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Liu J, Sun L, Hong Y, Deng J, Luo Q, Zeng R, Chen W. Near-infrared fluorescent probe for sensitive detection and imaging of DNA G4s in living cells. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 318:124489. [PMID: 38788507 DOI: 10.1016/j.saa.2024.124489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 04/27/2024] [Accepted: 05/19/2024] [Indexed: 05/26/2024]
Abstract
G-quadruplexs (G4s), four-stranded nucleic acid secondary structures, which formed by guanine-rich sequences play a vital role in human biological systems. Studies have shown that the formation of G4s is closely related to tumor development and apoptosis, which is considered as a new target for the development of anti-tumor drugs. Therefore, it is important to develop novel probes for G4s imaging. In this article, we engineered a near-infrared fluorescent probe (TOH) which can be activated by DNA G4s in living cells and tumor. TOH exhibits high selectivity to the structure of DNA G4s with the limit of detection for DNA G4s (Mito-0.5-2) is calculated to be 0.43 nM. Imaging studies of different cell lines revealed that the brighter fluorescence in cancer cell lines than in normal, indicating that DNA G4s maybe highly express in tumor cell lines. Simultaneously, TOH is also introduced into live tumor tissue imaging and found that the fluorescence intensity of tumor is the brightest relative to normal tissue, further validating the high expression of DNA G4s structures in tumor tissue. These features demonstrate TOH not only have the ability to image DNA G4 structures in real time, but also may have tumor diagnostic capabilities.
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Affiliation(s)
- Junjie Liu
- College of Chemistry and Material Science, Hengyang Normal University, Hengyang 421001, PR China
| | - Leying Sun
- College of Chemistry and Material Science, Hengyang Normal University, Hengyang 421001, PR China
| | - Yongxiang Hong
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Jie Deng
- College of Chemistry and Material Science, Hengyang Normal University, Hengyang 421001, PR China
| | - Qingyun Luo
- College of Chemistry and Material Science, Hengyang Normal University, Hengyang 421001, PR China
| | - Rongying Zeng
- College of Chemistry and Material Science, Hengyang Normal University, Hengyang 421001, PR China.
| | - Wen Chen
- College of Chemistry and Material Science, Hengyang Normal University, Hengyang 421001, PR China; State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China.
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2
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Goehring L, Keegan S, Lahiri S, Xia W, Kong M, Jimenez-Sainz J, Gupta D, Drapkin R, Jensen RB, Smith DJ, Rothenberg E, Fenyö D, Huang TT. Dormant origin firing promotes head-on transcription-replication conflicts at transcription termination sites in response to BRCA2 deficiency. Nat Commun 2024; 15:4716. [PMID: 38830843 PMCID: PMC11148086 DOI: 10.1038/s41467-024-48286-1] [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: 08/19/2023] [Accepted: 04/24/2024] [Indexed: 06/05/2024] Open
Abstract
BRCA2 is a tumor suppressor protein responsible for safeguarding the cellular genome from replication stress and genotoxicity, but the specific mechanism(s) by which this is achieved to prevent early oncogenesis remains unclear. Here, we provide evidence that BRCA2 acts as a critical suppressor of head-on transcription-replication conflicts (HO-TRCs). Using Okazaki-fragment sequencing (Ok-seq) and computational analysis, we identified origins (dormant origins) that are activated near the transcription termination sites (TTS) of highly expressed, long genes in response to replication stress. Dormant origins are a source for HO-TRCs, and drug treatments that inhibit dormant origin firing led to a reduction in HO-TRCs, R-loop formation, and DNA damage. Using super-resolution microscopy, we showed that HO-TRC events track with elongating RNA polymerase II, but not with transcription initiation. Importantly, RNase H2 is recruited to sites of HO-TRCs in a BRCA2-dependent manner to help alleviate toxic R-loops associated with HO-TRCs. Collectively, our results provide a mechanistic basis for how BRCA2 shields against genomic instability by preventing HO-TRCs through both direct and indirect means occurring at predetermined genomic sites based on the pre-cancer transcriptome.
