race with marine microbes.
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Affiliation(s)
- Megan A. Barela Hudgell
- Department of Biological Sciences, George Washington University, Washington, DC 20052, USA; (M.A.B.H.); (F.M.)
| | - Farhana Momtaz
- Department of Biological Sciences, George Washington University, Washington, DC 20052, USA; (M.A.B.H.); (F.M.)
| | - Abiha Jafri
- Department of Biological Sciences, George Washington University, Washington, DC 20052, USA; (M.A.B.H.); (F.M.)
| | - Max A. Alekseyev
- Department of Mathematics and the Computational Biology Institute, George Washington University, Washington, DC 20052, USA;
| | - L. Courtney Smith
- Department of Biological Sciences, George Washington University, Washington, DC 20052, USA; (M.A.B.H.); (F.M.)
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6
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Dabral P, Uppal T, Verma SC. G-quadruplexes of KSHV oriLyt play important roles in promoting lytic DNA replication. Microbiol Spectr 2023; 11:e0531622. [PMID: 37800915 PMCID: PMC10714766 DOI: 10.1128/spectrum.05316-22] [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: 12/26/2022] [Accepted: 08/15/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE Biological processes originating from the DNA and RNA can be regulated by the secondary structures present in the stretch of nucleic acids, and the G-quadruplexes are shown to regulate transcription, translation, and replication. In this study, we identified the presence of multiple G-quadruplex sites in the region (oriLyt) of Kaposi's sarcoma-associated herpesvirus (KSHV) DNA, which is essential for DNA replication during the lytic cycle. We demonstrated the roles of these G-quadruplexes through multiple biochemical and biophysical assays in controlling replication and efficient virus production. We demonstrated that KSHV achieves this by recruiting RecQ1 (helicase) at those G-quadruplex sites for efficient viral DNA replication. Analysis of the replicated DNA through nucleoside labeling and immunostaining showed a reduced initiation of DNA replication in cells with a pharmacologic stabilizer of G-quadruplexes. Overall, this study confirmed the role of the G-quadruplex in regulating viral DNA replication, which can be exploited for controlling viral DNA replication.
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Affiliation(s)
- Prerna Dabral
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
- Vitalant Research Institute, San Francisco, California, USA
| | - Timsy Uppal
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
| | - Subhash C. Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
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7
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Lorenzatti A, Piga EJ, Gismondi M, Binolfi A, Margarit E, Calcaterra N, Armas P. Genetic variations in G-quadruplex forming sequences affect the transcription of human disease-related genes. Nucleic Acids Res 2023; 51:12124-12139. [PMID: 37930868 PMCID: PMC10711447 DOI: 10.1093/nar/gkad948] [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: 08/12/2022] [Revised: 09/22/2023] [Accepted: 10/12/2023] [Indexed: 11/08/2023] Open
Abstract
Guanine-rich DNA strands can fold into non-canonical four-stranded secondary structures named G-quadruplexes (G4s). G4s folded in proximal promoter regions (PPR) are associated either with positive or negative transcriptional regulation. Given that single nucleotide variants (SNVs) affecting G4 folding (G4-Vars) may alter gene transcription, and that SNVs are associated with the human diseases' onset, we undertook a novel comprehensive study of the G4-Vars genome-wide (G4-variome) to find disease-associated G4-Vars located into PPRs. We developed a bioinformatics strategy to find disease-related SNVs located into PPRs simultaneously overlapping with putative G4-forming sequences (PQSs). We studied five G4-Vars disturbing in vitro the folding and stability of the G4s located into PPRs, which had been formerly associated with sporadic Alzheimer's disease (GRIN2B), a severe familiar coagulopathy (F7), atopic dermatitis (CSF2), myocardial infarction (SIRT1) and deafness (LHFPL5). Results obtained in cultured cells for these five G4-Vars suggest that the changes in the G4s affect the transcription, potentially contributing to the development of the mentioned diseases. Collectively, data reinforce the general idea that G4-Vars may impact on the different susceptibilities to human genetic diseases' onset, and could be novel targets for diagnosis and drug design in precision medicine.
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Affiliation(s)
- Agustín Lorenzatti
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
| | - Ernesto J Piga
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
| | - Mauro Gismondi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 531, Rosario, Santa Fe, Argentina
| | - Andrés Binolfi
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica (PLABEM), Ocampo y Esmeralda, Rosario S200EZP, Santa Fe, Argentina
| | - Ezequiel Margarit
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 531, Rosario, Santa Fe, Argentina
| | - Nora B Calcaterra
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
| | - Pablo Armas
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
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8
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Williams SL, Casas‐Delucchi CS, Raguseo F, Guneri D, Li Y, Minamino M, Fletcher EE, Yeeles JTP, Keyser UF, Waller ZAE, Di Antonio M, Coster G. Replication-induced DNA secondary structures drive fork uncoupling and breakage. EMBO J 2023; 42:e114334. [PMID: 37781931 PMCID: PMC10646557 DOI: 10.15252/embj.2023114334] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/03/2023] Open
Abstract
Sequences that form DNA secondary structures, such as G-quadruplexes (G4s) and intercalated-Motifs (iMs), are abundant in the human genome and play various physiological roles. However, they can also interfere with replication and threaten genome stability. Multiple lines of evidence suggest G4s inhibit replication, but the underlying mechanism remains unclear. Moreover, evidence of how iMs affect the replisome is lacking. Here, we reconstitute replication of physiologically derived structure-forming sequences to find that a single G4 or iM arrest DNA replication. Direct single-molecule structure detection within solid-state nanopores reveals structures form as a consequence of replication. Combined genetic and biophysical characterisation establishes that structure stability and probability of structure formation are key determinants of replisome arrest. Mechanistically, replication arrest is caused by impaired synthesis, resulting in helicase-polymerase uncoupling. Significantly, iMs also induce breakage of nascent DNA. Finally, stalled forks are only rescued by a specialised helicase, Pif1, but not Rrm3, Sgs1, Chl1 or Hrq1. Altogether, we provide a mechanism for quadruplex structure formation and resolution during replication and highlight G4s and iMs as endogenous sources of replication stress.
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Affiliation(s)
- Sophie L Williams
- Genome Replication Lab, Division of Cancer Biology, Institute of Cancer ResearchChester Beatty LaboratoriesLondonUK
| | - Corella S Casas‐Delucchi
- Genome Replication Lab, Division of Cancer Biology, Institute of Cancer ResearchChester Beatty LaboratoriesLondonUK
| | - Federica Raguseo
- Chemistry DepartmentImperial College London, MSRHLondonUK
- Institute of Chemical Biology, MSRHLondonUK
| | | | - Yunxuan Li
- Cavendish LaboratoryUniversity of CambridgeCambridgeUK
| | | | | | | | | | | | - Marco Di Antonio
- Chemistry DepartmentImperial College London, MSRHLondonUK
- Institute of Chemical Biology, MSRHLondonUK
- Francis Crick InstituteLondonUK
| | - Gideon Coster
- Genome Replication Lab, Division of Cancer Biology, Institute of Cancer ResearchChester Beatty LaboratoriesLondonUK
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9
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Sato K, Knipscheer P. G-quadruplex resolution: From molecular mechanisms to physiological relevance. DNA Repair (Amst) 2023; 130:103552. [PMID: 37572578 DOI: 10.1016/j.dnarep.2023.103552] [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: 05/24/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023]
Abstract
Guanine-rich DNA sequences can fold into stable four-stranded structures called G-quadruplexes or G4s. Research in the past decade demonstrated that G4 structures are widespread in the genome and prevalent in regulatory regions of actively transcribed genes. The formation of G4s has been tightly linked to important biological processes including regulation of gene expression and genome maintenance. However, they can also pose a serious threat to genome integrity especially by impeding DNA replication, and G4-associated somatic mutations have been found accumulated in the cancer genomes. Specialised DNA helicases and single stranded DNA binding proteins that can resolve G4 structures play a crucial role in preventing genome instability. The large variety of G4 unfolding proteins suggest the presence of multiple G4 resolution mechanisms in cells. Recently, there has been considerable progress in our detailed understanding of how G4s are resolved, especially during DNA replication. In this review, we first discuss the current knowledge of the genomic G4 landscapes and the impact of G4 structures on DNA replication and genome integrity. We then describe the recent progress on the mechanisms that resolve G4 structures and their physiological relevance. Finally, we discuss therapeutic opportunities to target G4 structures.
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Affiliation(s)
- Koichi Sato
- Oncode Institute, Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Puck Knipscheer
- Oncode Institute, Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, the Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.
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10
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van Dijk EL, Naquin D, Gorrichon K, Jaszczyszyn Y, Ouazahrou R, Thermes C, Hernandez C. Genomics in the long-read sequencing era. Trends Genet 2023; 39:649-671. [PMID: 37230864 DOI: 10.1016/j.tig.2023.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
Long-read sequencing (LRS) technologies have provided extremely powerful tools to explore genomes. While in the early years these methods suffered technical limitations, they have recently made significant progress in terms of read length, throughput, and accuracy and bioinformatics tools have strongly improved. Here, we aim to review the current status of LRS technologies, the development of novel methods, and the impact on genomics research. We will explore the most impactful recent findings made possible by these technologies focusing on high-resolution sequencing of genomes and transcriptomes and the direct detection of DNA and RNA modifications. We will also discuss how LRS methods promise a more comprehensive understanding of human genetic variation, transcriptomics, and epigenetics for the coming years.
