1
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Gaggioli V, Lo CSY, Reverón-Gómez N, Jasencakova Z, Domenech H, Nguyen H, Sidoli S, Tvardovskiy A, Uruci S, Slotman JA, Chai Y, Gonçalves JGSCS, Manolika EM, Jensen ON, Wheeler D, Sridharan S, Chakrabarty S, Demmers J, Kanaar R, Groth A, Taneja N. Dynamic de novo heterochromatin assembly and disassembly at replication forks ensures fork stability. Nat Cell Biol 2023; 25:1017-1032. [PMID: 37414849 PMCID: PMC10344782 DOI: 10.1038/s41556-023-01167-z] [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: 11/11/2022] [Accepted: 05/16/2023] [Indexed: 07/08/2023]
Abstract
Chromatin is dynamically reorganized when DNA replication forks are challenged. However, the process of epigenetic reorganization and its implication for fork stability is poorly understood. Here we discover a checkpoint-regulated cascade of chromatin signalling that activates the histone methyltransferase EHMT2/G9a to catalyse heterochromatin assembly at stressed replication forks. Using biochemical and single molecule chromatin fibre approaches, we show that G9a together with SUV39h1 induces chromatin compaction by accumulating the repressive modifications, H3K9me1/me2/me3, in the vicinity of stressed replication forks. This closed conformation is also favoured by the G9a-dependent exclusion of the H3K9-demethylase JMJD1A/KDM3A, which facilitates heterochromatin disassembly upon fork restart. Untimely heterochromatin disassembly from stressed forks by KDM3A enables PRIMPOL access, triggering single-stranded DNA gap formation and sensitizing cells towards chemotherapeutic drugs. These findings may help in explaining chemotherapy resistance and poor prognosis observed in patients with cancer displaying elevated levels of G9a/H3K9me3.
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Affiliation(s)
- Vincent Gaggioli
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Calvin S Y Lo
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Nazaret Reverón-Gómez
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zuzana Jasencakova
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Heura Domenech
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Hong Nguyen
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Simone Sidoli
- Department of Biochemistry & Molecular Biology, VILLUM Centre for Bioanalytical Sciences and Centre for Epigenetics, University of Southern Denmark, Odense, Denmark
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Andrey Tvardovskiy
- Department of Biochemistry & Molecular Biology, VILLUM Centre for Bioanalytical Sciences and Centre for Epigenetics, University of Southern Denmark, Odense, Denmark
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum Munchen, Neuherberg, Germany
| | - Sidrit Uruci
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Johan A Slotman
- Department of Pathology, Erasmus Optical Imaging Centre, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Yi Chai
- Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | | | - Eleni Maria Manolika
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Ole N Jensen
- Department of Biochemistry & Molecular Biology, VILLUM Centre for Bioanalytical Sciences and Centre for Epigenetics, University of Southern Denmark, Odense, Denmark
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sriram Sridharan
- Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Jeroen Demmers
- Proteomics Center and Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nitika Taneja
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
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Pauzaite T, Tollitt J, Sopaci B, Caprani L, Iwanowytsch O, Thacker U, Hardy JG, Allinson SL, Copeland NA. Dbf4-Cdc7 (DDK) Inhibitor PHA-767491 Displays Potent Anti-Proliferative Effects via Crosstalk with the CDK2-RB-E2F Pathway. Biomedicines 2022; 10:biomedicines10082012. [PMID: 36009559 PMCID: PMC9405858 DOI: 10.3390/biomedicines10082012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
Precise regulation of DNA replication complex assembly requires cyclin-dependent kinase (CDK) and Dbf4-dependent kinase (DDK) activities to activate the replicative helicase complex and initiate DNA replication. Chemical probes have been essential in the molecular analysis of DDK-mediated regulation of MCM2-7 activation and the initiation phase of DNA replication. Here, the inhibitory activity of two distinct DDK inhibitor chemotypes, PHA-767491 and XL-413, were assessed in cell-free and cell-based proliferation assays. PHA-767491 and XL-413 show distinct effects at the level of cellular proliferation, initiation of DNA replication and replisome activity. XL-413 and PHA-767491 both reduce DDK-specific phosphorylation of MCM2 but show differential potency in prevention of S-phase entry. DNA combing and DNA replication assays show that PHA-767491 is a potent inhibitor of the initiation phase of DNA replication but XL413 has weak activity. Importantly, PHA-767491 decreased E2F-mediated transcription of the G1/S regulators cyclin A2, cyclin E1 and cyclin E2, and this effect was independent of CDK9 inhibition. Significantly, the enhanced inhibitory profile of PHA-767491 is mediated by potent inhibition of both DDK and the CDK2-Rb-E2F transcriptional network, that provides the molecular basis for its increased anti-proliferative effects in RB+ cancer cell lines.
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Affiliation(s)
- Tekle Pauzaite
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YQ, UK
| | - James Tollitt
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YQ, UK
| | - Betul Sopaci
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YQ, UK
| | - Louise Caprani
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YQ, UK
| | - Olivia Iwanowytsch
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YQ, UK
| | - Urvi Thacker
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YQ, UK
| | - John G. Hardy
- Materials Science Institute, Lancaster University, Lancaster LA1 4YW, UK
- Department of Chemistry, Faculty of Science and Technology, Lancaster University, Lancaster LA1 4YB, UK
| | - Sarah L. Allinson
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YQ, UK
| | - Nikki A. Copeland
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YQ, UK
- Materials Science Institute, Lancaster University, Lancaster LA1 4YW, UK
- Correspondence:
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3
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Moore G, Jimenez Sainz J, Jensen RB. DNA fiber combing protocol using in-house reagents and coverslips to analyze replication fork dynamics in mammalian cells. STAR Protoc 2022; 3:101371. [PMID: 35573479 PMCID: PMC9092994 DOI: 10.1016/j.xpro.2022.101371] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
DNA fiber combing is a versatile technique that provides insight into replication fork dynamics at single-molecule resolution. DNA fibers are bound to silanized coverslips and combed, which straightens and aligns the fibers along a single axis. Here, we present a DNA fiber combing protocol that does not use commercial kits; we detail the steps to prepare all materials, reagents, and silanized coverslips. We describe the use of DLD-1 cells, but the protocol is amenable to other cell types.
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Affiliation(s)
- Gemma Moore
- Department of Therapeutic Radiology, Yale University School of Medicine, 15 York Street, New Haven, CT 06520, USA
- Corresponding author
| | - Judit Jimenez Sainz
- Department of Therapeutic Radiology, Yale University School of Medicine, 15 York Street, New Haven, CT 06520, USA
| | - Ryan B. Jensen
- Department of Therapeutic Radiology, Yale University School of Medicine, 15 York Street, New Haven, CT 06520, USA
- Corresponding author
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4
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A simple cut and stretch assay to detect antimicrobial resistance genes on bacterial plasmids by single-molecule fluorescence microscopy. Sci Rep 2022; 12:9301. [PMID: 35660772 PMCID: PMC9166776 DOI: 10.1038/s41598-022-13315-w] [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: 02/10/2022] [Accepted: 05/17/2022] [Indexed: 11/21/2022] Open
Abstract
Antimicrobial resistance (AMR) is a fast-growing threat to global health. The genes conferring AMR to bacteria are often located on plasmids, circular extrachromosomal DNA molecules that can be transferred between bacterial strains and species. Therefore, effective methods to characterize bacterial plasmids and detect the presence of resistance genes can assist in managing AMR, for example, during outbreaks in hospitals. However, existing methods for plasmid analysis either provide limited information or are expensive and challenging to implement in low-resource settings. Herein, we present a simple assay based on CRISPR/Cas9 excision and DNA combing to detect antimicrobial resistance genes on bacterial plasmids. Cas9 recognizes the gene of interest and makes a double-stranded DNA cut, causing the circular plasmid to linearize. The change in plasmid configuration from circular to linear, and hence the presence of the AMR gene, is detected by stretching the plasmids on a glass surface and visualizing by fluorescence microscopy. This single-molecule imaging based assay is inexpensive, fast, and in addition to detecting the presence of AMR genes, it provides detailed information on the number and size of plasmids in the sample. We demonstrate the detection of several β-lactamase-encoding genes on plasmids isolated from clinical samples. Furthermore, we demonstrate that the assay can be performed using standard microbiology and clinical laboratory equipment, making it suitable for low-resource settings.
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5
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Punt AM, Wieman JC, van der Elst KC, Huitema AD, Lentjes EG. An easy, fast, and efficient assay for the quantification of peptide Hepcidin-25 in serum and plasma with LC-MS/MS. Ann Clin Biochem 2022; 59:330-337. [PMID: 35392660 DOI: 10.1177/00045632221095490] [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: 11/16/2022]
Abstract
BACKGROUND The peptide hormone hepcidin-25 plays an important role in iron metabolism. Low or high levels of hepcidin-25 are associated with various iron disorders; therefore, hepcidin-25 is an important biomarker. This study describes an easy and fast analytical assay for the quantification of hepcidin-25 with liquid chromatography-tandem mass spectrometry (LC-MS/MS). METHODS Sample preparation was performed by protein precipitation with trichloroacetic acid, and injection onto a LC-MS/MS was directly conducted from a LoBind 96-well plate. RESULTS The concentration range covered by the quality control samples, ranged from 0.25 nmol/L (12.3% CV) to 11.9 nmol/L (CV < 9%). Matrix effect was limited (mean recovery of 99.9% with a CV of 6.4%). The assay was validated for serum, EDTA and heparin plasma. An international secondary reference material was used for calibration. The reference interval (90% CL) was estimated for hepcidin-25 by analysing serum and plasma samples from 156 healthy subjects with a lower limit: 0.12 (0.07-0.19) and upper limit: 11.2 nmol/L (9.5-13.0). CONCLUSIONS We present a fast and easy assay for the quantification of hepcidin-25 in serum and plasma samples. The assay was successfully used for the detection of various forms of hereditary haemolytic anaemias, to characterize the interplay between erythropoiesis and iron levels.