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Affiliation(s)
- Liana Goehring
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Sarah Keegan
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Institute for Systems Genetics, New York University School of Medicine, New York University School of Medicine, New York, NY, USA
| | - Sudipta Lahiri
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Wenxin Xia
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Michael Kong
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | | | - Dipika Gupta
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ryan B Jensen
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Duncan J Smith
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Eli Rothenberg
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - David Fenyö
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Institute for Systems Genetics, New York University School of Medicine, New York University School of Medicine, New York, NY, USA
| | - Tony T Huang
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
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3
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Madakashira BP, Magnani E, Ranjan S, Sadler KC. DNA hypomethylation activates Cdk4/6 and Atr to induce DNA replication and cell cycle arrest to constrain liver outgrowth in zebrafish. Nucleic Acids Res 2024; 52:3069-3087. [PMID: 38321933 PMCID: PMC11014291 DOI: 10.1093/nar/gkae031] [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: 08/07/2023] [Revised: 12/12/2023] [Accepted: 01/16/2024] [Indexed: 02/08/2024] Open
Abstract
Coordinating epigenomic inheritance and cell cycle progression is essential for organogenesis. UHRF1 connects these functions during development by facilitating maintenance of DNA methylation and cell cycle progression. Here, we provide evidence resolving the paradoxical phenotype of uhrf1 mutant zebrafish embryos which have activation of pro-proliferative genes and increased number of hepatocytes in S-phase, but the liver fails to grow. We uncover decreased Cdkn2a/b and persistent Cdk4/6 activation as the mechanism driving uhrf1 mutant hepatocytes into S-phase. This induces replication stress, DNA damage and Atr activation. Palbociclib treatment of uhrf1 mutants prevented aberrant S-phase entry, reduced DNA damage, and rescued most cellular and developmental phenotypes, but it did not rescue DNA hypomethylation, transposon expression or the interferon response. Inhibiting Atr reduced DNA replication and increased liver size in uhrf1 mutants, suggesting that Atr activation leads to dormant origin firing and prevents hepatocyte proliferation. Cdkn2a/b was downregulated pro-proliferative genes were also induced in a Cdk4/6 dependent fashion in the liver of dnmt1 mutants, suggesting DNA hypomethylation as a mechanism of Cdk4/6 activation during development. This shows that the developmental defects caused by DNA hypomethylation are attributed to persistent Cdk4/6 activation, DNA replication stress, dormant origin firing and cell cycle inhibition.
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4
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Tian M, Wang Z, Su Z, Shibata E, Shibata Y, Dutta A, Zang C. Integrative analysis of DNA replication origins and ORC-/MCM-binding sites in human cells reveals a lack of overlap. eLife 2024; 12:RP89548. [PMID: 38567819 PMCID: PMC10990492 DOI: 10.7554/elife.89548] [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] [Indexed: 04/05/2024] Open
Abstract
Based on experimentally determined average inter-origin distances of ~100 kb, DNA replication initiates from ~50,000 origins on human chromosomes in each cell cycle. The origins are believed to be specified by binding of factors like the origin recognition complex (ORC) or CTCF or other features like G-quadruplexes. We have performed an integrative analysis of 113 genome-wide human origin profiles (from five different techniques) and five ORC-binding profiles to critically evaluate whether the most reproducible origins are specified by these features. Out of ~7.5 million union origins identified by all datasets, only 0.27% (20,250 shared origins) were reproducibly obtained in at least 20 independent SNS-seq datasets and contained in initiation zones identified by each of three other techniques, suggesting extensive variability in origin usage and identification. Also, 21% of the shared origins overlap with transcriptional promoters, posing a conundrum. Although the shared origins overlap more than union origins with constitutive CTCF-binding sites, G-quadruplex sites, and activating histone marks, these overlaps are comparable or less than that of known transcription start sites, so that these features could be enriched in origins because of the overlap of origins with epigenetically open, promoter-like sequences. Only 6.4% of the 20,250 shared origins were within 1 kb from any of the ~13,000 reproducible ORC-binding sites in human cancer cells, and only 4.5% were within 1 kb of the ~11,000 union MCM2-7-binding sites in contrast to the nearly 100% overlap in the two comparisons in the yeast, Saccharomyces cerevisiae. Thus, in human cancer cell lines, replication origins appear to be specified by highly variable stochastic events dependent on the high epigenetic accessibility around promoters, without extensive overlap between the most reproducible origins and currently known ORC- or MCM-binding sites.