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Affiliation(s)
- Erwin L van Dijk
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Delphine Naquin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Kévin Gorrichon
- National Center of Human Genomics Research (CNRGH), 91000 Évry-Courcouronnes, France
| | - Yan Jaszczyszyn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Rania Ouazahrou
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Claude Thermes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Céline Hernandez
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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11
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Li G, Su G, Wang Y, Wang W, Shi J, Li D, Sui G. Integrative genomic analyses of promoter G-quadruplexes reveal their selective constraint and association with gene activation. Commun Biol 2023; 6:625. [PMID: 37301913 PMCID: PMC10257653 DOI: 10.1038/s42003-023-05015-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023] Open
Abstract
G-quadruplexes (G4s) regulate DNA replication and gene transcription, and are enriched in promoters without fully appreciated functional relevance. Here we show high selection pressure on putative G4 (pG4) forming sequences in promoters through investigating genetic and genomic data. Analyses of 76,156 whole-genome sequences reveal that G-tracts and connecting loops in promoter pG4s display lower or higher allele frequencies, respectively, than pG4-flanking regions, and central guanines (Gs) in G-tracts show higher selection pressure than other Gs. Additionally, pG4-promoters produce over 72.4% of transcripts, and promoter G4-containing genes are expressed at relatively high levels. Most genes repressed by TMPyP4, a G4-ligand, regulate epigenetic processes, and promoter G4s are enriched with gene activation histone marks, chromatin remodeler and transcription factor binding sites. Consistently, cis-expression quantitative trait loci (cis-eQTLs) are enriched in promoter pG4s and their G-tracts. Overall, our study demonstrates selective constraint of promoter G4s and reinforces their stimulative role in gene expression.
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Affiliation(s)
- Guangyue Li
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Gongbo Su
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Yunxuan Wang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Wenmeng Wang
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Jinming Shi
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Dangdang Li
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Guangchao Sui
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.
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12
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Vijay Kumar MJ, Morales R, Tsvetkov AS. G-quadruplexes and associated proteins in aging and Alzheimer's disease. FRONTIERS IN AGING 2023; 4:1164057. [PMID: 37323535 PMCID: PMC10267416 DOI: 10.3389/fragi.2023.1164057] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Abstract
Aging is a prominent risk factor for many neurodegenerative disorders, such as Alzheimer's disease (AD). Alzheimer's disease is characterized by progressive cognitive decline, memory loss, and neuropsychiatric and behavioral symptoms, accounting for most of the reported dementia cases. This disease is now becoming a major challenge and burden on modern society, especially with the aging population. Over the last few decades, a significant understanding of the pathophysiology of AD has been gained by studying amyloid deposition, hyperphosphorylated tau, synaptic dysfunction, oxidative stress, calcium dysregulation, and neuroinflammation. This review focuses on the role of non-canonical secondary structures of DNA/RNA G-quadruplexes (G4s, G4-DNA, and G4-RNA), G4-binding proteins (G4BPs), and helicases, and their roles in aging and AD. Being critically important for cellular function, G4s are involved in the regulation of DNA and RNA processes, such as replication, transcription, translation, RNA localization, and degradation. Recent studies have also highlighted G4-DNA's roles in inducing DNA double-strand breaks that cause genomic instability and G4-RNA's participation in regulating stress granule formation. This review emphasizes the significance of G4s in aging processes and how their homeostatic imbalance may contribute to the pathophysiology of AD.
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Affiliation(s)
- M. J. Vijay Kumar
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
| | - Rodrigo Morales
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- Centro Integrativo de Biologia y Quimica Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago, Chile
| | - Andrey S. Tsvetkov
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
- UTHealth Consortium on Aging, The University of Texas McGovern Medical School, Houston, TX, United States
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13
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Wang G, Vasquez KM. Dynamic alternative DNA structures in biology and disease. Nat Rev Genet 2023; 24:211-234. [PMID: 36316397 DOI: 10.1038/s41576-022-00539-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Repetitive elements in the human genome, once considered 'junk DNA', are now known to adopt more than a dozen alternative (that is, non-B) DNA structures, such as self-annealed hairpins, left-handed Z-DNA, three-stranded triplexes (H-DNA) or four-stranded guanine quadruplex structures (G4 DNA). These dynamic conformations can act as functional genomic elements involved in DNA replication and transcription, chromatin organization and genome stability. In addition, recent studies have revealed a role for these alternative structures in triggering error-generating DNA repair processes, thereby actively enabling genome plasticity. As a driving force for genetic variation, non-B DNA structures thus contribute to both disease aetiology and evolution.
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Affiliation(s)
- Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA.
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14
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A non-genetic switch triggers alternative telomere lengthening and cellular immortalization in ATRX deficient cells. Nat Commun 2023; 14:939. [PMID: 36805596 PMCID: PMC9941109 DOI: 10.1038/s41467-023-36294-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 01/25/2023] [Indexed: 02/22/2023] Open
Abstract
Alternative Lengthening of Telomeres (ALT) is an aberrant DNA recombination pathway which grants replicative immortality to approximately 10% of all cancers. Despite this high prevalence of ALT in cancer, the mechanism and genetics by which cells activate this pathway remain incompletely understood. A major challenge in dissecting the events that initiate ALT is the extremely low frequency of ALT induction in human cell systems. Guided by the genetic lesions that have been associated with ALT from cancer sequencing studies, we genetically engineered primary human pluripotent stem cells to deterministically induce ALT upon differentiation. Using this genetically defined system, we demonstrate that disruption of the p53 and Rb pathways in combination with ATRX loss-of-function is sufficient to induce all hallmarks of ALT and results in functional immortalization in a cell type-specific manner. We further demonstrate that ALT can be induced in the presence of telomerase, is neither dependent on telomere shortening nor crisis, but is rather driven by continuous telomere instability triggered by the induction of differentiation in ATRX-deficient stem cells.
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15
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Chung WC, Ravichandran S, Park D, Lee GM, Kim YE, Choi Y, Song MJ, Kim KK, Ahn JH. G-quadruplexes formed by Varicella-Zoster virus reiteration sequences suppress expression of glycoprotein C and regulate viral cell-to-cell spread. PLoS Pathog 2023; 19:e1011095. [PMID: 36630443 PMCID: PMC9873165 DOI: 10.1371/journal.ppat.1011095] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/24/2023] [Accepted: 01/02/2023] [Indexed: 01/12/2023] Open
Abstract
G-quadruplex (G4) formed by repetitive guanosine-rich sequences plays important roles in diverse cellular processes; however, its roles in viral infection are not fully understood. In this study, we investigated the genome-wide distribution of G4-forming sequences (G4 motifs) in Varicella-Zoster virus (VZV) and found that G4 motifs are enriched in the internal repeat short and the terminal repeat short regions flanking the unique short region and also in some reiteration (R) sequence regions. A high density of G4 motifs in the R2 region was found on the template strand of ORF14, which encodes glycoprotein C (gC), a virulent factor for viral growth in skin. Analyses such as circular dichroism spectroscopy, thermal difference spectra, and native polyacrylamide gel electrophoresis with oligodeoxynucleotides demonstrated that several G4 motifs in ORF14 form stable G4 structures. In transfection assays, gC expression from the G4-disrupted ORF14 gene was increased at the transcriptional level and became more resistant to suppression by G4-ligand treatment. The recombinant virus containing the G4-disrupted ORF14 gene expressed a higher level of gC mRNA, while it showed a slightly reduced growth. This G4-disrupted ORF14 virus produced smaller plaques than the wild-type virus. Our results demonstrate that G4 formation via reiteration sequences suppresses gC expression during VZV infection and regulates viral cell-to-cell spread.
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Affiliation(s)
- Woo-Chang Chung
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Subramaniyam Ravichandran
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Daegyu Park
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Gwang Myeong Lee
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Young-Eui Kim
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Youngju Choi
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Moon Jung Song
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
- Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Jin-Hyun Ahn
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
- Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
- * E-mail:
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16
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Sister chromatid exchanges induced by perturbed replication can form independently of BRCA1, BRCA2 and RAD51. Nat Commun 2022; 13:6722. [PMID: 36344511 PMCID: PMC9640580 DOI: 10.1038/s41467-022-34519-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 10/27/2022] [Indexed: 11/09/2022] Open
Abstract
Sister chromatid exchanges (SCEs) are products of joint DNA molecule resolution, and are considered to form through homologous recombination (HR). Indeed, SCE induction upon irradiation requires the canonical HR factors BRCA1, BRCA2 and RAD51. In contrast, replication-blocking agents, including PARP inhibitors, induce SCEs independently of BRCA1, BRCA2 and RAD51. PARP inhibitor-induced SCEs are enriched at difficult-to-replicate genomic regions, including common fragile sites (CFSs). PARP inhibitor-induced replication lesions are transmitted into mitosis, suggesting that SCEs can originate from mitotic processing of under-replicated DNA. Proteomics analysis reveals mitotic recruitment of DNA polymerase theta (POLQ) to synthetic DNA ends. POLQ inactivation results in reduced SCE numbers and severe chromosome fragmentation upon PARP inhibition in HR-deficient cells. Accordingly, analysis of CFSs in cancer genomes reveals frequent allelic deletions, flanked by signatures of POLQ-mediated repair. Combined, we show PARP inhibition generates under-replicated DNA, which is processed into SCEs during mitosis, independently of canonical HR factors.