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Affiliation(s)
- Arjen M Punt
- Department of Clinical Pharmacy, Division of Laboratory Medicine and Pharmacy, 8124University Medical Center Utrecht, Utrecht, The Netherlands.,Central Diagnostic Laboratory, 8124University Medical Center Utrecht, Utrecht, The Netherlands
| | - Joëlle C Wieman
- Central Diagnostic Laboratory, 8124University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kim Cm van der Elst
- Department of Clinical Pharmacy, Division of Laboratory Medicine and Pharmacy, 8124University Medical Center Utrecht, Utrecht, The Netherlands
| | - Alwin Dr Huitema
- Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht.,Department of Pharmacology, 541199Princess Máxima Center for Pediatric Oncology.,Department of Pharmacy & Pharmacology, 541199Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Eef Gwm Lentjes
- Central Diagnostic Laboratory, 8124University Medical Center Utrecht, Utrecht, The Netherlands
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6
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Thiriet C. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2536-2548. [PMID: 35137186 PMCID: PMC8934661 DOI: 10.1093/nar/gkac060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/25/2022] [Indexed: 11/13/2022] Open
Abstract
DNA replication occurring in S-phase is critical for the maintenance of the cell fate from one generation to the next, and requires the duplication of epigenetic information. The integrity of the epigenome is, in part, insured by the recycling of parental histones and de novo deposition of newly synthesized histones. While the histone variants have revealed important functions in epigenetic regulations, the deposition in chromatin during S-phase of newly synthesized histone variants remains unclear. The identification of histone variants of H3 and unique features of Physarum polycephalum provides a powerful system for investigating de novo deposition of newly synthesized histones by tracking the incorporation of exogenous histones within cells. The analyses revealed that the rate of deposition of H3.1 and H3.3 is anticorrelated as S-phase progresses, H3.3 is predominately produced and utilized in early S and dropped throughout S-phase, while H3.1 behaved in the opposite way. Disturbing the expression of H3 variants by siRNAs revealed mutual compensation of histone transcripts. Interestingly, the incorporation of pre-formed constrained histone complexes showed that tetramers of H3/H4 are more efficiently utilized by the cell than dimers. These results support the model whereby the histone variant distribution is established upon replication and new histone deposition.
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7
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KK S, Lin YL, Sewunet T, Wrande M, Sandegren L, Giske CG, Westerlund F. A Parallelized Nanofluidic Device for High-Throughput Optical DNA Mapping of Bacterial Plasmids. MICROMACHINES 2021; 12:1234. [PMID: 34683285 PMCID: PMC8538381 DOI: 10.3390/mi12101234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 12/03/2022]
Abstract
Optical DNA mapping (ODM) has developed into an important technique for DNA analysis, where single DNA molecules are sequence-specifically labeled and stretched, for example, in nanofluidic channels. We have developed an ODM assay to analyze bacterial plasmids-circular extrachromosomal DNA that often carry genes that make bacteria resistant to antibiotics. As for most techniques, the next important step is to increase throughput and automation. In this work, we designed and fabricated a nanofluidic device that, together with a simple automation routine, allows parallel analysis of up to 10 samples at the same time. Using plasmids encoding extended-spectrum beta-lactamases (ESBL), isolated from Escherichiacoli and Klebsiellapneumoniae, we demonstrate the multiplexing capabilities of the device when it comes to both many samples in parallel and different resistance genes. As a final example, we combined the device with a novel protocol for rapid cultivation and extraction of plasmids from fecal samples collected from patients. This combined protocol will make it possible to analyze many patient samples in one device already on the day the sample is collected, which is an important step forward for the ODM analysis of plasmids in clinical diagnostics.
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Affiliation(s)
- Sriram KK
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.)
| | - Yii-Lih Lin
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.)
| | - Tsegaye Sewunet
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, 141 52 Stockholm, Sweden; (T.S.); (C.G.G.)
| | - Marie Wrande
- Department of Medical Biochemistry and Microbiology, Uppsala University, 752 37 Uppsala, Sweden; (M.W.); (L.S.)
| | - Linus Sandegren
- Department of Medical Biochemistry and Microbiology, Uppsala University, 752 37 Uppsala, Sweden; (M.W.); (L.S.)
| | - Christian G. Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, 141 52 Stockholm, Sweden; (T.S.); (C.G.G.)
- Clinical Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Fredrik Westerlund
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.)
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8
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Öz R, Wang JL, Guerois R, Goyal G, KK S, Ropars V, Sharma R, Koca F, Charbonnier JB, Modesti M, Strick TR, Westerlund F. Dynamics of Ku and bacterial non-homologous end-joining characterized using single DNA molecule analysis. Nucleic Acids Res 2021; 49:2629-2641. [PMID: 33590005 PMCID: PMC7969030 DOI: 10.1093/nar/gkab083] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 01/20/2021] [Accepted: 01/29/2021] [Indexed: 01/29/2023] Open
Abstract
We use single-molecule techniques to characterize the dynamics of prokaryotic DNA repair by non-homologous end-joining (NHEJ), a system comprised only of the dimeric Ku and Ligase D (LigD). The Ku homodimer alone forms a ∼2 s synapsis between blunt DNA ends that is increased to ∼18 s upon addition of LigD, in a manner dependent on the C-terminal arms of Ku. The synapsis lifetime increases drastically for 4 nt complementary DNA overhangs, independently of the C-terminal arms of Ku. These observations are in contrast to human Ku, which is unable to bridge either of the two DNA substrates. We also demonstrate that bacterial Ku binds the DNA ends in a cooperative manner for synapsis initiation and remains stably bound at DNA junctions for several hours after ligation is completed, indicating that a system for removal of the proteins is active in vivo. Together these experiments shed light on the dynamics of bacterial NHEJ in DNA end recognition and processing. We speculate on the evolutionary similarities between bacterial and eukaryotic NHEJ and discuss how an increased understanding of bacterial NHEJ can open the door for future antibiotic therapies targeting this mechanism.
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Affiliation(s)
- Robin Öz
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 41296, Sweden
| | - Jing L Wang
- Institut Jacques Monod, Université de Paris, CNRS, UMR7592, Paris, France
- Ecole Normale Supérieure, IBENS, CNRS, INSERM, PSL Research University, Paris 75005 France
| | - Raphael Guerois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Gaurav Goyal
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 41296, Sweden
| | - Sriram KK
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 41296, Sweden
| | - Virginie Ropars
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Rajhans Sharma
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 41296, Sweden
| | - Firat Koca
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 41296, Sweden
| | - Jean-Baptiste Charbonnier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille 13009, France
- Equipe Labélisée, Ligue Nationale Contre le Cancer, Paris 75013, France
| | - Terence R Strick
- Institut Jacques Monod, Université de Paris, CNRS, UMR7592, Paris, France
- Ecole Normale Supérieure, IBENS, CNRS, INSERM, PSL Research University, Paris 75005 France
- Equipe Labélisée, Ligue Nationale Contre le Cancer, Paris 75013, France
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 41296, Sweden
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9
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Żabka A, Winnicki K, Polit JT, Bernasińska-Słomczewska J, Maszewski J. 5-Aminouracil and other inhibitors of DNA replication induce biphasic interphase-mitotic cells in apical root meristems of Allium cepa. PLANT CELL REPORTS 2020; 39:1013-1028. [PMID: 32328702 PMCID: PMC7359111 DOI: 10.1007/s00299-020-02545-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
Induction of biphasic interphase-mitotic cells and PCC is connected with an increased level of metabolism in root meristem cells of Allium cepa. Previous experiments using primary roots of Allium cepa exposed to low concentrations of hydroxyurea have shown that long-term DNA replication stress (DRS) disrupts essential links of the S-M checkpoint mechanism, leading meristem cells either to premature chromosome condensation (PCC) or to a specific form of chromatin condensation, establishing biphasic organization of cell nuclei with both interphase and mitotic domains (IM cells). The present study supplements and extends these observations by describing general conditions under which both abnormal types of M-phase cells may occur. The analysis of root apical meristem (RAM) cell proliferation after prolonged mild DRS indicates that a broad spectrum of inhibitors is capable of generating PCC and IM organization of cell nuclei. These included: 5-aminouracil (5-AU, a thymine antagonist), characterized by the highest efficiency in creating cells with the IM phenotype, aphidicolin (APH), an inhibitor of DNA polymerase α, 5-fluorodeoxyuridine (FUdR), an inhibitor of thymidylate synthetase, methotrexate (MTX), a folic acid analog that inhibits purine and pyrimidine synthesis, and cytosine arabinoside (Ara-C), which inhibits DNA replication by forming cleavage complexes with topoisomerase I. As evidenced using fluorescence-based click chemistry assays, continuous treatment of onion RAM cells with 5-AU is associated with an accelerated dynamics of the DNA replication machinery and significantly enhanced levels of transcription and translation. Furthermore, DRS conditions bring about an intensified production of hydrogen peroxide (H2O2), depletion of reduced glutathione (GSH), and some increase in DNA fragmentation, associated with only a slight increase in apoptosis-like programmed cell death events.