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Affiliation(s)
- Mengxue Tian
- Center for Public Health Genomics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Zhenjia Wang
- Center for Public Health Genomics, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Zhangli Su
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Genetics, University of Alabama at BirminghamBirminghamUnited States
| | - Etsuko Shibata
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Genetics, University of Alabama at BirminghamBirminghamUnited States
| | - Yoshiyuki Shibata
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Genetics, University of Alabama at BirminghamBirminghamUnited States
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Genetics, University of Alabama at BirminghamBirminghamUnited States
| | - Chongzhi Zang
- Center for Public Health Genomics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Public Health Sciences, University of VirginiaCharlottesvilleUnited States
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5
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Martins F, Rosspopoff O, Carlevaro-Fita J, Forey R, Offner S, Planet E, Pulver C, Pak H, Huber F, Michaux J, Bassani-Sternberg M, Turelli P, Trono D. A Cluster of Evolutionarily Recent KRAB Zinc Finger Proteins Protects Cancer Cells from Replicative Stress-Induced Inflammation. Cancer Res 2024; 84:808-826. [PMID: 38345497 PMCID: PMC10940857 DOI: 10.1158/0008-5472.can-23-1237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 10/15/2023] [Accepted: 01/19/2024] [Indexed: 03/16/2024]
Abstract
Heterochromatin loss and genetic instability enhance cancer progression by favoring clonal diversity, yet uncontrolled replicative stress leads to mitotic catastrophe and inflammatory responses that promote immune rejection. KRAB domain-containing zinc finger proteins (KZFP) contribute to heterochromatin maintenance at transposable elements (TE). Here, we identified an association of upregulation of a cluster of primate-specific KZFPs with poor prognosis, increased copy-number alterations, and changes in the tumor microenvironment in diffuse large B-cell lymphoma (DLBCL). Depleting two of these KZFPs targeting evolutionarily recent TEs, ZNF587 and ZNF417, impaired the proliferation of cells derived from DLBCL and several other tumor types. ZNF587 and ZNF417 depletion led to heterochromatin redistribution, replicative stress, and cGAS-STING-mediated induction of an interferon/inflammatory response, which enhanced susceptibility to macrophage-mediated phagocytosis and increased surface expression of HLA-I, together with presentation of a neoimmunopeptidome. Thus, cancer cells can exploit KZFPs to dampen TE-originating surveillance mechanisms, which likely facilitates clonal expansion, diversification, and immune evasion. SIGNIFICANCE Upregulation of a cluster of primate-specific KRAB zinc finger proteins in cancer cells prevents replicative stress and inflammation by regulating heterochromatin maintenance, which could facilitate the development of improved biomarkers and treatments.
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Affiliation(s)
- Filipe Martins
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Clinics of Medical Oncology, Cantonal Hospital of Fribourg (HFR), Fribourg, Switzerland
| | - Olga Rosspopoff
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Joana Carlevaro-Fita
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Romain Forey
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sandra Offner
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Cyril Pulver
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - HuiSong Pak
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Florian Huber
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Justine Michaux
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Priscilla Turelli
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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6
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González-Acosta D, Lopes M. DNA replication and replication stress response in the context of nuclear architecture. Chromosoma 2024; 133:57-75. [PMID: 38055079 PMCID: PMC10904558 DOI: 10.1007/s00412-023-00813-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 12/07/2023]
Abstract
The DNA replication process needs to be coordinated with other DNA metabolism transactions and must eventually extend to the full genome, regardless of chromatin status, gene expression, secondary structures and DNA lesions. Completeness and accuracy of DNA replication are crucial to maintain genome integrity, limiting transformation in normal cells and offering targeting opportunities for proliferating cancer cells. DNA replication is thus tightly coordinated with chromatin dynamics and 3D genome architecture, and we are only beginning to understand the underlying molecular mechanisms. While much has recently been discovered on how DNA replication initiation is organised and modulated in different genomic regions and nuclear territories-the so-called "DNA replication program"-we know much less on how the elongation of ongoing replication forks and particularly the response to replication obstacles is affected by the local nuclear organisation. Also, it is still elusive how specific components of nuclear architecture participate in the replication stress response. Here, we review known mechanisms and factors orchestrating replication initiation, and replication fork progression upon stress, focusing on recent evidence linking genome organisation and nuclear architecture with the cellular responses to replication interference, and highlighting open questions and future challenges to explore this exciting new avenue of research.