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17
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Mellor C, Perez C, Sale JE. Creation and resolution of non-B-DNA structural impediments during replication. Crit Rev Biochem Mol Biol 2022; 57:412-442. [PMID: 36170051 PMCID: PMC7613824 DOI: 10.1080/10409238.2022.2121803] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 08/02/2022] [Accepted: 08/25/2022] [Indexed: 01/27/2023]
Abstract
During replication, folding of the DNA template into non-B-form secondary structures provides one of the most abundant impediments to the smooth progression of the replisome. The core replisome collaborates with multiple accessory factors to ensure timely and accurate duplication of the genome and epigenome. Here, we discuss the forces that drive non-B structure formation and the evidence that secondary structures are a significant and frequent source of replication stress that must be actively countered. Taking advantage of recent advances in the molecular and structural biology of the yeast and human replisomes, we examine how structures form and how they may be sensed and resolved during replication.
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Affiliation(s)
- Christopher Mellor
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Consuelo Perez
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Julian E Sale
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
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18
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Osia B, Twarowski J, Jackson T, Lobachev K, Liu L, Malkova A. Migrating bubble synthesis promotes mutagenesis through lesions in its template. Nucleic Acids Res 2022; 50:6870-6889. [PMID: 35748867 PMCID: PMC9262586 DOI: 10.1093/nar/gkac520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/23/2022] [Accepted: 06/10/2022] [Indexed: 12/24/2022] Open
Abstract
Break-induced replication (BIR) proceeds via a migrating D-loop for hundreds of kilobases and is highly mutagenic. Previous studies identified long single-stranded (ss) nascent DNA that accumulates during leading strand synthesis to be a target for DNA damage and a primary source of BIR-induced mutagenesis. Here, we describe a new important source of mutagenic ssDNA formed during BIR: the ssDNA template for leading strand BIR synthesis formed during D-loop migration. Specifically, we demonstrate that this D-loop bottom template strand (D-BTS) is susceptible to APOBEC3A (A3A)-induced DNA lesions leading to mutations associated with BIR. Also, we demonstrate that BIR-associated ssDNA promotes an additional type of genetic instability: replication slippage between microhomologies stimulated by inverted DNA repeats. Based on our results we propose that these events are stimulated by both known sources of ssDNA formed during BIR, nascent DNA formed by leading strand synthesis, and the D-BTS that we describe here. Together we report a new source of mutagenesis during BIR that may also be shared by other homologous recombination pathways driven by D-loop repair synthesis.
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Affiliation(s)
| | | | - Tyler Jackson
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kirill Lobachev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GE 30332, USA
| | - Liping Liu
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA
| | - Anna Malkova
- To whom correspondence should be addressed. Tel: +1 319 384 1285;
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19
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Georgakopoulos-Soares I, Parada GE, Hemberg M. Secondary structures in RNA synthesis, splicing and translation. Comput Struct Biotechnol J 2022; 20:2871-2884. [PMID: 35765654 PMCID: PMC9198270 DOI: 10.1016/j.csbj.2022.05.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/19/2022] [Accepted: 05/21/2022] [Indexed: 11/30/2022] Open
Abstract
Even though the functional role of mRNA molecules is primarily decided by the nucleotide sequence, several properties are determined by secondary structure conformations. Examples of secondary structures include long range interactions, hairpins, R-loops and G-quadruplexes and they are formed through interactions of non-adjacent nucleotides. Here, we discuss advances in our understanding of how secondary structures can impact RNA synthesis, splicing, translation and mRNA half-life. During RNA synthesis, secondary structures determine RNA polymerase II (RNAPII) speed, thereby influencing splicing. Splicing is also determined by RNA binding proteins and their binding rates are modulated by secondary structures. For the initiation of translation, secondary structures can control the choice of translation start site. Here, we highlight the mechanisms by which secondary structures modulate these processes, discuss advances in technologies to detect and study them systematically, and consider the roles of RNA secondary structures in disease.
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20
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Xue C, Salunkhe SJ, Tomimatsu N, Kawale AS, Kwon Y, Burma S, Sung P, Greene EC. Bloom helicase mediates formation of large single-stranded DNA loops during DNA end processing. Nat Commun 2022; 13:2248. [PMID: 35473934 PMCID: PMC9042962 DOI: 10.1038/s41467-022-29937-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 03/14/2022] [Indexed: 01/27/2023] Open
Abstract
Bloom syndrome (BS) is associated with a profoundly increased cancer risk and is caused by mutations in the Bloom helicase (BLM). BLM is involved in the nucleolytic processing of the ends of DNA double-strand breaks (DSBs), to yield long 3' ssDNA tails that serve as the substrate for break repair by homologous recombination (HR). Here, we use single-molecule imaging to demonstrate that BLM mediates formation of large ssDNA loops during DNA end processing. A BLM mutant lacking the N-terminal domain (NTD) retains vigorous in vitro end processing activity but fails to generate ssDNA loops. This same mutant supports DSB end processing in cells, however, these cells do not form RAD51 DNA repair foci and the processed DSBs are channeled into synthesis-dependent strand annealing (SSA) instead of HR-mediated repair, consistent with a defect in RAD51 filament formation. Together, our results provide insights into BLM functions during homologous recombination.
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Affiliation(s)
- Chaoyou Xue
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Sameer J Salunkhe
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Nozomi Tomimatsu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Ajinkya S Kawale
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Sandeep Burma
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Department of Neurosurgery, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
- The Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
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21
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Hamadeh Z, Hanlon V, Lansdorp PM. Mapping of sister chromatid exchange events and genome alterations in single cells. Methods 2022; 204:64-72. [PMID: 35483548 DOI: 10.1016/j.ymeth.2022.04.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/08/2022] [Accepted: 04/22/2022] [Indexed: 12/14/2022] Open
Abstract
Mammalian genomes encode over a hundred different helicases, many of which are implicated in the repair of DNA lesions by acting on DNA structures arising during DNA replication, recombination or transcription. Defining the in vivo substrates of such DNA helicases is a major challenge given the large number of helicases in the genome, the breadth of potential substrates in the genome and the degree of genetic pleiotropy among DNA helicases in resolving diverse substrates. Helicases such as WRN, BLM and RECQL5 are implicated in the resolution of error-free recombination events known as sister chromatid exchange events (SCEs). Single cell Strand-seq can be used to map the genomic location of individual SCEs at a resolution that exceeds that of classical cytogenetic techniques by several orders of magnitude. By mapping the genomic locations of SCEs in the absence of different helicases, it should in principle be possible to infer the substrate specificity of specific helicases. Here we describe how the genome can be interrogated for such DNA repair events using single-cell template strand sequencing (Strand-seq) and bioinformatic tools. SCEs and copy-number alterations were mapped to genomic locations at kilobase resolution in haploid KBM7 cells. Strategies, possibilities, and limitations of Strand-seq to study helicase function are illustrated using these cells before and after CRISPR/Cas9 knock out of WRN, BLM and/or RECQL5.
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Affiliation(s)
- Zeid Hamadeh
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Genome Science and Technology, University of British Columbia, Vancouver, BC, Canada
| | - Vincent Hanlon
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Peter M Lansdorp
- Departments of Medical Genetics and Hematology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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22
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A POLD3/BLM dependent pathway handles DSBs in transcribed chromatin upon excessive RNA:DNA hybrid accumulation. Nat Commun 2022; 13:2012. [PMID: 35440629 PMCID: PMC9019021 DOI: 10.1038/s41467-022-29629-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 03/25/2022] [Indexed: 12/03/2022] Open
Abstract
Transcriptionally active loci are particularly prone to breakage and mounting evidence suggests that DNA Double-Strand Breaks arising in active genes are handled by a dedicated repair pathway, Transcription-Coupled DSB Repair (TC-DSBR), that entails R-loop accumulation and dissolution. Here, we uncover a function for the Bloom RecQ DNA helicase (BLM) in TC-DSBR in human cells. BLM is recruited in a transcription dependent-manner at DSBs where it fosters resection, RAD51 binding and accurate Homologous Recombination repair. However, in an R-loop dissolution-deficient background, we find that BLM promotes cell death. We report that upon excessive RNA:DNA hybrid accumulation, DNA synthesis is enhanced at DSBs, in a manner that depends on BLM and POLD3. Altogether our work unveils a role for BLM at DSBs in active chromatin, and highlights the toxic potential of RNA:DNA hybrids that accumulate at transcription-associated DSBs. DNA Double Strand breaks in transcriptionally active loci (TC-DSBs) undergo a dedicated repair pathway. Here, the authors show that excessive RNA:DNA hybrid accumulation at TC-DSBs elicits POLD3/BLM-dependent DNA synthesis that induces cell toxicity.