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Affiliation(s)
- Aneta Żabka
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Konrad Winnicki
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Justyna Teresa Polit
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Joanna Bernasińska-Słomczewska
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Janusz Maszewski
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
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10
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van Dijk CG, Louzao-Martinez L, van Mulligen E, Boermans B, Demmers JA, van den Bosch TP, Goumans MJ, Duncker DJ, Verhaar MC, Cheng C. Extracellular Matrix Analysis of Human Renal Arteries in Both Quiescent and Active Vascular State. Int J Mol Sci 2020; 21:E3905. [PMID: 32486169 PMCID: PMC7313045 DOI: 10.3390/ijms21113905] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 01/30/2023] Open
Abstract
In vascular tissue engineering strategies, the addition of vascular-specific extracellular matrix (ECM) components may better mimic the in vivo microenvironment and potentially enhance cell-matrix interactions and subsequent tissue growth. For this purpose, the exact composition of the human vascular ECM first needs to be fully characterized. Most research has focused on characterizing ECM components in mature vascular tissue; however, the developing fetal ECM matches the active environment required in vascular tissue engineering more closely. Consequently, we characterized the ECM protein composition of active (fetal) and quiescent (mature) renal arteries using a proteome analysis of decellularized tissue. The obtained human fetal renal artery ECM proteome dataset contains higher levels of 15 ECM proteins versus the mature renal artery ECM proteome, whereas 16 ECM proteins showed higher levels in the mature tissue compared to fetal. Elastic ECM proteins EMILIN1 and FBN1 are significantly enriched in fetal renal arteries and are mainly produced by cells of mesenchymal origin. We functionally tested the role of EMILIN1 and FBN1 by anchoring the ECM secreted by vascular smooth muscle cells (SMCs) to glass coverslips. This ECM layer was depleted from either EMILIN1 or FBN1 by using siRNA targeting of the SMCs. Cultured endothelial cells (ECs) on this modified ECM layer showed alterations on the transcriptome level of multiple pathways, especially the Rho GTPase controlled pathways. However, no significant alterations in adhesion, migration or proliferation were observed when ECs were cultured on EMILIN1- or FNB1-deficient ECM. To conclude, the proteome analysis identified unique ECM proteins involved in the embryonic development of renal arteries. Alterations in transcriptome levels of ECs cultured on EMILIN1- or FBN1-deficient ECM showed that these candidate proteins could affect the endothelial (regenerative) response.
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Affiliation(s)
- Christian G.M. van Dijk
- Department of Nephrology and Hypertension, Division of Internal Medicine and Dermatology, University Medical Center Utrecht, PO Box 85500, 3508 GA Utrecht, The Netherlands; (C.G.M.v.D.); (E.v.M.); (B.B.); (M.C.V.)
| | - Laura Louzao-Martinez
- Center for Proteomics, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands; (L.L.-M.); (J.A.A.D.)
| | - Elise van Mulligen
- Department of Nephrology and Hypertension, Division of Internal Medicine and Dermatology, University Medical Center Utrecht, PO Box 85500, 3508 GA Utrecht, The Netherlands; (C.G.M.v.D.); (E.v.M.); (B.B.); (M.C.V.)
| | - Bart Boermans
- Department of Nephrology and Hypertension, Division of Internal Medicine and Dermatology, University Medical Center Utrecht, PO Box 85500, 3508 GA Utrecht, The Netherlands; (C.G.M.v.D.); (E.v.M.); (B.B.); (M.C.V.)
| | - Jeroen A.A. Demmers
- Center for Proteomics, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands; (L.L.-M.); (J.A.A.D.)
| | | | - Marie-José Goumans
- Department of Cell and Chemical Biology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands;
| | - Dirk J. Duncker
- Experimental Cardiology, Department of Cardiology, Thorax center, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, The Netherlands;
| | - Marianne C. Verhaar
- Department of Nephrology and Hypertension, Division of Internal Medicine and Dermatology, University Medical Center Utrecht, PO Box 85500, 3508 GA Utrecht, The Netherlands; (C.G.M.v.D.); (E.v.M.); (B.B.); (M.C.V.)
| | - Caroline Cheng
- Department of Nephrology and Hypertension, Division of Internal Medicine and Dermatology, University Medical Center Utrecht, PO Box 85500, 3508 GA Utrecht, The Netherlands; (C.G.M.v.D.); (E.v.M.); (B.B.); (M.C.V.)
- Experimental Cardiology, Department of Cardiology, Thorax center, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, The Netherlands;
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11
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Salazar-Cavazos E, Nitta CF, Mitra ED, Wilson BS, Lidke KA, Hlavacek WS, Lidke DS. Multisite EGFR phosphorylation is regulated by adaptor protein abundances and dimer lifetimes. Mol Biol Cell 2020; 31:695-708. [PMID: 31913761 PMCID: PMC7202077 DOI: 10.1091/mbc.e19-09-0548] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Differential epidermal growth factor receptor (EGFR) phosphorylation is thought to couple receptor activation to distinct signaling pathways. However, the molecular mechanisms responsible for biased signaling are unresolved due to a lack of insight into the phosphorylation patterns of full-length EGFR. We extended a single-molecule pull-down technique previously used to study protein-protein interactions to allow for robust measurement of receptor phosphorylation. We found that EGFR is predominantly phosphorylated at multiple sites, yet phosphorylation at specific tyrosines is variable and only a subset of receptors share phosphorylation at the same site, even with saturating ligand concentrations. We found distinct populations of receptors as soon as 1 min after ligand stimulation, indicating early diversification of function. To understand this heterogeneity, we developed a mathematical model. The model predicted that variations in phosphorylation are dependent on the abundances of signaling partners, while phosphorylation levels are dependent on dimer lifetimes. The predictions were confirmed in studies of cell lines with different expression levels of signaling partners, and in experiments comparing low- and high-affinity ligands and oncogenic EGFR mutants. These results reveal how ligand-regulated receptor dimerization dynamics and adaptor protein concentrations play critical roles in EGFR signaling.
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Affiliation(s)
| | | | - Eshan D Mitra
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545
| | | | - Keith A Lidke
- Comprehensive Cancer Center, and.,Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131
| | - William S Hlavacek
- Comprehensive Cancer Center, and.,Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Diane S Lidke
- Department of Pathology.,Comprehensive Cancer Center, and
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12
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Varapula D, LaBouff E, Raseley K, Uppuluri L, Ehrlich GD, Noh M, Xiao M. A micropatterned substrate for on-surface enzymatic labelling of linearized long DNA molecules. Sci Rep 2019; 9:15059. [PMID: 31636335 PMCID: PMC6803683 DOI: 10.1038/s41598-019-51507-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/02/2019] [Indexed: 12/22/2022] Open
Abstract
Optical mapping of linearized DNA molecules is a promising new technology for sequence assembly and scaffolding, large structural variant detection, and diagnostics. This is currently achieved either using nanochannel confinement or by stretching single DNA molecules on a solid surface. While the first method necessitates DNA labelling before linearization, the latter allows for modification post-linearization, thereby affording increased process flexibility. Each method is constrained by various physical and chemical limitations. One of the most common techniques for linearization of DNA uses a hydrophobic surface and a receding meniscus, termed molecular combing. Here, we report the development of a microfabricated surface that can not only comb the DNA molecules efficiently but also provides for sequence-specific enzymatic fluorescent DNA labelling. By modifying a glass surface with two contrasting functionalities, such that DNA binds selectively to one of the two regions, we can control DNA extension, which is known to be critical for sequence-recognition by an enzyme. Moreover, the surface modification provides enzymatic access to the DNA backbone, as well as minimizing non-specific fluorescent dye adsorption. These enhancements make the designed surface suitable for large-scale and high-resolution single DNA molecule studies.
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Affiliation(s)
- Dharma Varapula
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Eric LaBouff
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Kaitlin Raseley
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Lahari Uppuluri
- Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, PA, 19104, USA
| | - Garth D Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Moses Noh
- Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, PA, 19104, USA
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA.
- Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA.
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13
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Louzao-Martinez L, van Dijk CG, Xu YJ, Korn A, Bekker NJ, Brouwhuis R, Nicese MN, Demmers JA, Goumans MJT, Masereeuw R, Duncker DJ, Verhaar MC, Cheng C. A proteome comparison between human fetal and mature renal extracellular matrix identifies EMILIN1 as a regulator of renal epithelial cell adhesion. Matrix Biol Plus 2019; 4:100011. [PMID: 33543009 PMCID: PMC7852202 DOI: 10.1016/j.mbplus.2019.100011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/08/2019] [Accepted: 07/18/2019] [Indexed: 12/27/2022] Open
Abstract
Cell-based approaches using tissue engineering and regenerative medicine to replace damaged renal tissue with 3D constructs is a promising emerging therapy for kidney disease. Besides living cells, a template provided by a scaffold based on biomaterials and bioactive factors is needed for successful kidney engineering. Nature's own template for a scaffolding system is the extracellular matrix (ECM). Research has focused on mapping the mature renal ECM; however, the developing fetal ECM matches more the active environment required in 3D renal constructs. Here, we characterized the differences between the human fetal and mature renal ECM using spectrometry-based proteomics of decellularized tissue. We identified 99 different renal ECM proteins of which the majority forms an overlapping core, but also includes proteins enriched in either the fetal or mature ECM. Relative protein quantification showed a significant dominance of EMILIN1 in the fetal ECM. We functionally tested the role of EMILIN1 in the ECM using a novel methodology that permits the reliable anchorage of native cell-secreted ECM to glass coverslips. Depletion of EMILIN1 from the ECM layer using siRNA mediated knock-down technologies does not affect renal epithelial cell growth, but does promote migration. Lack of EMILIN1 in the ECM layer reduces the adhesion strength of renal epithelial cells, shown by a decrease in focal adhesion points and associated stress fibers. We showed in this study the importance of a human renal fetal and mature ECM catalogue for identifying promising ECM components that have high implementation potential in scaffolds for 3D renal constructs. Proteomics revealed the differences between the renal fetal and mature extracellular matrix. EMILIN1 has a significant dominance in the fetal extracellular matrix. EMILIN1 depletion from the extracellular matrix reduces the adhesion strength and promotes migration of renal epithelial cells.