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Affiliation(s)
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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7
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Lee CSK, Weiβ M, Hamperl S. Where and when to start: Regulating DNA replication origin activity in eukaryotic genomes. Nucleus 2023; 14:2229642. [PMID: 37469113 PMCID: PMC10361152 DOI: 10.1080/19491034.2023.2229642] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
In eukaryotic genomes, hundreds to thousands of potential start sites of DNA replication named origins are dispersed across each of the linear chromosomes. During S-phase, only a subset of origins is selected in a stochastic manner to assemble bidirectional replication forks and initiate DNA synthesis. Despite substantial progress in our understanding of this complex process, a comprehensive 'identity code' that defines origins based on specific nucleotide sequences, DNA structural features, the local chromatin environment, or 3D genome architecture is still missing. In this article, we review the genetic and epigenetic features of replication origins in yeast and metazoan chromosomes and highlight recent insights into how this flexibility in origin usage contributes to nuclear organization, cell growth, differentiation, and genome stability.
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Affiliation(s)
- Clare S K Lee
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Matthias Weiβ
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Stephan Hamperl
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
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8
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Abstract
Transcription and replication both require large macromolecular complexes to act on a DNA template, yet these machineries cannot simultaneously act on the same DNA sequence. Conflicts between the replication and transcription machineries (transcription-replication conflicts, or TRCs) are widespread in both prokaryotes and eukaryotes and have the capacity to both cause DNA damage and compromise complete, faithful replication of the genome. This review will highlight recent studies investigating the genomic locations of TRCs and the mechanisms by which they may be prevented, mitigated, or resolved. We address work from both model organisms and mammalian systems but predominantly focus on multicellular eukaryotes owing to the additional complexities inherent in the coordination of replication and transcription in the context of cell type-specific gene expression and higher-order chromatin organization.
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Affiliation(s)
- Liana Goehring
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA;
| | - Tony T Huang
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA;
| | - Duncan J Smith
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA;
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9
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da Costa-Nunes JA, Gierlinski M, Sasaki T, Haagensen EJ, Gilbert DM, Blow JJ. The location and development of Replicon Cluster Domains in early replicating DNA. Wellcome Open Res 2023; 8:158. [PMID: 37766844 PMCID: PMC10521077 DOI: 10.12688/wellcomeopenres.18742.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Background: It has been known for many years that in metazoan cells, replication origins are organised into clusters where origins within each cluster fire near-synchronously. Despite clusters being a fundamental organising principle of metazoan DNA replication, the genomic location of origin clusters has not been documented. Methods: We synchronised human U2OS by thymidine block and release followed by L-mimosine block and release to create a population of cells progressing into S phase with a high degree of synchrony. At different times after release into S phase, cells were pulsed with EdU; the EdU-labelled DNA was then pulled down, sequenced and mapped onto the human genome. Results: The early replicating DNA showed features at a range of scales. Wavelet analysis showed that the major feature of the early replicating DNA was at a size of 500 kb, consistent with clusters of replication origins. Over the first two hours of S phase, these Replicon Cluster Domains broadened in width, consistent with their being enlarged by the progression of replication forks at their outer boundaries. The total replication signal associated with each Replicon Cluster Domain varied considerably, and this variation was reproducible and conserved over time. We provide evidence that this variability in replication signal was at least in part caused by Replicon Cluster Domains being activated at different times in different cells in the population. We also provide evidence that adjacent clusters had a statistical preference for being activated in sequence across a group, consistent with the 'domino' model of replication focus activation order observed by microscopy. Conclusions: We show that early replicating DNA is organised into Replicon Cluster Domains that behave as expected of replicon clusters observed by DNA fibre analysis. The coordinated activation of different Replicon Cluster Domains can generate the replication timing programme by which the genome is duplicated.