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23
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Wang KB, Liu Y, Li Y, Dickerhoff J, Li J, Yang MH, Yang D, Kong LY. Oxidative Damage Induces a Vacancy G-Quadruplex That Binds Guanine Metabolites: Solution Structure of a cGMP Fill-in Vacancy G-Quadruplex in the Oxidized BLM Gene Promoter. J Am Chem Soc 2022; 144:6361-6372. [PMID: 35352895 PMCID: PMC9904417 DOI: 10.1021/jacs.2c00435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Guanine (G)-oxidation to 8-oxo-7,8-dihydroguanine (OG) by reactive oxygen species in genomic DNA has been implicated with various human diseases. G-quadruplex (G4)-forming sequences in gene promoters are highly susceptible to G-oxidation, which can subsequently cause gene activation. However, the underlying G4 structural changes that result from OG modifications remain poorly understood. Herein, we investigate the effect of G-oxidation on the BLM gene promoter G4. For the first time, we show that OG can induce a G-vacancy-containing G4 (vG4), which can be filled in and stabilized by guanine metabolites and derivatives. We determined the NMR solution structure of the cGMP-fill-in oxidized BLM promoter vG4. This is the first complex structure of an OG-induced vG4 from a human gene promoter sequence with a filled-in guanine metabolite. The high-resolution structure elucidates the structural features of the specific 5'-end cGMP-fill-in for the OG-induced vG4. Interestingly, the OG is removed from the G-core and becomes part of the 3'-end capping structure. A series of guanine metabolites and derivatives are evaluated for fill-in activity to the oxidation-induced vG4. Significantly, cellular guanine metabolites, such as cGMP and GTP, can bind and stabilize the OG-induced vG4, suggesting their potential regulatory role in response to oxidative damage in physiological and pathological processes. Our work thus provides exciting insights into how oxidative damage and cellular metabolites may work together through a G4-based epigenetic feature for gene regulation. Furthermore, the NMR structure can guide the rational design of small-molecule inhibitors that specifically target the oxidation-induced vG4s.
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Affiliation(s)
| | | | - Yipu Li
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
| | - Jonathan Dickerhoff
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jinzhu Li
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
| | - Ming-Hua Yang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
| | - Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Department of Chemistry, and Purdue Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ling-Yi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
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24
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The Dynamic Regulation of G-Quadruplex DNA Structures by Cytosine Methylation. Int J Mol Sci 2022; 23:ijms23052407. [PMID: 35269551 PMCID: PMC8910436 DOI: 10.3390/ijms23052407] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 02/01/2023] Open
Abstract
It is well known that certain non B-DNA structures, including G-quadruplexes, are key elements that can regulate gene expression. Here, we explore the theory that DNA modifications, such as methylation of cytosine, could act as a dynamic switch by promoting or alleviating the structural formation of G-quadruplex structures in DNA or RNA. The interaction between epigenetic DNA modifications, G4 formation, and the 3D architecture of the genome is a complex and developing area of research. Although there is growing evidence for such interactions, a great deal still remains to be discovered. In vivo, the potential effect that cytosine methylation may have on the formation of DNA structures has remained largely unresearched, despite this being a potential mechanism through which epigenetic factors could regulate gene activity. Such interactions could represent novel mechanisms for important biological functions, including altering nucleosome positioning or regulation of gene expression. Furthermore, promotion of strand-specific G-quadruplex formation in differentially methylated genes could have a dynamic role in directing X-inactivation or the control of imprinting, and would be a worthwhile focus for future research.
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25
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Hodson C, Low JKK, van Twest S, Jones SE, Swuec P, Murphy V, Tsukada K, Fawkes M, Bythell-Douglas R, Davies A, Holien JK, O'Rourke JJ, Parker BL, Glaser A, Parker MW, Mackay JP, Blackford AN, Costa A, Deans AJ. Mechanism of Bloom syndrome complex assembly required for double Holliday junction dissolution and genome stability. Proc Natl Acad Sci U S A 2022; 119:e2109093119. [PMID: 35115399 PMCID: PMC8832983 DOI: 10.1073/pnas.2109093119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 12/17/2021] [Indexed: 12/29/2022] Open
Abstract
The RecQ-like helicase BLM cooperates with topoisomerase IIIα, RMI1, and RMI2 in a heterotetrameric complex (the "Bloom syndrome complex") for dissolution of double Holliday junctions, key intermediates in homologous recombination. Mutations in any component of the Bloom syndrome complex can cause genome instability and a highly cancer-prone disorder called Bloom syndrome. Some heterozygous carriers are also predisposed to breast cancer. To understand how the activities of BLM helicase and topoisomerase IIIα are coupled, we purified the active four-subunit complex. Chemical cross-linking and mass spectrometry revealed a unique architecture that links the helicase and topoisomerase domains. Using biochemical experiments, we demonstrated dimerization mediated by the N terminus of BLM with a 2:2:2:2 stoichiometry within the Bloom syndrome complex. We identified mutations that independently abrogate dimerization or association of BLM with RMI1, and we show that both are dysfunctional for dissolution using in vitro assays and cause genome instability and synthetic lethal interactions with GEN1/MUS81 in cells. Truncated BLM can also inhibit the activity of full-length BLM in mixed dimers, suggesting a putative mechanism of dominant-negative action in carriers of BLM truncation alleles. Our results identify critical molecular determinants of Bloom syndrome complex assembly required for double Holliday junction dissolution and maintenance of genome stability.
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Affiliation(s)
- Charlotte Hodson
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Sylvie van Twest
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Samuel E Jones
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | - Paolo Swuec
- Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Vincent Murphy
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Kaima Tsukada
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
- Laboratory for Zero-Carbon Energy, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Matthew Fawkes
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Rohan Bythell-Douglas
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Department of Medicine (St. Vincent's), University of Melbourne, Fitzroy, VIC 3065, Australia
| | | | - Jessica K Holien
- Department of Medicine (St. Vincent's), University of Melbourne, Fitzroy, VIC 3065, Australia
- School of Science, RMIT University, Melbourne, VIC 3001, Australia
- Structural Biology Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Julienne J O'Rourke
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Benjamin L Parker
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Astrid Glaser
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Michael W Parker
- Structural Biology Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Bio21 Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Andrew N Blackford
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | | | - Andrew J Deans
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia;
- Department of Medicine (St. Vincent's), University of Melbourne, Fitzroy, VIC 3065, Australia
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26
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Sun X, Bai J, Xu J, Xi X, Gu M, Zhu C, Xue H, Chen C, Dong J. Multiple DSB Resection Activities Redundantly Promote Alternative End Joining-Mediated Class Switch Recombination. Front Cell Dev Biol 2021; 9:767624. [PMID: 34926456 PMCID: PMC8671047 DOI: 10.3389/fcell.2021.767624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/25/2021] [Indexed: 01/13/2023] Open
Abstract
Alternative end joining (A-EJ) catalyzes substantial level of antibody class switch recombination (CSR) in B cells deficient for classical non-homologous end joining, featuring increased switch (S) region DSB resection and junctional microhomology (MH). While resection has been suggested to initiate A-EJ in model DSB repair systems using engineered endonucleases, the contribution of resection factors to A-EJ-mediated CSR remains unclear. In this study, we systematically dissected the requirement for individual DSB resection factors in A-EJ-mediated class switching with a cell-based assay system and high-throughput sequencing. We show that while CtIP and Mre11 both are mildly required for CSR in WT cells, they play more critical roles in mediating A-EJ CSR, which depend on the exonuclease activity of Mre11. While DNA2 and the helicase/HRDC domain of BLM are required for A-EJ by mediating long S region DSB resection, in contrast, Exo1's resection-related function does not play any obvious roles for class switching in either c-NHEJ or A-EJ cells, or mediated in an AID-independent manner by joining of Cas9 breaks. Furthermore, ATM and its kinase activity functions at least in part independent of CtIP/Mre11 to mediate A-EJ switching in Lig4-deficient cells. In stark contrast to Lig4 deficiency, 53BP1-deficient cells do not depend on ATM/Mre11/CtIP for residual joining. We discuss the roles for each resection factor in A-EJ-mediated CSR and suggest that the extent of requirements for resection is context dependent.