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Affiliation(s)
- Laura Louzao-Martinez
- Department of Nephrology and Hypertension, University Medical Center Utrecht, the Netherlands
| | - Christian G.M. van Dijk
- Department of Nephrology and Hypertension, University Medical Center Utrecht, the Netherlands
| | - Yan Juan Xu
- Department of Nephrology and Hypertension, University Medical Center Utrecht, the Netherlands
| | - Amber Korn
- Department of Nephrology and Hypertension, University Medical Center Utrecht, the Netherlands
| | - Nicolaas J. Bekker
- Department of Nephrology and Hypertension, University Medical Center Utrecht, the Netherlands
| | - Romi Brouwhuis
- Department of Nephrology and Hypertension, University Medical Center Utrecht, the Netherlands
| | - Maria Novella Nicese
- Department of Nephrology and Hypertension, University Medical Center Utrecht, the Netherlands
| | | | | | - Rosalinde Masereeuw
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht, the Netherlands
| | - Dirk J. Duncker
- Experimental Cardiology, Department of Cardiology, Erasmus University Medical Center, the Netherlands
| | - Marianne C. Verhaar
- Department of Nephrology and Hypertension, University Medical Center Utrecht, the Netherlands
| | - Caroline Cheng
- Department of Nephrology and Hypertension, University Medical Center Utrecht, the Netherlands
- Experimental Cardiology, Department of Cardiology, Erasmus University Medical Center, the Netherlands
- Corresponding author at: Department of Nephrology and Hypertension, University Medical Center Utrecht, PO Box 85500, 3508 GA Utrecht, the Netherlands, Experimental Cardiology, Thoraxcenter, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, the Netherlands.
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14
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Transcription-dependent regulation of replication dynamics modulates genome stability. Nat Struct Mol Biol 2018; 26:58-66. [PMID: 30598553 DOI: 10.1038/s41594-018-0170-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 11/16/2018] [Indexed: 01/17/2023]
Abstract
Common fragile sites (CFSs) are loci that are hypersensitive to replication stress and hotspots for chromosomal rearrangements in cancers. CFSs replicate late in S phase, are cell-type specific and nest in large genes. The relative impact of transcription-replication conflicts versus a low density in initiation events on fragility is currently debated. Here we addressed the relationships between transcription, replication, and instability by manipulating the transcription of endogenous large genes in chicken and human cells. We found that inducing low transcription with a weak promoter destabilized large genes, whereas stimulating their transcription with strong promoters alleviated instability. Notably, strong promoters triggered a switch to an earlier replication timing, supporting a model in which high transcription levels give cells more time to complete replication before mitosis. Transcription could therefore contribute to maintaining genome integrity, challenging the dominant view that it is exclusively a threat.
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15
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Davis JL, Dong B, Sun C, Zhang HF. Method to identify and minimize artifacts induced by fluorescent impurities in single-molecule localization microscopy. JOURNAL OF BIOMEDICAL OPTICS 2018; 23:1-14. [PMID: 30334394 PMCID: PMC6210800 DOI: 10.1117/1.jbo.23.10.106501] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/21/2018] [Indexed: 05/04/2023]
Abstract
The existence of fluorescent impurities has been a long-standing obstacle in single-molecule imaging, which results in sample misidentification and higher localization uncertainty. Spectroscopic single-molecule localization microscopy can record the full fluorescent spectrum of every stochastic single-molecule emission event. This capability allows us to quantify the spatial and spectral characteristics of fluorescent impurities introduced by sample preparation steps, based on which we developed a method to effectively separate fluorescent impurities from target molecules.
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Affiliation(s)
- Janel L. Davis
- Northwestern University, Department of Biomedical Engineering, Evanston, Illinois, United States
| | - Biqin Dong
- Northwestern University, Department of Biomedical Engineering, Evanston, Illinois, United States
- Northwestern University, Department of Mechanical Engineering, Evanston, Illinois, United States
| | - Cheng Sun
- Northwestern University, Department of Mechanical Engineering, Evanston, Illinois, United States
| | - Hao F. Zhang
- Northwestern University, Department of Biomedical Engineering, Evanston, Illinois, United States
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16
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Yadav H, Sharma P. A simple and novel DNA combing methodology for Fiber-FISH and optical mapping. Genomics 2018; 111:567-578. [PMID: 29550497 DOI: 10.1016/j.ygeno.2018.03.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/09/2018] [Accepted: 03/12/2018] [Indexed: 02/02/2023]
Abstract
Single molecule analysis can help us study genomics efficiently. It involves studying single DNA molecules for genomic studies. DNA combing is one of such techniques which allowed us to study single DNA molecules for multiple uses. DNA combing technology can be used to perform Fiber-FISH and optical mapping. Physical mapping of genomes can be studied by restriction digestion of combed DNA on glass slides. Restriction fragments can be arranged into optical maps by gathering fluorescent intensity data by CCD camera and image analysis by softwares. Physical mapping and DNA segment rearrangements can be studied by Fiber-FISH which involves application of probes on genomic DNA combed over glass slides. We developed a novel methodology involving combing solution optimization, denatured combed DNA and performed restriction digestion of combed DNA. Thus we provided an efficient and robust combing platform for its application in Fiber-FISH and optical mapping.
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Affiliation(s)
- Hemendra Yadav
- Department of Botany, University of Rajasthan, Jaipur, India.
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17
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Yadav H, Sharma P. Enhanced post wash retention of combed DNA molecules by varying multiple combing parameters. Anal Biochem 2017; 536:45-50. [PMID: 28821423 DOI: 10.1016/j.ab.2017.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/07/2017] [Accepted: 08/14/2017] [Indexed: 01/01/2023]
Abstract
Recent advances in genomics have created a need for efficient techniques for deciphering information hidden in various genomes. Single molecule analysis is one such technique to understand molecular processes at single molecule level. Fiber- FISH performed with the help of DNA combing can help us in understanding genetic rearrangements and changes in genome at single DNA molecule level. For performing Fiber-FISH we need high retention of combed DNA molecules post wash as Fiber-FISH requires profuse washing. We optimized combing process involving combing solution, method of DNA mounting on glass slides and coating of glass slides to enhance post-wash retention of DNA molecules. It was found that average number of DNA molecules observed post-wash per field of view was maximum with our optimized combing solution. APTES coated glass slides showed lesser retention than PEI surface but fluorescent intensity was higher in case of APTES coated surface. Capillary method used to mount DNA on glass slides also showed lesser retention but straight DNA molecules were observed as compared to force flow method.
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Affiliation(s)
- Hemendra Yadav
- Department of Botany, University of Rajasthan, Jaipur, India.
| | - Pulkit Sharma
- Bioinventree Pvt Ltd., SB 17 Bhawani Singh Road, Bapunagar, Jaipur 302015 India
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18
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Hoory E, Budassi J, Pfeffer E, Cho N, Thalappillil J, Andersen J, Rafailovich M, Sokolov J. Discrimination of Adsorbed Double-Stranded and Single-Stranded DNA Molecules on Surfaces by Fluorescence Emission Spectroscopy Using Acridine Orange Dye. J Fluoresc 2017; 27:2153-2158. [DOI: 10.1007/s10895-017-2154-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/31/2017] [Indexed: 10/19/2022]
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19
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Tourrière H, Saksouk J, Lengronne A, Pasero P. Single-molecule Analysis of DNA Replication Dynamics in Budding Yeast and Human Cells by DNA Combing. Bio Protoc 2017; 7:e2305. [PMID: 34541074 DOI: 10.21769/bioprotoc.2305] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/01/2017] [Accepted: 04/24/2017] [Indexed: 11/02/2022] Open
Abstract
The DNA combing method allows the analysis of DNA replication at the level of individual DNA molecules stretched along silane-coated glass coverslips. Before DNA extraction, ongoing DNA synthesis is labeled with halogenated analogues of thymidine. Replication tracks are visualized by immunofluorescence using specific antibodies. Unlike biochemical and NGS-based methods, DNA combing provides unique information on cell-to-cell variations in DNA replication profiles, including initiation and elongation. Finally, this assay can be used to monitor the effect of DNA lesions on fork progression, arrest and restart.
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Affiliation(s)
- Hélène Tourrière
- Institute of Human Genetics, CNRS UMR 9002 and University of Montpellier, Equipe labéllisée LIGUE 2017, Montpellier, France
| | - Julie Saksouk
- Institute of Human Genetics, CNRS UMR 9002 and University of Montpellier, Equipe labéllisée LIGUE 2017, Montpellier, France
| | - Armelle Lengronne
- Institute of Human Genetics, CNRS UMR 9002 and University of Montpellier, Equipe labéllisée LIGUE 2017, Montpellier, France
| | - Philippe Pasero
- Institute of Human Genetics, CNRS UMR 9002 and University of Montpellier, Equipe labéllisée LIGUE 2017, Montpellier, France
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20
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Abstract
High resolution fiber-Fluorescence in situ hybridization (FISH) is an advanced FISH technology that can effectively bridge the resolution gap between probe hybridizing on DNA molecules and chromosomal regions. Since various types of DNA and chromatin fibers can be generated reflecting different degrees of DNA/chromatin packaging status, fiber-FISH technology has been successfully used in diverse molecular cytogenetic/cytogenomic studies. Following a brief review of this technology, including its major development and increasing applications, typical protocols to generate DNA/chromatin fiber will be described, coupled with rationales, as well as technical tips. These released DNA/chromatin fibers are suitable for an array of cytogenetic/cytogenomic analyses.