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Affiliation(s)
- José A. da Costa-Nunes
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Marek Gierlinski
- Data Analysis Group, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Takayo Sasaki
- San Diego Biomedical Research Institute, San Diego, California, CA 92121, USA
| | - Emma J. Haagensen
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Present address: School of Medical Education, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - David M. Gilbert
- San Diego Biomedical Research Institute, San Diego, California, CA 92121, USA
| | - J. Julian Blow
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
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10
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Poulet-Benedetti J, Tonnerre-Doncarli C, Valton AL, Laurent M, Gérard M, Barinova N, Parisis N, Massip F, Picard F, Prioleau MN. Dimeric G-quadruplex motifs-induced NFRs determine strong replication origins in vertebrates. Nat Commun 2023; 14:4843. [PMID: 37563125 PMCID: PMC10415359 DOI: 10.1038/s41467-023-40441-4] [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: 03/27/2023] [Accepted: 07/28/2023] [Indexed: 08/12/2023] Open
Abstract
Replication of vertebrate genomes is tightly regulated to ensure accurate duplication, but our understanding of the interplay between genetic and epigenetic factors in this regulation remains incomplete. Here, we investigated the involvement of three elements enriched at gene promoters and replication origins: guanine-rich motifs potentially forming G-quadruplexes (pG4s), nucleosome-free regions (NFRs), and the histone variant H2A.Z, in the firing of origins of replication in vertebrates. We show that two pG4s on the same DNA strand (dimeric pG4s) are sufficient to induce the assembly of an efficient minimal replication origin without inducing transcription in avian DT40 cells. Dimeric pG4s in replication origins are associated with formation of an NFR next to precisely-positioned nucleosomes enriched in H2A.Z on this minimal origin and genome-wide. Thus, our data suggest that dimeric pG4s are important for the organization and duplication of vertebrate genomes. It supports the hypothesis that a nucleosome close to an NFR is a shared signal for the formation of replication origins in eukaryotes.
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Affiliation(s)
| | | | - Anne-Laure Valton
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Marc Laurent
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Marie Gérard
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Natalja Barinova
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Nikolaos Parisis
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Florian Massip
- MINES ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, 75006, Paris, France
- Institut Curie, Paris, Cedex, France
- INSERM, U900, Paris, Cedex, France
| | - Franck Picard
- Laboratory of Biology and Modelling of the Cell, Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France.
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11
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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: 42] [Impact Index Per Article: 42.0] [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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12
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Hu Y, Stillman B. Origins of DNA replication in eukaryotes. Mol Cell 2023; 83:352-372. [PMID: 36640769 PMCID: PMC9898300 DOI: 10.1016/j.molcel.2022.12.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023]
Abstract
Errors occurring during DNA replication can result in inaccurate replication, incomplete replication, or re-replication, resulting in genome instability that can lead to diseases such as cancer or disorders such as autism. A great deal of progress has been made toward understanding the entire process of DNA replication in eukaryotes, including the mechanism of initiation and its control. This review focuses on the current understanding of how the origin recognition complex (ORC) contributes to determining the location of replication initiation in the multiple chromosomes within eukaryotic cells, as well as methods for mapping the location and temporal patterning of DNA replication. Origin specification and configuration vary substantially between eukaryotic species and in some cases co-evolved with gene-silencing mechanisms. We discuss the possibility that centromeres and origins of DNA replication were originally derived from a common element and later separated during evolution.