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Affiliation(s)
- Xikui Sun
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Jingning Bai
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Jiejie Xu
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Xiaoli Xi
- Department of Gastroenterology, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Mingyu Gu
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Chengming Zhu
- Research Center of the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Hongman Xue
- Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Chun Chen
- Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Junchao Dong
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China.,Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
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27
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Chen JN, He YD, Liang HT, Cai TT, Chen Q, Zheng KW. Regulation of PDGFR-β gene expression by targeting the G-vacancy bearing G-quadruplex in promoter. Nucleic Acids Res 2021; 49:12634-12643. [PMID: 34850916 PMCID: PMC8682790 DOI: 10.1093/nar/gkab1154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/14/2021] [Accepted: 11/09/2021] [Indexed: 12/31/2022] Open
Abstract
G-quadruplex is an essential element in gene transcription that serves as a promising drug target. Guanine-vacancy-bearing G-quadruplex (GVBQ) is a newly identified G-quadruplex that has distinct structural features from the canonical G-quadruplex. Potential GVBQ-forming motifs are widely distributed in gene promoter regions. However, whether GVBQ can form in genomic DNA and be an effective target for manipulating gene expression is unknown. Using photo-crosslinking, dimethyl sulfate footprinting, exonuclease digestion and in vitro transcription, we demonstrated the formation of a GVBQ in the G-rich nuclease hypersensitivity element within the human PDGFR-β gene promoter region in both single-stranded and double-stranded DNA. The formation of GVBQ in dsDNA could be induced by negative supercoiling created by downstream transcription. We also found that the PDGFR-β GVBQ was specifically recognized and stabilized by a new synthetic porphyrin guanine conjugate (mPG). Targeting the PDGFR-β GVBQ in human cancer cells using the mPG could specifically alter PDGFR-β gene expression. Our work illustrates that targeting GVBQ with mPG in human cells can regulate the expression level of a specific gene, thus indicating a novel strategy for drug development.
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Affiliation(s)
- Juan-Nan Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Yi-de He
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China.,School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - Hui-Ting Liang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Ting-Ting Cai
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Qi Chen
- School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Ke-Wei Zheng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China
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28
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Brosh RM, Wu Y. An emerging picture of FANCJ's role in G4 resolution to facilitate DNA replication. NAR Cancer 2021; 3:zcab034. [PMID: 34873585 DOI: 10.1093/narcan/zcab034] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/28/2021] [Accepted: 08/13/2021] [Indexed: 02/06/2023] Open
Abstract
A well-accepted hallmark of cancer is genomic instability, which drives tumorigenesis. Therefore, understanding the molecular and cellular defects that destabilize chromosomal integrity is paramount to cancer diagnosis, treatment and cure. DNA repair and the replication stress response are overarching paradigms for maintenance of genomic stability, but the devil is in the details. ATP-dependent helicases serve to unwind DNA so it is replicated, transcribed, recombined and repaired efficiently through coordination with other nucleic acid binding and metabolizing proteins. Alternatively folded DNA structures deviating from the conventional anti-parallel double helix pose serious challenges to normal genomic transactions. Accumulating evidence suggests that G-quadruplex (G4) DNA is problematic for replication. Although there are multiple human DNA helicases that can resolve G4 in vitro, it is debated which helicases are truly important to resolve such structures in vivo. Recent advances have begun to elucidate the principal helicase actors, particularly in cellular DNA replication. FANCJ, a DNA helicase implicated in cancer and the chromosomal instability disorder Fanconi Anemia, takes center stage in G4 resolution to allow smooth DNA replication. We will discuss FANCJ's role with its protein partner RPA to remove G4 obstacles during DNA synthesis, highlighting very recent advances and implications for cancer therapy.
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Affiliation(s)
- Robert M Brosh
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
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29
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Patil KM, Chin D, Seah HL, Shi Q, Lim KW, Phan AT. G4-PROTAC: targeted degradation of a G-quadruplex binding protein. Chem Commun (Camb) 2021; 57:12816-12819. [PMID: 34783801 DOI: 10.1039/d1cc05025g] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
G-quadruplex (G4) binding proteins regulate important biological processes, but their interaction networks are poorly understood. We report the first use of G4 as a warhead of a proteolysis-targeting chimera (G4-PROTAC) for targeted degradation of a G4-binding protein (RHAU/DHX36). G4-PROTAC provides a new way to explore G4-protein networks and to develop potential therapeutics.
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Affiliation(s)
- Kiran M Patil
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore.
| | - Danielle Chin
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore.
| | - Hui Ling Seah
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore.
| | - Qi Shi
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore.
| | - Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore.
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore. .,NTU Institute of Structural Biology, Nanyang Technological University, 636921, Singapore
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30
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Liu Y, Zhu X, Wang K, Zhang B, Qiu S. The Cellular Functions and Molecular Mechanisms of G-Quadruplex Unwinding Helicases in Humans. Front Mol Biosci 2021; 8:783889. [PMID: 34912850 PMCID: PMC8667583 DOI: 10.3389/fmolb.2021.783889] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/02/2021] [Indexed: 01/19/2023] Open
Abstract
G-quadruplexes (G4s) are stable non-canonical secondary structures formed by G-rich DNA or RNA sequences. They play various regulatory roles in many biological processes. It is commonly agreed that G4 unwinding helicases play key roles in G4 metabolism and function, and these processes are closely related to physiological and pathological processes. In recent years, more and more functional and mechanistic details of G4 helicases have been discovered; therefore, it is necessary to carefully sort out the current research efforts. Here, we provide a systematic summary of G4 unwinding helicases from the perspective of functions and molecular mechanisms. First, we provide a general introduction about helicases and G4s. Next, we comprehensively summarize G4 unfolding helicases in humans and their proposed cellular functions. Then, we review their study methods and molecular mechanisms. Finally, we share our perspective on further prospects. We believe this review will provide opportunities for researchers to reach the frontiers in the functions and molecular mechanisms of human G4 unwinding helicases.
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Affiliation(s)
- Yang Liu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Xinting Zhu
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Kejia Wang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Bo Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Shuyi Qiu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
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31
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Linke R, Limmer M, Juranek SA, Heine A, Paeschke K. The Relevance of G-Quadruplexes for DNA Repair. Int J Mol Sci 2021; 22:12599. [PMID: 34830478 PMCID: PMC8620898 DOI: 10.3390/ijms222212599] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 01/28/2023] Open
Abstract
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.
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Affiliation(s)
- Rebecca Linke
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michaela Limmer
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
| | - Stefan A. Juranek
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
| | - Annkristin Heine
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
| | - Katrin Paeschke
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
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32
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Marilovtseva EV, Studitsky VM. Guanine Quadruplexes in Cell Nucleus Metabolism. Mol Biol 2021. [DOI: 10.1134/s0026893321040075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Chovanec P, Yin Y. A mapping platform for mitotic crossover by single-cell multi-omics. Methods Enzymol 2021; 661:183-204. [PMID: 34776212 DOI: 10.1016/bs.mie.2021.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Mitotic crossovers have the potential to cause large-scale genome rearrangements. Here, we describe high-throughput, single-cell, whole-genome sequencing methods for mapping crossovers genome-wide at scale. The methods are generalizable to various eukaryotes and to other end points requiring high-throughput, high-coverage single cell sequencing.
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Affiliation(s)
- Peter Chovanec
- Department of Human Genetics, University of California, Los Angeles, CA, Unites States
| | - Yi Yin
- Department of Human Genetics, University of California, Los Angeles, CA, Unites States.
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34
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Caterino M, Paeschke K. Action and function of helicases on RNA G-quadruplexes. Methods 2021; 204:110-125. [PMID: 34509630 PMCID: PMC9236196 DOI: 10.1016/j.ymeth.2021.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/02/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022] Open
Abstract
Methodological progresses and piling evidence prove the rG4 biology in vivo. rG4s step in virtually every aspect of RNA biology. Helicases unwinding of rG4s is a fine regulatory layer to the downstream processes and general cell homeostasis. The current knowledge is however limited to a few cell lines. The regulation of helicases themselves is delineating as a important question. Non-helicase rG4-processing proteins likely play a role.
The nucleic acid structure called G-quadruplex (G4) is currently discussed to function in nucleic acid-based mechanisms that influence several cellular processes. They can modulate the cellular machinery either positively or negatively, both at the DNA and RNA level. The majority of what we know about G4 biology comes from DNA G4 (dG4) research. RNA G4s (rG4), on the other hand, are gaining interest as researchers become more aware of their role in several aspects of cellular homeostasis. In either case, the correct regulation of G4 structures within cells is essential and demands specialized proteins able to resolve them. Small changes in the formation and unfolding of G4 structures can have severe consequences for the cells that could even stimulate genome instability, apoptosis or proliferation. Helicases are the most relevant negative G4 regulators, which prevent and unfold G4 formation within cells during different pathways. Yet, and despite their importance only a handful of rG4 unwinding helicases have been identified and characterized thus far. This review addresses the current knowledge on rG4s-processing helicases with a focus on methodological approaches. An example of a non-helicase rG4s-unwinding protein is also briefly described.
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Affiliation(s)
- Marco Caterino
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany.
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35
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Polleys EJ, Freudenreich CH. Homologous recombination within repetitive DNA. Curr Opin Genet Dev 2021; 71:143-153. [PMID: 34464817 DOI: 10.1016/j.gde.2021.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/06/2021] [Accepted: 08/12/2021] [Indexed: 12/16/2022]
Abstract
Many microsatellite DNA sequences are able to form non-B form DNA secondary structures, such as hairpin loops, cruciforms, triplex DNA or G-quadruplexes. These DNA structures can form a significant impediment to DNA replication and repair, leading to DNA nicks, gaps, and breaks, which can be repaired by homologous recombination (HR). Recent work understanding HR at structure-forming repeats has focused on genetic requirements for replication fork restart, break induced replication (BIR) at broken forks, recombination during and after relocalization of breaks or stalled forks to the nuclear periphery, and how repair pathway choice and kinetics are navigated in the presence of a repeat tract. In this review, we summarize recent developments that illuminate the role of recombination in repairing DNA damage or causing tract length changes within repetitive DNA and its role in maintaining genome stability.