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Affiliation(s)
- Christine J Ye
- The Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Henry H Heng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 3226 Scott Hall, 540 E, Detroit, MI, 48201, USA.
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
- Karmanos Cancer Institute, Detroit, MI, 48201, USA.
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21
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Eles JR, Vazquez AL, Snyder NR, Lagenaur C, Murphy MC, Kozai TDY, Cui XT. Neuroadhesive L1 coating attenuates acute microglial attachment to neural electrodes as revealed by live two-photon microscopy. Biomaterials 2016; 113:279-292. [PMID: 27837661 DOI: 10.1016/j.biomaterials.2016.10.054] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/26/2016] [Accepted: 10/30/2016] [Indexed: 12/15/2022]
Abstract
Implantable neural electrode technologies for chronic neural recordings can restore functional control to paralysis and limb loss victims through brain-machine interfaces. These probes, however, have high failure rates partly due to the biological responses to the probe which generate an inflammatory scar and subsequent neuronal cell death. L1 is a neuronal specific cell adhesion molecule and has been shown to minimize glial scar formation and promote electrode-neuron integration when covalently attached to the surface of neural probes. In this work, the acute microglial response to L1-coated neural probes was evaluated in vivo by implanting coated devices into the cortex of mice with fluorescently labeled microglia, and tracking microglial dynamics with multi-photon microscopy for the ensuing 6 h in order to understand L1's cellular mechanisms of action. Microglia became activated immediately after implantation, extending processes towards both L1-coated and uncoated control probes at similar velocities. After the processes made contact with the probes, microglial processes expanded to cover 47.7% of the control probes' surfaces. For L1-coated probes, however, there was a statistically significant 83% reduction in microglial surface coverage. This effect was sustained through the experiment. At 6 h post-implant, the radius of microglia activation was reduced for the L1 probes by 20%, shifting from 130.0 to 103.5 μm with the coating. Microglia as far as 270 μm from the implant site displayed significantly lower morphological characteristics of activation for the L1 group. These results suggest that the L1 surface treatment works in an acute setting by microglial mediated mechanisms.
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Affiliation(s)
- James R Eles
- Bioengineering, University of Pittsburgh, United States; Center for the Neural Basis of Cognition, University of Pittsburgh and Carnegie Mellon University, United States
| | - Alberto L Vazquez
- Bioengineering, University of Pittsburgh, United States; Radiology, University of Pittsburgh, United States; Neurobiology, University of Pittsburgh, United States
| | - Noah R Snyder
- Bioengineering, University of Pittsburgh, United States; Center for the Neural Basis of Cognition, University of Pittsburgh and Carnegie Mellon University, United States
| | - Carl Lagenaur
- Neurobiology, University of Pittsburgh, United States
| | | | - Takashi D Y Kozai
- Bioengineering, University of Pittsburgh, United States; Center for the Neural Basis of Cognition, University of Pittsburgh and Carnegie Mellon University, United States; McGowan Institute for Regenerative Medicine, University of Pittsburgh, United States; NeuroTech Center of the University of Pittsburgh Brain Institute, United States.
| | - X Tracy Cui
- Bioengineering, University of Pittsburgh, United States; Center for the Neural Basis of Cognition, University of Pittsburgh and Carnegie Mellon University, United States; McGowan Institute for Regenerative Medicine, University of Pittsburgh, United States.
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22
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Lacroix J, Pélofy S, Blatché C, Pillaire MJ, Huet S, Chapuis C, Hoffmann JS, Bancaud A. Analysis of DNA Replication by Optical Mapping in Nanochannels. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:5963-5970. [PMID: 27624455 DOI: 10.1002/smll.201503795] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 06/21/2016] [Indexed: 06/06/2023]
Abstract
DNA replication is essential to maintain genome integrity in S phase of the cell division cycle. Accumulation of stalled replication forks is a major source of genetic instability, and likely constitutes a key driver of tumorigenesis. The mechanisms of regulation of replication fork progression have therefore been extensively investigated, in particular with DNA combing, an optical mapping technique that allows the stretching of single molecules and the mapping of active region for DNA synthesis by fluorescence microscopy. DNA linearization in nanochannels has been successfully used to probe genomic information patterns along single chromosomes, and has been proposed to be a competitive alternative to DNA combing. Yet this conjecture remains to be confirmed experimentally. Here, two complementary techniques are established to detect the genomic distribution of tracks of newly synthesized DNA in human cells by optical mapping in nanochannels. Their respective advantages and limitations are compared, and applied them to detect deregulations of the replication program induced by the antitumor drug hydroxyurea. The developments here thus broaden the field of applications accessible to nanofluidic technologies, and can be used in the future as part for molecular diagnostics in the context of high throughput cancer drug screening.
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Affiliation(s)
- Joris Lacroix
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
| | - Sandrine Pélofy
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
| | - Charline Blatché
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
| | - Marie-Jeanne Pillaire
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
- Equipe "Labellisée LA LIGUE CONTRE LE CANCER 2013" - Laboratoire d'Excellence Toulouse Cancer LABEX TOUCAN - Cancer Research Center of Toulouse, Inserm U1037, CNRS ERL5294, 2 Avenue Hubert Curien, CS 53717, 31037, Toulouse, France
| | - Sébastien Huet
- CNRS, UMR 6061, Institut Génétique et Développement de Rennes, F-35043, Rennes, France
- Université Rennes 1, UEB, UMR 6290, Faculté de Médecine, F-35043, Rennes, France
| | - Catherine Chapuis
- CNRS, UMR 6061, Institut Génétique et Développement de Rennes, F-35043, Rennes, France
- Université Rennes 1, UEB, UMR 6290, Faculté de Médecine, F-35043, Rennes, France
| | - Jean-Sébastien Hoffmann
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
- Equipe "Labellisée LA LIGUE CONTRE LE CANCER 2013" - Laboratoire d'Excellence Toulouse Cancer LABEX TOUCAN - Cancer Research Center of Toulouse, Inserm U1037, CNRS ERL5294, 2 Avenue Hubert Curien, CS 53717, 31037, Toulouse, France
| | - Aurélien Bancaud
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
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23
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Direct and precise length measurement of single, stretched DNA fragments by dynamic molecular combing and STED nanoscopy. Anal Bioanal Chem 2016; 408:6453-9. [DOI: 10.1007/s00216-016-9764-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/25/2016] [Accepted: 07/04/2016] [Indexed: 11/25/2022]
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24
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PERK inhibits DNA replication during the Unfolded Protein Response via Claspin and Chk1. Oncogene 2016; 36:678-686. [DOI: 10.1038/onc.2016.239] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 05/06/2016] [Accepted: 06/03/2016] [Indexed: 12/20/2022]
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25
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Teperek M, Simeone A, Gaggioli V, Miyamoto K, Allen GE, Erkek S, Kwon T, Marcotte EM, Zegerman P, Bradshaw CR, Peters AHFM, Gurdon JB, Jullien J. Sperm is epigenetically programmed to regulate gene transcription in embryos. Genome Res 2016; 26:1034-46. [PMID: 27034506 PMCID: PMC4971762 DOI: 10.1101/gr.201541.115] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/29/2016] [Indexed: 12/02/2022]
Abstract
For a long time, it has been assumed that the only role of sperm at fertilization is to introduce the male genome into the egg. Recently, ideas have emerged that the epigenetic state of the sperm nucleus could influence transcription in the embryo. However, conflicting reports have challenged the existence of epigenetic marks on sperm genes, and there are no functional tests supporting the role of sperm epigenetic marking on embryonic gene expression. Here, we show that sperm is epigenetically programmed to regulate embryonic gene expression. By comparing the development of sperm- and spermatid-derived frog embryos, we show that the programming of sperm for successful development relates to its ability to regulate transcription of a set of developmentally important genes. During spermatid maturation into sperm, these genes lose H3K4me2/3 and retain H3K27me3 marks. Experimental removal of these epigenetic marks at fertilization de-regulates gene expression in the resulting embryos in a paternal chromatin-dependent manner. This demonstrates that epigenetic instructions delivered by the sperm at fertilization are required for correct regulation of gene expression in the future embryos. The epigenetic mechanisms of developmental programming revealed here are likely to relate to the mechanisms involved in transgenerational transmission of acquired traits. Understanding how parental experience can influence development of the progeny has broad potential for improving human health.