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Affiliation(s)
- Yixin Hu
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; Program in Molecular and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Bruce Stillman
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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13
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Jodkowska K, Pancaldi V, Rigau M, Almeida R, Fernández-Justel J, Graña-Castro O, Rodríguez-Acebes S, Rubio-Camarillo M, Carrillo-de Santa Pau E, Pisano D, Al-Shahrour F, Valencia A, Gómez M, Méndez J. 3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells. Nucleic Acids Res 2022; 50:12149-12165. [PMID: 36453993 PMCID: PMC9757045 DOI: 10.1093/nar/gkac1111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 10/31/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
In mammalian cells, chromosomal replication starts at thousands of origins at which replisomes are assembled. Replicative stress triggers additional initiation events from 'dormant' origins whose genomic distribution and regulation are not well understood. In this study, we have analyzed origin activity in mouse embryonic stem cells in the absence or presence of mild replicative stress induced by aphidicolin, a DNA polymerase inhibitor, or by deregulation of origin licensing factor CDC6. In both cases, we observe that the majority of stress-responsive origins are also active in a small fraction of the cell population in a normal S phase, and stress increases their frequency of activation. In a search for the molecular determinants of origin efficiency, we compared the genetic and epigenetic features of origins displaying different levels of activation, and integrated their genomic positions in three-dimensional chromatin interaction networks derived from high-depth Hi-C and promoter-capture Hi-C data. We report that origin efficiency is directly proportional to the proximity to transcriptional start sites and to the number of contacts established between origin-containing chromatin fragments, supporting the organization of origins in higher-level DNA replication factories.
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Affiliation(s)
| | | | | | | | - José M Fernández-Justel
- Functional Organization of the Mammalian Genome Group, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Madrid, Spain
| | - Osvaldo Graña-Castro
- Bioinformatics Unit, Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain,Institute of Applied Molecular Medicine (IMMA-Nemesio Díez), San Pablo-CEU University, Boadilla del Monte, Madrid, Spain
| | - Sara Rodríguez-Acebes
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Miriam Rubio-Camarillo
- Bioinformatics Unit, Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - David Pisano
- Bioinformatics Unit, Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Fátima Al-Shahrour
- Bioinformatics Unit, Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Alfonso Valencia
- Computational Biology Life Sciences Group, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - María Gómez
- Correspondence may also be addressed to María Gómez. Tel: +34 911964724; Fax: +34 911964420;
| | - Juan Méndez
- To whom correspondence should be addressed. Tel: +34 917328000; Fax: +34 917328033;
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14
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Murat P, Perez C, Crisp A, van Eijk P, Reed SH, Guilbaud G, Sale JE. DNA replication initiation shapes the mutational landscape and expression of the human genome. SCIENCE ADVANCES 2022; 8:eadd3686. [PMID: 36351018 PMCID: PMC9645720 DOI: 10.1126/sciadv.add3686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
The interplay between active biological processes and DNA repair is central to mutagenesis. Here, we show that the ubiquitous process of replication initiation is mutagenic, leaving a specific mutational footprint at thousands of early and efficient replication origins. The observed mutational pattern is consistent with two distinct mechanisms, reflecting the two-step process of origin activation, triggering the formation of DNA breaks at the center of origins and local error-prone DNA synthesis in their immediate vicinity. We demonstrate that these replication initiation-dependent mutational processes exert an influence on phenotypic diversity in humans that is disproportionate to the origins' genomic size: By increasing mutational loads at gene promoters and splice junctions, the presence of an origin significantly influences both gene expression and mRNA isoform usage. Last, we show that mutagenesis at origins not only drives the evolution of origin sequences but also contributes to sculpting regulatory domains of the human genome.
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Affiliation(s)
- Pierre Murat
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Consuelo Perez
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Alastair Crisp
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Patrick van Eijk
- Broken String Biosciences Ltd., BioData Innovation Centre, Unit AB3-03, Level 3, Wellcome Genome Campus, Hinxton, Cambridge CB10 1DR, UK
- Division of Cancer & Genetics School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Simon H. Reed
- Broken String Biosciences Ltd., BioData Innovation Centre, Unit AB3-03, Level 3, Wellcome Genome Campus, Hinxton, Cambridge CB10 1DR, UK
- Division of Cancer & Genetics School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Guillaume Guilbaud
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Julian E. Sale
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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15
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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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