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Affiliation(s)
- Erica J Polleys
- Department of Biology, Tufts University, Medford MA 02155, United States
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford MA 02155, United States; Program in Genetics, Tufts University, Boston MA 02111, United States.
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36
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St Germain C, Zhao H, Barlow JH. Transcription-Replication Collisions-A Series of Unfortunate Events. Biomolecules 2021; 11:1249. [PMID: 34439915 PMCID: PMC8391903 DOI: 10.3390/biom11081249] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Transcription-replication interactions occur when DNA replication encounters genomic regions undergoing transcription. Both replication and transcription are essential for life and use the same DNA template making conflicts unavoidable. R-loops, DNA supercoiling, DNA secondary structure, and chromatin-binding proteins are all potential obstacles for processive replication or transcription and pose an even more potent threat to genome integrity when these processes co-occur. It is critical to maintaining high fidelity and processivity of transcription and replication while navigating through a complex chromatin environment, highlighting the importance of defining cellular pathways regulating transcription-replication interaction formation, evasion, and resolution. Here we discuss how transcription influences replication fork stability, and the safeguards that have evolved to navigate transcription-replication interactions and maintain genome integrity in mammalian cells.
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Affiliation(s)
- Commodore St Germain
- School of Mathematics and Science, Solano Community College, 4000 Suisun Valley Road, Fairfield, CA 94534, USA
- Department of Microbiology and Molecular Genetics, University of California Davis, One Shields Avenue, Davis, CA 95616, USA;
| | - Hongchang Zhao
- Department of Microbiology and Molecular Genetics, University of California Davis, One Shields Avenue, Davis, CA 95616, USA;
| | - Jacqueline H. Barlow
- Department of Microbiology and Molecular Genetics, University of California Davis, One Shields Avenue, Davis, CA 95616, USA;
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37
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Shastri VM, Subramanian V, Schmidt KH. A novel cell-cycle-regulated interaction of the Bloom syndrome helicase BLM with Mcm6 controls replication-linked processes. Nucleic Acids Res 2021; 49:8699-8713. [PMID: 34370039 PMCID: PMC8421143 DOI: 10.1093/nar/gkab663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/16/2021] [Accepted: 07/22/2021] [Indexed: 11/13/2022] Open
Abstract
The Bloom syndrome DNA helicase BLM contributes to chromosome stability through its roles in double-strand break repair by homologous recombination and DNA replication fork restart during the replication stress response. Loss of BLM activity leads to Bloom syndrome, which is characterized by extraordinary cancer risk and small stature. Here, we have analyzed the composition of the BLM complex during unperturbed S-phase and identified a direct physical interaction with the Mcm6 subunit of the minichromosome maintenance (MCM) complex. Using distinct binding sites, BLM interacts with the N-terminal domain of Mcm6 in G1 phase and switches to the C-terminal Cdt1-binding domain of Mcm6 in S-phase, with a third site playing a role for Mcm6 binding after DNA damage. Disruption of Mcm6-binding to BLM in S-phase leads to supra-normal DNA replication speed in unperturbed cells, and the helicase activity of BLM is required for this increased replication speed. Upon disruption of BLM/Mcm6 interaction, repair of replication-dependent DNA double-strand breaks is delayed and cells become hypersensitive to DNA damage and replication stress. Our findings reveal that BLM not only plays a role in the response to DNA damage and replication stress, but that its physical interaction with Mcm6 is required in unperturbed cells, most notably in S-phase as a negative regulator of replication speed.
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Affiliation(s)
- Vivek M Shastri
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
| | - Veena Subramanian
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
| | - Kristina H Schmidt
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA.,Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
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38
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Transcription/Replication Conflicts in Tumorigenesis and Their Potential Role as Novel Therapeutic Targets in Multiple Myeloma. Cancers (Basel) 2021; 13:cancers13153755. [PMID: 34359660 PMCID: PMC8345052 DOI: 10.3390/cancers13153755] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/13/2021] [Accepted: 07/22/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Multiple myeloma is a hematologic cancer characterized by the accumulation of malignant plasma cells in the bone marrow. It remains a mostly incurable disease due to the inability to overcome refractory disease and drug-resistant relapse. Oncogenic transformation of PC in multiple myeloma is thought to occur within the secondary lymphoid organs. However, the precise molecular events leading to myelomagenesis remain obscure. Here, we identified genes involved in the prevention and the resolution of conflicts between the replication and transcription significantly overexpressed during the plasma cell differentiation process and in multiple myeloma cells. We discussed the potential role of these factors in myelomagenesis and myeloma biology. The specific targeting of these factors might constitute a new therapeutic strategy in multiple myeloma. Abstract Plasma cells (PCs) have an essential role in humoral immune response by secretion of antibodies, and represent the final stage of B lymphocytes differentiation. During this differentiation, the pre-plasmablastic stage is characterized by highly proliferative cells that start to secrete immunoglobulins (Igs). Thus, replication and transcription must be tightly regulated in these cells to avoid transcription/replication conflicts (TRCs), which could increase replication stress and lead to genomic instability. In this review, we analyzed expression of genes involved in TRCs resolution during B to PC differentiation and identified 41 genes significantly overexpressed in the pre-plasmablastic stage. This illustrates the importance of mechanisms required for adequate processing of TRCs during PCs differentiation. Furthermore, we identified that several of these factors were also found overexpressed in purified PCs from patients with multiple myeloma (MM) compared to normal PCs. Malignant PCs produce high levels of Igs concomitantly with cell cycle deregulation. Therefore, increasing the TRCs occurring in MM cells could represent a potent therapeutic strategy for MM patients. Here, we describe the potential roles of TRCs resolution factors in myelomagenesis and discuss the therapeutic interest of targeting the TRCs resolution machinery in MM.
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Bossaert M, Pipier A, Riou JF, Noirot C, Nguyên LT, Serre RF, Bouchez O, Defrancq E, Calsou P, Britton S, Gomez D. Transcription-associated topoisomerase 2α (TOP2A) activity is a major effector of cytotoxicity induced by G-quadruplex ligands. eLife 2021; 10:65184. [PMID: 34180392 PMCID: PMC8279764 DOI: 10.7554/elife.65184] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/16/2021] [Indexed: 12/11/2022] Open
Abstract
G-quadruplexes (G4) are non-canonical DNA structures found in the genome of most species including human. Small molecules stabilizing these structures, called G4 ligands, have been identified and, for some of them, shown to induce cytotoxic DNA double-strand breaks. Through the use of an unbiased genetic approach, we identify here topoisomerase 2α (TOP2A) as a major effector of cytotoxicity induced by two clastogenic G4 ligands, pyridostatin and CX-5461, the latter molecule currently undergoing phase I/II clinical trials in oncology. We show that both TOP2 activity and transcription account for DNA break production following G4 ligand treatments. In contrast, clastogenic activity of these G4 ligands is countered by topoisomerase 1 (TOP1), which limits co-transcriptional G4 formation, and by factors promoting transcriptional elongation. Altogether our results support that clastogenic G4 ligands act as DNA structure-driven TOP2 poisons at transcribed regions bearing G4 structures.
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Affiliation(s)
- Madeleine Bossaert
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Angélique Pipier
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Jean-Francois Riou
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, CNRS, INSERM, Paris, France
| | - Céline Noirot
- INRAE, UR 875, Unité de Mathématique et Informatique Appliquées, Genotoul Bioinfo, Castanet-Tolosan, France
| | - Linh-Trang Nguyên
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | | | - Olivier Bouchez
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Eric Defrancq
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Grenoble Alpes, Grenoble, France
| | - Patrick Calsou
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Sébastien Britton
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Dennis Gomez
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
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40
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Teng YC, Sundaresan A, O'Hara R, Gant VU, Li M, Martire S, Warshaw JN, Basu A, Banaszynski LA. ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress. Nat Commun 2021; 12:3887. [PMID: 34162889 PMCID: PMC8222256 DOI: 10.1038/s41467-021-24206-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 06/07/2021] [Indexed: 12/15/2022] Open
Abstract
ATRX is a tumor suppressor that has been associated with protection from DNA replication stress, purportedly through resolution of difficult-to-replicate G-quadruplex (G4) DNA structures. While several studies demonstrate that loss of ATRX sensitizes cells to chemical stabilizers of G4 structures, the molecular function of ATRX at G4 regions during replication remains unknown. Here, we demonstrate that ATRX associates with a number of the MCM replication complex subunits and that loss of ATRX leads to G4 structure accumulation at newly synthesized DNA. We show that both the helicase domain of ATRX and its H3.3 chaperone function are required to protect cells from G4-induced replicative stress. Furthermore, these activities are upstream of heterochromatin formation mediated by the histone methyltransferase, ESET, which is the critical molecular event that protects cells from G4-mediated stress. In support, tumors carrying mutations in either ATRX or ESET show increased mutation burden at G4-enriched DNA sequences. Overall, our study provides new insights into mechanisms by which ATRX promotes genome stability with important implications for understanding impacts of its loss on human disease. ATRX is a chromatin remodeling protein, which loss has been associated to replication stress, DNA damage, and DNA repair failures that drive genome instability. Here the authors reveal that ATRX protects genomic integrity at G4-containing regions by maintaining these regions in a closed heterochromatic state.