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Affiliation(s)
- Marta Teperek
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, United Kingdom; Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom
| | - Angela Simeone
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, United Kingdom; Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom
| | - Vincent Gaggioli
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, United Kingdom; Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom
| | - Kei Miyamoto
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, United Kingdom; Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom
| | - George E Allen
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, United Kingdom
| | - Serap Erkek
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4001 Basel, Switzerland
| | - Taejoon Kwon
- Department of Molecular Bioscience, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Edward M Marcotte
- Department of Molecular Bioscience, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Philip Zegerman
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, United Kingdom; Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom
| | - Charles R Bradshaw
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, United Kingdom
| | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4001 Basel, Switzerland
| | - John B Gurdon
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, United Kingdom; Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom
| | - Jerome Jullien
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, United Kingdom; Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom
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26
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Gallo D, Wang G, Yip CM, Brown GW. Analysis of Replicating Yeast Chromosomes by DNA Combing. Cold Spring Harb Protoc 2016; 2016:pdb.prot085118. [PMID: 26832684 DOI: 10.1101/pdb.prot085118] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Molecular combing of DNA fibers is a powerful technique to monitor origin usage and DNA replication fork progression in the budding yeast Saccharomyces cerevisiae. In contrast to traditional flow cytometry, microarray, or sequencing techniques, which provide population-level data, DNA combing provides DNA replication profiles of individual molecules. DNA combing uses yeast strains that express human thymidine kinase, which facilitates the incorporation of thymidine analogs into nascent DNA. First, DNA is isolated and stretched uniformly onto silanized glass coverslips. Following immunodetection with antibodies that recognize the thymidine analog and the DNA, the DNA fibers are imaged using a fluorescence microscope. Finally, the lengths of newly replicated DNA tracks are measured and converted to base pairs, allowing calculations of the speed of the replication fork and of interorigin distances. DNA combing can be applied to monitor replication defects caused by gene mutations or by chemical agents that induce replication stress. Here, we present a methodology for studying replicating yeast chromosomes by molecular DNA combing. We begin with procedures for the preparation of silanized coverslips and for assembly of a DNA combing machine (DCM) and conclude by presenting a detailed protocol for molecular DNA combing in yeast.
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Affiliation(s)
- David Gallo
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Gang Wang
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Christopher M Yip
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada; Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Grant W Brown
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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27
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Bialic M, Coulon V, Drac M, Gostan T, Schwob E. Analyzing the dynamics of DNA replication in Mammalian cells using DNA combing. Methods Mol Biol 2015; 1300:67-78. [PMID: 25916705 DOI: 10.1007/978-1-4939-2596-4_4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
How cells duplicate their chromosomes is a key determinant of cell identity and genome stability. DNA replication can initiate from more than 100,000 sites distributed along mammalian chromosomes, yet a given cell uses only a subset of these origins due to inefficient origin activation and regulation by developmental or environmental cues. An impractical consequence of cell-to-cell variations in origin firing is that population-based techniques do not accurately describe how chromosomes are replicated in single cells. DNA combing is a biophysical DNA fiber stretching method which permits visualization of ongoing DNA synthesis along Mb-sized single-DNA molecules purified from cells that were previously pulse-labeled with thymidine analogues. This allows quantitative measurements of several salient features of chromosome replication dynamics, such as fork velocity, fork asymmetry, inter-origin distances, and global instant fork density. In this chapter we describe how to obtain this information from asynchronous cultures of mammalian cells.
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Affiliation(s)
- Marta Bialic
- Institute of Molecular Genetics, CNRS UMR5535 & Université Montpellier, 1919 route de Mende, Montpellier, 34293, France
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28
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Dugyala VR, Basavaraj MG. Control over coffee-ring formation in evaporating liquid drops containing ellipsoids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:8680-6. [PMID: 25003833 DOI: 10.1021/la500803h] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A control over the nature of deposit pattern obtained after the evaporation of solvent from a sessile drop containing dispersed materials has been demonstrated to have applications in materials engineering, separation technology, printing technology, manufacture of printed circuit boards, biology, and agriculture. In this article, we report an experimental investigation of the effect of particle shape and DLVO (Derjaguin-Landau-Verwey-Overbeek) interactions on evaporation-driven pattern formation in sessile drops. The use of a model system containing monodisperse particles where particle aspect ratio and surface charge can be adjusted reveals that a control over the nature of deposit pattern can be achieved by tuning the particle-particle and particle-substrate interactions. A clear coffee-ring formation is observed when the strength of particle-particle repulsion is higher than the particle-substrate attraction. However, complete suppression of ringlike deposits leading to a uniform film is achieved when particle-substrate and particle-particle interactions are attractive. Results illustrate that for the system of submicron ellipsoids that are hydrophilic, the nature of deposit patterns obtained after evaporation depends on the nature of interactions and not on particle shape.
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Affiliation(s)
- Venkateshwar Rao Dugyala
- Polymer Engineering and Colloid Science Lab (PECS Lab), Department of Chemical Engineering, Indian Institute of Technology-Madras , Chennai 600 036, India
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29
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Neupane GP, Dhakal KP, Kim MS, Lee H, Guthold M, Joseph VS, Hong JD, Kim J. Simple method of DNA stretching on glass substrate for fluorescence imaging and spectroscopy. JOURNAL OF BIOMEDICAL OPTICS 2014; 19:051210. [PMID: 24407597 DOI: 10.1117/1.jbo.19.5.051210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 12/13/2013] [Indexed: 06/03/2023]
Abstract
We demonstrate a simple method of stretching DNA to its full length, suitable for optical imaging and atomic force microscopy (AFM). Two competing forces on the DNA molecules, which are the electrostatic attraction between positively charged dye molecules (YOYO-1) intercalated into DNA and the negatively charged surface of glass substrate, and the centrifugal force of the rotating substrate, are mainly responsible for the effective stretching and the dispersion of single strands of DNA. The density of stretched DNA molecules could be controlled by the concentration of the dye-stained DNA solution. Stretching of single DNA molecules was confirmed by AFM imaging and the photoluminescence spectra of single DNA molecule stained with YOYO-1 were obtained, suggesting that our method is useful for spectroscopic analysis of DNA at the single molecule level.
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Affiliation(s)
- Guru P Neupane
- IBS Center for Integrated Nanostructure Physics, Institute for Basic Science (IBS), Daejeon 305-701, Republic of KoreabSungkyunkwan University, Department of Energy Science, Suwon 440-746, Republic of Korea
| | - Krishna P Dhakal
- IBS Center for Integrated Nanostructure Physics, Institute for Basic Science (IBS), Daejeon 305-701, Republic of KoreabSungkyunkwan University, Department of Energy Science, Suwon 440-746, Republic of Korea
| | - Min Su Kim
- IBS Center for Integrated Nanostructure Physics, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea
| | - Hyunsoo Lee
- Wake Forest University, Department of Physics, Winston-Salem, North Carolina 27109
| | - Martin Guthold
- Wake Forest University, Department of Physics, Winston-Salem, North Carolina 27109
| | - Vincent S Joseph
- Incheon National University, Department of Chemistry, Incheon 406-772, Republic of Korea
| | - Jong-Dal Hong
- Incheon National University, Department of Chemistry, Incheon 406-772, Republic of Korea
| | - Jeongyong Kim
- IBS Center for Integrated Nanostructure Physics, Institute for Basic Science (IBS), Daejeon 305-701, Republic of KoreabSungkyunkwan University, Department of Energy Science, Suwon 440-746, Republic of KoreaeIncheon National University, Department of Physi
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30
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Gaggioli V, Zeiser E, Rivers D, Bradshaw CR, Ahringer J, Zegerman P. CDK phosphorylation of SLD-2 is required for replication initiation and germline development in C. elegans. ACTA ACUST UNITED AC 2014; 204:507-22. [PMID: 24535824 PMCID: PMC3926958 DOI: 10.1083/jcb.201310083] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Timely phosphorylation of SLD-2 by CDK is essential for proper replication initiation and cell proliferation in the germline of C. elegans. Cyclin-dependent kinase (CDK) plays a vital role in proliferation control across eukaryotes. Despite this, how CDK mediates cell cycle and developmental transitions in metazoa is poorly understood. In this paper, we identify orthologues of Sld2, a CDK target that is important for DNA replication in yeast, and characterize SLD-2 in the nematode worm Caenorhabditis elegans. We demonstrate that SLD-2 is required for replication initiation and the nuclear retention of a critical component of the replicative helicase CDC-45 in embryos. SLD-2 is a CDK target in vivo, and phosphorylation regulates the interaction with another replication factor, MUS-101. By mutation of the CDK sites in sld-2, we show that CDK phosphorylation of SLD-2 is essential in C. elegans. Finally, using a phosphomimicking sld-2 mutant, we demonstrate that timely CDK phosphorylation of SLD-2 is an important control mechanism to allow normal proliferation in the germline. These results determine an essential function of CDK in metazoa and identify a developmental role for regulated SLD-2 phosphorylation.
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Affiliation(s)
- Vincent Gaggioli
- Wellcome Trust/Cancer Research UK Gurdon Institute, 2 Department of Genetics, and 3 Department of Zoology, University of Cambridge, Cambridge CB2 1QN, England, UK
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31
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Gaggioli V, Le Viet B, Germe T, Hyrien O. DNA topoisomerase IIα controls replication origin cluster licensing and firing time in Xenopus egg extracts. Nucleic Acids Res 2013; 41:7313-31. [PMID: 23757188 PMCID: PMC3753627 DOI: 10.1093/nar/gkt494] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Sperm chromatin incubated in Xenopus egg extracts undergoes origin licensing and nuclear assembly before DNA replication. We found that depletion of DNA topoisomerase IIα (topo IIα), the sole topo II isozyme of eggs and its inhibition by ICRF-193, which clamps topo IIα around DNA have opposite effects on these processes. ICRF-193 slowed down replication origin cluster activation and fork progression in a checkpoint-independent manner, without altering replicon size. In contrast, topo IIα depletion accelerated origin cluster activation, and topo IIα add-back negated overinitiation. Therefore, topo IIα is not required for DNA replication, but topo IIα clamps slow replication, probably by forming roadblocks. ICRF-193 had no effect on DNA synthesis when added after nuclear assembly, confirming that topo IIα activity is dispensable for replication and revealing that topo IIα clamps formed on replicating DNA do not block replication, presumably because topo IIα acts behind and not in front of forks. Topo IIα depletion increased, and topo IIα addition reduced, chromatin loading of MCM2-7 replicative helicase, whereas ICRF-193 did not affect MCM2-7 loading. Therefore, topo IIα restrains MCM2-7 loading in an ICRF-193-resistant manner during origin licensing, suggesting a model for establishing the sequential firing of origin clusters.
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Affiliation(s)
- Vincent Gaggioli
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), S2-Génomique Fonctionnelle, CNRS UMR8197, Inserm U1024, 46 rue d'Ulm, 75005 Paris, France
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32
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Técher H, Koundrioukoff S, Azar D, Wilhelm T, Carignon S, Brison O, Debatisse M, Le Tallec B. Replication dynamics: biases and robustness of DNA fiber analysis. J Mol Biol 2013; 425:4845-55. [PMID: 23557832 DOI: 10.1016/j.jmb.2013.03.040] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 03/22/2013] [Accepted: 03/25/2013] [Indexed: 12/11/2022]
Abstract
The factors that govern replication programs are still poorly identified in metazoans, especially in mammalian cells. Thanks to molecular combing, the dynamics of DNA replication can be assessed at the genome-scale level from the cumulative analysis of single DNA fibers. This technique notably enables measurement of replication fork speed and fork asymmetry and that of distances separating either initiation or termination events. The results presented here aim to evaluate requirements critical to accurate measurement of replication parameters by molecular combing. We show that sample size, fiber length and DNA counterstaining are crucial to gain robust information concerning replication dynamics. Our results thus provide a methodological frame to investigate the DNA replication program through molecular combing analyses.
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Affiliation(s)
- Hervé Técher
- Institut Curie, Centre de Recherche, 26 rue d'Ulm, 75248 Paris Cedex 05, France; Université Pierre et Marie Curie Paris 06, 4 Place Jussieu, 75005 Paris, France; Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3244, 75248 Paris Cedex 05, France
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33
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Dvořáková M, Karafiát V, Pajer P, Kluzáková E, Jarkovská K, Peková S, Krutílková L, Dvořák M. DNA released by leukemic cells contributes to the disruption of the bone marrow microenvironment. Oncogene 2012; 32:5201-9. [PMID: 23222712 DOI: 10.1038/onc.2012.553] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 10/01/2012] [Accepted: 10/02/2012] [Indexed: 12/22/2022]
Abstract
Reciprocal interactions between a tumor and its microenvironment control expansion of tumor cells. Here we show a specific type of interaction in which blasts of experimental leukemia destroy the bone marrow (BM) structures and kill stromal cells. The in vitro experiments showed that the cytotoxic agent released by leukemic cells is the fragmented DNA derived from their genome and occurring in nucleosome-like complexes. This DNA entered nuclei of BM or other cells and induced H2A.X phosphorylation at serine 139, similar to double-strand break-inducing agents. There was a correlation between large amounts of acquired DNA and death of recipient cells. Moreover, the DNA integrated into chromosomal DNA of recipient cells. Primary human acute myeloid leukemia cells also released fragmented DNA that penetrated the nuclei of other cells both in vitro and in vivo. We suggest that DNA fragments released from leukemic and also perhaps other types of tumor cells can activate DNA repair mechanisms or death in recipient cells of a tumor microenvironment, depending on the amount of the acquired DNA. This can impair DNA stability and viability of tumor stromal cells, undermine homeostatic capacity of tumor microenvironment and facilitate tumor progression.
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Affiliation(s)
- M Dvořáková
- Institute of Molecular Genetics, AS CR, Prague, Czech Republic
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34
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Bianco JN, Poli J, Saksouk J, Bacal J, Silva MJ, Yoshida K, Lin YL, Tourrière H, Lengronne A, Pasero P. Analysis of DNA replication profiles in budding yeast and mammalian cells using DNA combing. Methods 2012; 57:149-57. [PMID: 22579803 DOI: 10.1016/j.ymeth.2012.04.007] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Revised: 04/11/2012] [Accepted: 04/14/2012] [Indexed: 11/17/2022] Open
Abstract
DNA combing is a powerful method developed by Bensimon and colleagues to stretch DNA molecules on silanized glass coverslips. This technique provides a unique way to monitor the activation of replication origins and the progression of replication forks at the level of single DNA molecules, after incorporation of thymidine analogs, such as 5-bromo-2'-deoxyuridine (BrdU), 5-iodo-2'-deoxyuridine (IdU) and 5-chloro-2'-deoxyuridine (CldU) in newly-synthesized DNA. Unlike microarray-based approaches, this assay gives access to the variability of replication profiles in individual cells. It can also be used to monitor the effect of DNA lesions on fork progression, arrest and restart. In this review, we propose standard DNA combing methods to analyze DNA replication in budding yeast and in human cells. We also show that 5-ethynyl-2'-deoxyuridine (EdU) can be used as a good alternative to BrdU for DNA combing analysis, as unlike halogenated nucleotides, it can be detected without prior denaturation of DNA.
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Affiliation(s)
- Julien N Bianco
- Institute of Human Genetics, CNRS UPR 1142, Montpellier F-34396, France
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35
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Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome. PLoS Comput Biol 2011; 7:e1002322. [PMID: 22219720 PMCID: PMC3248390 DOI: 10.1371/journal.pcbi.1002322] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 11/07/2011] [Indexed: 12/28/2022] Open
Abstract
Genome-wide replication timing studies have suggested that mammalian chromosomes consist of megabase-scale domains of coordinated origin firing separated by large originless transition regions. Here, we report a quantitative genome-wide analysis of DNA replication kinetics in several human cell types that contradicts this view. DNA combing in HeLa cells sorted into four temporal compartments of S phase shows that replication origins are spaced at 40 kb intervals and fire as small clusters whose synchrony increases during S phase and that replication fork velocity (mean 0.7 kb/min, maximum 2.0 kb/min) remains constant and narrowly distributed through S phase. However, multi-scale analysis of a genome-wide replication timing profile shows a broad distribution of replication timing gradients with practically no regions larger than 100 kb replicating at less than 2 kb/min. Therefore, HeLa cells lack large regions of unidirectional fork progression. Temporal transition regions are replicated by sequential activation of origins at a rate that increases during S phase and replication timing gradients are set by the delay and the spacing between successive origin firings rather than by the velocity of single forks. Activation of internal origins in a specific temporal transition region is directly demonstrated by DNA combing of the IGH locus in HeLa cells. Analysis of published origin maps in HeLa cells and published replication timing and DNA combing data in several other cell types corroborate these findings, with the interesting exception of embryonic stem cells where regions of unidirectional fork progression seem more abundant. These results can be explained if origins fire independently of each other but under the control of long-range chromatin structure, or if replication forks progressing from early origins stimulate initiation in nearby unreplicated DNA. These findings shed a new light on the replication timing program of mammalian genomes and provide a general model for their replication kinetics. Eukaryotic chromosomes replicate from multiple replication origins that fire at different times in S phase. The mechanisms that specify origin position and firing time and coordinate origins to ensure complete genome duplication are unclear. Previous studies proposed either that origins are arranged in temporally coordinated groups or fire independently of each other in a stochastic manner. Here, we have performed a quantitative analysis of human genome replication kinetics using a combination of DNA combing, which reveals local patterns of origin firing and replication fork progression on single DNA molecules, and massive sequencing of newly replicated DNA, which reveals the population-averaged replication timing profile of the entire genome. We show that origins are activated synchronously in large regions of uniform replication timing but more gradually in temporal transition regions and that the rate of origin firing increases as replication progresses. Large regions of unidirectional fork progression are abundant in embryonic stem cells but rare in differentiated cells. We propose a model in which replication forks progressing from early origins stimulate initiation in nearby unreplicated DNA in a manner that explains the shape of the replication timing profile. These results provide a fundamental insight into the temporal regulation of mammalian genome replication.
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36
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Ma E, Hyrien O, Goldar A. Do replication forks control late origin firing in Saccharomyces cerevisiae? Nucleic Acids Res 2011; 40:2010-9. [PMID: 22086957 PMCID: PMC3300028 DOI: 10.1093/nar/gkr982] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Recent studies of eukaryotic DNA replication timing profiles suggest that the time-dependent rate of origin firing, I(t), has a universal shape, which ensures a reproducible replication completion time. However, measurements of I(t) are based on population averages, which may bias the shape of the I(t) because of imperfect cell synchrony and cell-to-cell variability. Here, we measure the population-averaged I(t) profile from synchronized Saccharomyces cerevisiae cells using DNA combing and we extract the single-cell I(t) profile using numerical deconvolution. The single cell I(t) and the population-averaged I(t) extracted from DNA combing and replication timing profiles are similar, indicating a genome scale invariance of the replication process, and excluding cell-to-cell variability in replication time as an explanation for the shape of I(t). The single cell I(t) correlates with fork density in wild-type cells, which is specifically loosened in late S phase in the clb5Δ mutant. A previously proposed numerical model that reproduces the wild-type I(t) profile, could also describe the clb5Δ mutant I(t) once modified to incorporate the decline in CDK activity and the looser dependency of initiation on fork density in the absence of Clb5p. Overall, these results suggest that the replication forks emanating from early fired origins facilitate origin firing in later-replicating regions.