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Affiliation(s)
- Yu-Ching Teng
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Medical Center Research Institute, Harold. C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Aishwarya Sundaresan
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Medical Center Research Institute, Harold. C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ryan O'Hara
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Medical Center Research Institute, Harold. C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vincent U Gant
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Medical Center Research Institute, Harold. C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Minhua Li
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Medical Center Research Institute, Harold. C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sara Martire
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Medical Center Research Institute, Harold. C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jane N Warshaw
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Medical Center Research Institute, Harold. C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Amrita Basu
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Laura A Banaszynski
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Medical Center Research Institute, Harold. C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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41
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Meier B, Volkova NV, Hong Y, Bertolini S, González-Huici V, Petrova T, Boulton S, Campbell PJ, Gerstung M, Gartner A. Protection of the C. elegans germ cell genome depends on diverse DNA repair pathways during normal proliferation. PLoS One 2021; 16:e0250291. [PMID: 33905417 PMCID: PMC8078821 DOI: 10.1371/journal.pone.0250291] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/01/2021] [Indexed: 12/13/2022] Open
Abstract
Maintaining genome integrity is particularly important in germ cells to ensure faithful transmission of genetic information across generations. Here we systematically describe germ cell mutagenesis in wild-type and 61 DNA repair mutants cultivated over multiple generations. ~44% of the DNA repair mutants analysed showed a >2-fold increased mutagenesis with a broad spectrum of mutational outcomes. Nucleotide excision repair deficiency led to higher base substitution rates, whereas polh-1(Polη) and rev-3(Polζ) translesion synthesis polymerase mutants resulted in 50-400 bp deletions. Signatures associated with defective homologous recombination fall into two classes: 1) brc-1/BRCA1 and rad-51/RAD51 paralog mutants showed increased mutations across all mutation classes, 2) mus-81/MUS81 and slx-1/SLX1 nuclease, and him-6/BLM, helq-1/HELQ or rtel-1/RTEL1 helicase mutants primarily accumulated structural variants. Repetitive and G-quadruplex sequence-containing loci were more frequently mutated in specific DNA repair backgrounds. Tandem duplications embedded in inverted repeats were observed in helq-1 helicase mutants, and a unique pattern of 'translocations' involving homeologous sequences occurred in rip-1 recombination mutants. atm-1/ATM checkpoint mutants harboured structural variants specifically enriched in subtelomeric regions. Interestingly, locally clustered mutagenesis was only observed for combined brc-1 and cep-1/p53 deficiency. Our study provides a global view of how different DNA repair pathways contribute to prevent germ cell mutagenesis.
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Affiliation(s)
- Bettina Meier
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland
| | - Nadezda V. Volkova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Ye Hong
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland
| | - Simone Bertolini
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland
| | | | - Tsvetana Petrova
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland
| | | | - Peter J. Campbell
- Cancer, Ageing and Somatic Mutation Program, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Anton Gartner
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
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42
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Construction of Whole Genomes from Scaffolds Using Single Cell Strand-Seq Data. Int J Mol Sci 2021; 22:ijms22073617. [PMID: 33807210 PMCID: PMC8037727 DOI: 10.3390/ijms22073617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/23/2021] [Accepted: 03/27/2021] [Indexed: 12/26/2022] Open
Abstract
Accurate reference genome sequences provide the foundation for modern molecular biology and genomics as the interpretation of sequence data to study evolution, gene expression, and epigenetics depends heavily on the quality of the genome assembly used for its alignment. Correctly organising sequenced fragments such as contigs and scaffolds in relation to each other is a critical and often challenging step in the construction of robust genome references. We previously identified misoriented regions in the mouse and human reference assemblies using Strand-seq, a single cell sequencing technique that preserves DNA directionality Here we demonstrate the ability of Strand-seq to build and correct full-length chromosomes by identifying which scaffolds belong to the same chromosome and determining their correct order and orientation, without the need for overlapping sequences. We demonstrate that Strand-seq exquisitely maps assembly fragments into large related groups and chromosome-sized clusters without using new assembly data. Using template strand inheritance as a bi-allelic marker, we employ genetic mapping principles to cluster scaffolds that are derived from the same chromosome and order them within the chromosome based solely on directionality of DNA strand inheritance. We prove the utility of our approach by generating improved genome assemblies for several model organisms including the ferret, pig, Xenopus, zebrafish, Tasmanian devil and the Guinea pig.
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43
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Kaur E, Agrawal R, Sengupta S. Functions of BLM Helicase in Cells: Is It Acting Like a Double-Edged Sword? Front Genet 2021; 12:634789. [PMID: 33777104 PMCID: PMC7994599 DOI: 10.3389/fgene.2021.634789] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/11/2021] [Indexed: 12/14/2022] Open
Abstract
DNA damage repair response is an important biological process involved in maintaining the fidelity of the genome in eukaryotes and prokaryotes. Several proteins that play a key role in this process have been identified. Alterations in these key proteins have been linked to different diseases including cancer. BLM is a 3′−5′ ATP-dependent RecQ DNA helicase that is one of the most essential genome stabilizers involved in the regulation of DNA replication, recombination, and both homologous and non-homologous pathways of double-strand break repair. BLM structure and functions are known to be conserved across many species like yeast, Drosophila, mouse, and human. Genetic mutations in the BLM gene cause a rare, autosomal recessive disorder, Bloom syndrome (BS). BS is a monogenic disease characterized by genomic instability, premature aging, predisposition to cancer, immunodeficiency, and pulmonary diseases. Hence, these characteristics point toward BLM being a tumor suppressor. However, in addition to mutations, BLM gene undergoes various types of alterations including increase in the copy number, transcript, and protein levels in multiple types of cancers. These results, along with the fact that the lack of wild-type BLM in these cancers has been associated with increased sensitivity to chemotherapeutic drugs, indicate that BLM also has a pro-oncogenic function. While a plethora of studies have reported the effect of BLM gene mutations in various model organisms, there is a dearth in the studies undertaken to investigate the effect of its oncogenic alterations. We propose to rationalize and integrate the dual functions of BLM both as a tumor suppressor and maybe as a proto-oncogene, and enlist the plausible mechanisms of its deregulation in cancers.
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Affiliation(s)
- Ekjot Kaur
- Signal Transduction Laboratory-2, National Institute of Immunology, New Delhi, India
| | - Ritu Agrawal
- Signal Transduction Laboratory-2, National Institute of Immunology, New Delhi, India
| | - Sagar Sengupta
- Signal Transduction Laboratory-2, National Institute of Immunology, New Delhi, India
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44
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Guiblet WM, Cremona MA, Harris RS, Chen D, Eckert KA, Chiaromonte F, Huang YF, Makova KD. Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome. Nucleic Acids Res 2021; 49:1497-1516. [PMID: 33450015 PMCID: PMC7897504 DOI: 10.1093/nar/gkaa1269] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 12/14/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
Approximately 13% of the human genome can fold into non-canonical (non-B) DNA structures (e.g. G-quadruplexes, Z-DNA, etc.), which have been implicated in vital cellular processes. Non-B DNA also hinders replication, increasing errors and facilitating mutagenesis, yet its contribution to genome-wide variation in mutation rates remains unexplored. Here, we conducted a comprehensive analysis of nucleotide substitution frequencies at non-B DNA loci within noncoding, non-repetitive genome regions, their ±2 kb flanking regions, and 1-Megabase windows, using human-orangutan divergence and human single-nucleotide polymorphisms. Functional data analysis at single-base resolution demonstrated that substitution frequencies are usually elevated at non-B DNA, with patterns specific to each non-B DNA type. Mirror, direct and inverted repeats have higher substitution frequencies in spacers than in repeat arms, whereas G-quadruplexes, particularly stable ones, have higher substitution frequencies in loops than in stems. Several non-B DNA types also affect substitution frequencies in their flanking regions. Finally, non-B DNA explains more variation than any other predictor in multiple regression models for diversity or divergence at 1-Megabase scale. Thus, non-B DNA substantially contributes to variation in substitution frequencies at small and large scales. Our results highlight the role of non-B DNA in germline mutagenesis with implications to evolution and genetic diseases.
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Affiliation(s)
- Wilfried M Guiblet
- Bioinformatics and Genomics Graduate Program, Penn State University, UniversityPark, PA 16802, USA
| | - Marzia A Cremona
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Operations and Decision Systems, Université Laval, Canada
- CHU de Québec – Université Laval Research Center, Canada
| | - Robert S Harris
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Di Chen
- Intercollege Graduate Degree Program in Genetics, Huck Institutes of the Life Sciences, Penn State University, UniversityPark, PA 16802, USA
| | - Kristin A Eckert
- Department of Pathology, Penn State University, College of Medicine, Hershey, PA 17033, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, PA, USA
| | - Francesca Chiaromonte
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, PA, USA
- EMbeDS, Sant’Anna School of Advanced Studies, 56127 Pisa, Italy
| | - Yi-Fei Huang
- Department of Biology, Penn State University, University Park, PA 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, PA, USA
| | - Kateryna D Makova
- Department of Biology, Penn State University, University Park, PA 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, PA, USA
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45
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Lejault P, Mitteaux J, Sperti FR, Monchaud D. How to untie G-quadruplex knots and why? Cell Chem Biol 2021; 28:436-455. [PMID: 33596431 DOI: 10.1016/j.chembiol.2021.01.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/08/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022]
Abstract
For over two decades, the prime objective of the chemical biology community studying G-quadruplexes (G4s) has been to use chemicals to interact with and stabilize G4s in cells to obtain mechanistic interpretations. This strategy has been undoubtedly successful, as demonstrated by recent advances. However, these insights have also led to a fundamental rethinking of G4-targeting strategies: due to the prevalence of G4s in the human genome, transcriptome, and ncRNAome (collectively referred to as the G4ome), and their involvement in human diseases, should we continue developing G4-stabilizing ligands or should we invest in designing molecular tools to unfold G4s? Here, we first focus on how, when, and where G4s fold in cells; then, we describe the enzymatic systems that have evolved to counteract G4 folding and how they have been used as tools to manipulate G4s in cells; finally, we present strategies currently being implemented to devise new molecular G4 unwinding agents.
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Affiliation(s)
- Pauline Lejault
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Jérémie Mitteaux
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France.
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46
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Zell J, Rota Sperti F, Britton S, Monchaud D. DNA folds threaten genetic stability and can be leveraged for chemotherapy. RSC Chem Biol 2021; 2:47-76. [PMID: 35340894 PMCID: PMC8885165 DOI: 10.1039/d0cb00151a] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/20/2020] [Indexed: 12/22/2022] Open
Abstract
Damaging DNA is a current and efficient strategy to fight against cancer cell proliferation. Numerous mechanisms exist to counteract DNA damage, collectively referred to as the DNA damage response (DDR) and which are commonly dysregulated in cancer cells. Precise knowledge of these mechanisms is necessary to optimise chemotherapeutic DNA targeting. New research on DDR has uncovered a series of promising therapeutic targets, proteins and nucleic acids, with application notably via an approach referred to as combination therapy or combinatorial synthetic lethality. In this review, we summarise the cornerstone discoveries which gave way to the DNA being considered as an anticancer target, and the manipulation of DDR pathways as a valuable anticancer strategy. We describe in detail the DDR signalling and repair pathways activated in response to DNA damage. We then summarise the current understanding of non-B DNA folds, such as G-quadruplexes and DNA junctions, when they are formed and why they can offer a more specific therapeutic target compared to that of canonical B-DNA. Finally, we merge these subjects to depict the new and highly promising chemotherapeutic strategy which combines enhanced-specificity DNA damaging and DDR targeting agents. This review thus highlights how chemical biology has given rise to significant scientific advances thanks to resolutely multidisciplinary research efforts combining molecular and cell biology, chemistry and biophysics. We aim to provide the non-specialist reader a gateway into this exciting field and the specialist reader with a new perspective on the latest results achieved and strategies devised.
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Affiliation(s)
- Joanna Zell
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
| | - Sébastien Britton
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS Toulouse France
- Équipe Labellisée la Ligue Contre le Cancer 2018 Toulouse France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
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47
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Shorrocks AMK, Jones SE, Tsukada K, Morrow CA, Belblidia Z, Shen J, Vendrell I, Fischer R, Kessler BM, Blackford AN. The Bloom syndrome complex senses RPA-coated single-stranded DNA to restart stalled replication forks. Nat Commun 2021; 12:585. [PMID: 33500419 PMCID: PMC7838300 DOI: 10.1038/s41467-020-20818-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023] Open
Abstract
The Bloom syndrome helicase BLM interacts with topoisomerase IIIα (TOP3A), RMI1 and RMI2 to form the BTR complex, which dissolves double Holliday junctions to produce non-crossover homologous recombination (HR) products. BLM also promotes DNA-end resection, restart of stalled replication forks, and processing of ultra-fine DNA bridges in mitosis. How these activities of the BTR complex are regulated in cells is still unclear. Here, we identify multiple conserved motifs within the BTR complex that interact cooperatively with the single-stranded DNA (ssDNA)-binding protein RPA. Furthermore, we demonstrate that RPA-binding is required for stable BLM recruitment to sites of DNA replication stress and for fork restart, but not for its roles in HR or mitosis. Our findings suggest a model in which the BTR complex contains the intrinsic ability to sense levels of RPA-ssDNA at replication forks, which controls BLM recruitment and activation in response to replication stress.
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Affiliation(s)
- Ann-Marie K Shorrocks
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Samuel E Jones
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Kaima Tsukada
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
- Department of Transdisciplinary Science and Engineering, School of Environment and Society, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Carl A Morrow
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Zoulikha Belblidia
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Johanna Shen
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Iolanda Vendrell
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Andrew N Blackford
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK.
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK.
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48
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Miglietta G, Russo M, Capranico G. G-quadruplex-R-loop interactions and the mechanism of anticancer G-quadruplex binders. Nucleic Acids Res 2020; 48:11942-11957. [PMID: 33137181 PMCID: PMC7708042 DOI: 10.1093/nar/gkaa944] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 12/17/2022] Open
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.
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Affiliation(s)
- Giulia Miglietta
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Marco Russo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126 Bologna, Italy
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49
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Masai H, Tanaka T. G-quadruplex DNA and RNA: Their roles in regulation of DNA replication and other biological functions. Biochem Biophys Res Commun 2020; 531:25-38. [PMID: 32826060 DOI: 10.1016/j.bbrc.2020.05.132] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 12/19/2022]
Abstract
G-quadruplex is one of the best-studied non-B type DNA that is now known to be prevalently present in the genomes of almost all the biological species. Recent studies reveal roles of G-quadruplex (G4) structures in various nucleic acids and chromosome transactions. In this short article, we will first describe recent findings on the roles of G4 in regulation of DNA replication. G4 is involved in regulation of spatio-temporal regulation of DNA replication through interaction with a specific binding protein, Rif1. This regulation is at least partially mediated by generation of specific chromatin architecture through Rif1-G4 interactions. We will also describe recent studies showing the potential roles of G4 in initiation of DNA replication. Next, we will present showcases of highly diversified roles of DNA G4 and RNA G4 in regulation of nucleic acid and chromosome functions. Finally, we will discuss how the formation of cellular G4 could be regulated.
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Affiliation(s)
- Hisao Masai
- Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
| | - Taku Tanaka
- Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
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50
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Ahmed A, Angell R, Oxenford S, Worthington J, Williams N, Barton N, Fowler TG, O’Flynn DE, Sunose M, McConville M, Vo T, Wilson WD, Karim SA, Morton JP, Neidle S. Asymmetrically Substituted Quadruplex-Binding Naphthalene Diimide Showing Potent Activity in Pancreatic Cancer Models. ACS Med Chem Lett 2020; 11:1634-1644. [PMID: 32832034 PMCID: PMC7429975 DOI: 10.1021/acsmedchemlett.0c00317] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/16/2020] [Indexed: 12/13/2022] Open
Abstract
Targeting of genomic quadruplexes is an approach to treating complex human cancers. We describe a series of tetra-substituted naphthalene diimide (ND) derivatives with a phenyl substituent directly attached to the ND core. The lead compound (SOP1812) has 10 times superior cellular and in vivo activity compared with previous ND compounds and nanomolar binding to human quadruplexes. The pharmacological properties of SOP1812 indicate good bioavailability, which is consistent with the in vivo activity in xenograft and genetic models for pancreatic cancer. Transcriptome analysis shows that it down-regulates several cancer gene pathways, including Wnt/β-catenin signaling.
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Affiliation(s)
- Ahmed
A. Ahmed
- School
of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Richard Angell
- School
of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Sally Oxenford
- School
of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Jenny Worthington
- Axis
Bio Discovery Services, Ltd., Coleraine, Northern Ireland BT51 3RP, United Kingdom
| | - Nicole Williams
- Axis
Bio Discovery Services, Ltd., Coleraine, Northern Ireland BT51 3RP, United Kingdom
| | - Naomi Barton
- Sygnature
Discovery Limited, Nottingham NG1 1GR, United Kingdom
| | | | | | - Mihiro Sunose
- Sygnature
Discovery Limited, Nottingham NG1 1GR, United Kingdom
| | | | - Tam Vo
- Department
of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - W. David Wilson
- Department
of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Saadia A. Karim
- Cancer
Research UK Beatson Institute, Glasgow G61 1BD, United
Kingdom
| | - Jennifer P. Morton
- Cancer
Research UK Beatson Institute, Glasgow G61 1BD, United
Kingdom
- Institute
of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, United Kingdom
| | - Stephen Neidle
- School
of Pharmacy, University College London, London WC1N 1AX, United Kingdom
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