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Affiliation(s)
- Emilie Ma
- Commissariat à l'Energie Atomique (CEA), iBiTec-S, 91191 Gif-sur-Yvette, France
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37
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Letessier A, Millot GA, Koundrioukoff S, Lachagès AM, Vogt N, Hansen RS, Malfoy B, Brison O, Debatisse M. Cell-type-specific replication initiation programs set fragility of the FRA3B fragile site. Nature 2011; 470:120-3. [DOI: 10.1038/nature09745] [Citation(s) in RCA: 338] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Accepted: 12/08/2010] [Indexed: 12/17/2022]
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38
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Lubelsky Y, Sasaki T, Kuipers MA, Lucas I, Le Beau MM, Carignon S, Debatisse M, Prinz JA, Dennis JH, Gilbert DM. Pre-replication complex proteins assemble at regions of low nucleosome occupancy within the Chinese hamster dihydrofolate reductase initiation zone. Nucleic Acids Res 2010; 39:3141-55. [PMID: 21148149 PMCID: PMC3082903 DOI: 10.1093/nar/gkq1276] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Genome-scale mapping of pre-replication complex proteins has not been reported in mammalian cells. Poor enrichment of these proteins at specific sites may be due to dispersed binding, poor epitope availability or cell cycle stage-specific binding. Here, we have mapped sites of biotin-tagged ORC and MCM protein binding in G1-synchronized populations of Chinese hamster cells harboring amplified copies of the dihydrofolate reductase (DHFR) locus, using avidin-affinity purification of biotinylated chromatin followed by high-density microarray analysis across the DHFR locus. We have identified several sites of significant enrichment for both complexes distributed throughout the previously identified initiation zone. Analysis of the frequency of initiations across stretched DNA fibers from the DHFR locus confirmed a broad zone of de-localized initiation activity surrounding the sites of ORC and MCM enrichment. Mapping positions of mononucleosomal DNA empirically and computing nucleosome-positioning information in silico revealed that ORC and MCM map to regions of low measured and predicted nucleosome occupancy. Our results demonstrate that specific sites of ORC and MCM enrichment can be detected within a mammalian intitiation zone, and suggest that initiation zones may be regions of generally low nucleosome occupancy where flexible nucleosome positioning permits flexible pre-RC assembly sites.
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Affiliation(s)
- Yoav Lubelsky
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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39
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Gay S, Lachages AM, Millot GA, Courbet S, Letessier A, Debatisse M, Brison O. Nucleotide supply, not local histone acetylation, sets replication origin usage in transcribed regions. EMBO Rep 2010; 11:698-704. [PMID: 20671737 DOI: 10.1038/embor.2010.112] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Revised: 06/24/2010] [Accepted: 06/25/2010] [Indexed: 12/25/2022] Open
Abstract
In eukaryotes, only a fraction of replication origins fire at each S phase. Local histone acetylation was proposed to control firing efficiency of origins, but conflicting results were obtained. We report that local histone acetylation does not reflect origin efficiencies along the adenosine monophosphate deaminase 2 locus in mammalian fibroblasts. Reciprocally, modulation of origin efficiency does not affect acetylation. However, treatment with a deacetylase inhibitor changes the initiation pattern. We demonstrate that this treatment alters pyrimidine biosynthesis and decreases fork speed, which recruits latent origins. Our findings reconcile results that seemed inconsistent and reveal an unsuspected effect of deacetylase inhibitors on replication dynamics.
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Affiliation(s)
- Sophie Gay
- Institut Curie, Centre de Recherche, 26 rue d'Ulm, 75248 Paris, France
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Despras E, Daboussi F, Hyrien O, Marheineke K, Kannouche PL. ATR/Chk1 pathway is essential for resumption of DNA synthesis and cell survival in UV-irradiated XP variant cells. Hum Mol Genet 2010; 19:1690-701. [PMID: 20123862 DOI: 10.1093/hmg/ddq046] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
DNA polymerase eta (poleta) performs translesion synthesis past ultraviolet (UV) photoproducts and is deficient in cancer-prone xeroderma pigmentosum variant (XP-V) syndrome. The slight sensitivity of XP-V cells to UV is dramatically enhanced by low concentrations of caffeine. So far, the biological explanation for this feature remains elusive. Using DNA combing, we showed that translesion synthesis defect leads to a strong reduction in the number of active replication forks and a high proportion of stalled forks in human cells, which contrasts with budding yeast. Moreover, extensive regions of single-strand DNA are formed during replication in irradiated XP-V cells, leading to an over-activation of ATR/Chk1 pathway after low UVC doses. Addition of a low concentration of caffeine post-irradiation, although inefficient to restore S-phase progression, significantly decreases Chk1 activation and abrogates DNA synthesis in XP-V cells. While inhibition of Chk1 activity by UCN-01 prevents UVC-induced S-phase delay in wild-type cells, it aggravates replication defect in XP-V cells by increasing fork stalling. Consequently, UCN-01 sensitizes XP-V cells to UVC as caffeine does. Our findings indicate that poleta acts at stalled forks to resume their progression, preventing the requirement for efficient replication checkpoint after low UVC doses. In the absence of poleta, Chk1 kinase becomes essential for replication resumption by alternative pathways, via fork stabilization.
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Affiliation(s)
- Emmanuelle Despras
- Centre Nationale de Recherche Scientifique (CNRS) UMR8200, Laboratoire Stabilité Génétique et Oncogenèse, Université Paris-Sud, Institut Gustave Roussy, 39 rue Camille Desmoulins, 94800 Villejuif, France
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Krude T, Christov CP, Hyrien O, Marheineke K. Y RNA functions at the initiation step of mammalian chromosomal DNA replication. J Cell Sci 2009; 122:2836-45. [PMID: 19657016 DOI: 10.1242/jcs.047563] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Non-coding Y RNAs have recently been identified as essential novel factors for chromosomal DNA replication in mammalian cell nuclei, but mechanistic details of their function have not been defined. Here, we identify the execution point for Y RNA function during chromosomal DNA replication in a mammalian cell-free system. We determined the effect of degradation of Y3 RNA on replication origin activation and on fork progression rates at single-molecule resolution by DNA combing and nascent-strand analysis. Degradation of Y3 RNA inhibits the establishment of new DNA replication forks at the G1- to S-phase transition and during S phase. This inhibition is negated by addition of exogenous Y1 RNA. By contrast, progression rates of DNA replication forks are not affected by degradation of Y3 RNA or supplementation with exogenous Y1 RNA. These data indicate that Y RNAs are required for the establishment, but not for the elongation, of chromosomal DNA replication forks in mammalian cell nuclei. We conclude that the execution point for non-coding Y RNA function is the activation of chromosomal DNA replication origins.
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Affiliation(s)
- Torsten Krude
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, UK.
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Reiss E, Hölzel R, Bier FF. Synthesis and stretching of rolling circle amplification products in a flow-through system. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2009; 5:2316-22. [PMID: 19492351 DOI: 10.1002/smll.200900319] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Enzymatic isothermal rolling circle amplification (RCA) produces long concatemeric single-stranded DNA (ssDNA) molecules if a small circular ssDNA molecule is applied as the template. A method is presented here in which the RCA reaction is carried out in a flow-through system, starting from isolated surface-tethered DNA primers. This approach combines gentle fluidic handling of the single-stranded RCA products, such as staining or stretching via a receding meniscus, with the option of simultaneous (fluorescence) microscopic observation. It is shown that the stretched and surface-attached RCA products are accessible for hybridization of complementary oligonucleotides, which demonstrates their addressability by complementary base pairing. The long RCA products should be well suited to bridge the gap between biomolecular nanoscale building-blocks and structures at the micro- and macroscale, especially at the single-molecule level presented here.
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Affiliation(s)
- Edda Reiss
- Fraunhofer Institute for Biomedical Engineering, Branch Potsdam-Golm, Department of Nanobiotechnology & Nanomedicine ,Am Mühlenberg 13, 14476 Potsdam, Germany.
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Marheineke K, Goldar A, Krude T, Hyrien O. Use of DNA combing to study DNA replication in Xenopus and human cell-free systems. Methods Mol Biol 2009; 521:575-603. [PMID: 19563130 DOI: 10.1007/978-1-60327-815-7_33] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The Xenopus egg extract has become the gold standard for in vitro studies of metazoan DNA replication. We have used this system to study the mechanisms that ensure rapid and complete DNA replication despite random initiation during Xenopus early development. To this end we adapted the DNA combing technique to investigate the distribution of replication bubbles along single DNA molecules. DNA replicating in egg extracts is labelled by addition of digoxigenin-11-dUTP and/or biotin-16-dUTP at precise times. These two dTTP analogues are efficiently incorporated into DNA during replication in the extract. After DNA purification and combing the DNA is visualized with appropriate fluorescent antibody/streptavidin molecules. Replicated DNA appears as green or red tracts whose pattern reveals how each molecule was replicated, allowing to follow the dynamics of DNA replication through S phase. We describe (a) the preparation and use of egg extracts and demembranated sperm chromatin templates; (b) a simple method for preparing silanized glass coverslips suitable for DNA combing and fluorescence detection; (c) two alternative replicative DNA labelling schemes and their respective advantages; and (d) a protocol for combining replicative labelling with detection of specific DNA sequences by fluorescent in situ hybridization (FISH). Although most observations made in Xenopus egg extracts are applicable to other eukaryotes, there are differences in cell-cycle regulation between mammalian somatic cells and embryonic amphibian cells, which led to the development of human cell-free systems that can initiate semi-conservative chromosomal DNA replication under cell-cycle control. We have employed the knowledge gained with Xenopus extracts to characterize DNA replication intermediates generated in human cell-free systems using DNA combing. We describe here (a) the preparation and use of human cell-free extracts and initiation-competent template nuclei for DNA combing studies; (b) an optimized labelling scheme for DNA replication intermediates by molecular combing and fluorescence microscopy.
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