1
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Fujikawa Y, Kawai H, Suzuki T, Kamiya H. Visualization of oxidized guanine nucleotides accumulation in living cells with split MutT. Nucleic Acids Res 2024; 52:6532-6542. [PMID: 38738661 PMCID: PMC11194108 DOI: 10.1093/nar/gkae371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/14/2024] [Accepted: 04/25/2024] [Indexed: 05/14/2024] Open
Abstract
Cancer cells produce vast quantities of reactive oxygen species, leading to the accumulation of toxic nucleotides as 8-oxo-7,8-dihydro-2'-deoxyguanosine 5'-triphosphate (8-oxo-dGTP). The human MTH1 protein catalyzes the hydrolysis of 8-oxo-dGTP, and cancer cells are dependent on MTH1 for their survival. MTH1 inhibitors are possible candidates for a class of anticancer drugs; however, a reliable screening system using live cells has not been developed. Here we report a visualization method for 8-oxo-dGTP and its related nucleotides in living cells. Escherichia coli MutT, a functional homologue of MTH1, is divided into the N-terminal (1-95) and C-terminal (96-129) parts (Mu95 and 96tT, respectively). Mu95 and 96tT were fused to Ash (assembly helper tag) and hAG (Azami Green), respectively, to visualize the nucleotides as fluorescent foci formed upon the Ash-hAG association. The foci were highly increased when human cells expressing Ash-Mu95 and hAG-96tT were treated with 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG) and 8-oxo-dGTP. The foci formation by 8-oxo-dG(TP) was strikingly enhanced by the MTH1 knockdown. Moreover, known MTH1 inhibitors and oxidizing reagents also increased foci. This is the first system that visualizes damaged nucleotides in living cells, provides an excellent detection method for the oxidized nucleotides and oxidative stress, and enables high throughput screening for MTH1 inhibitors.
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Affiliation(s)
- Yoshihiro Fujikawa
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Hidehiko Kawai
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Tetsuya Suzuki
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Hiroyuki Kamiya
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
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2
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Li J, Wang ZH, Dang YM, Li DN, Liu Z, Dai DP, Cai JP. MTH1 suppression enhances the stemness of MCF7 through upregulation of STAT3. Free Radic Biol Med 2022; 188:447-458. [PMID: 35809767 DOI: 10.1016/j.freeradbiomed.2022.06.240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/22/2022]
Abstract
MTH1 protein can sanitize the damaged (d)NTP pool and MTH1 inhibitors have been developed to impede the growth of rapidly proliferating tumor cells; however, the effect of MTH1 inhibition on breast cancer stemness has not been reported yet. Here, we constructed breast cancer cell lines with the stable depletion of MTH1. MTH1 suppression clearly increased the ratio of CD44+CD24-/low subpopulations and promoted the formation of tumorspheres in MCF7 and T47D cells. RNA expression profiling, RT-qPCR and Western blotting showed the upregulation of master stem cell transcription factors Sox2, Oct4 and Nanog in MTH1 knockdown cells. GSEA suggested and Western blotting verified that MTH1 knockdown increased the expression of phosphorylated STAT3 (Tyr705). Furthermore, we indirectly demonstrated that the increased concentration of 8-oxo-dGTP and 8-oxo-GTP in MTH1-knockdown cells and exogenous 8-oxoGTP, rather than 8-oxo-dGTP, could significantly increase the phosphorylation of STAT3. In conclusion, this work indicates that MTH1 inhibition increased the proportion of breast cancer stem cells (BCSCs) and promoted stemness properties in MCF7 cells.
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Affiliation(s)
- Jin Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China
| | - Zi-Hui Wang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, PR China
| | - Ya-Min Dang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, PR China
| | - Dan-Ni Li
- The Clinical Laboratory of Beijing Hospital, Ministry of Health, Beijing, PR China
| | - Zhen Liu
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, PR China
| | - Da-Peng Dai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China
| | - Jian-Ping Cai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
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3
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Nakamura K, Groth A, Alabert C. Investigating Mitotic Inheritance of Histone Posttranslational Modifications by Triple pSILAC Coupled to Nascent Chromatin Capture. Methods Mol Biol 2022; 2529:407-417. [PMID: 35733024 DOI: 10.1007/978-1-0716-2481-4_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Pulse stable isotope labeling with amino acids in cell culture (pSILAC) coupled to mass spectrometric analysis is a powerful tool to study propagation of histone post-translational modifications (PTMs). We describe the combination of triple pSILAC with pulse-chase labeling of newly replicated DNA by nascent chromatin capture (NCC). This technology tracks newly synthesized and recycled old histones, from deposition to transmission to daughter cells, unveiling principles of histone-based inheritance.
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Affiliation(s)
- Kyosuke Nakamura
- Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Constance Alabert
- Genome Regulation and Expression, School of Life Sciences, MSI/WTB Complex, University of Dundee, Dundee, UK.
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4
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Levchenko SM, Pliss A, Peng X, Prasad PN, Qu J. Fluorescence lifetime imaging for studying DNA compaction and gene activities. LIGHT, SCIENCE & APPLICATIONS 2021; 10:224. [PMID: 34728612 PMCID: PMC8563720 DOI: 10.1038/s41377-021-00664-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 10/04/2021] [Accepted: 10/18/2021] [Indexed: 05/04/2023]
Abstract
Optical imaging is a most useful and widespread technique for the investigation of the structure and function of the cellular genomes. However, an analysis of immensely convoluted and irregularly compacted DNA polymer is highly challenging even by modern super-resolution microscopy approaches. Here we propose fluorescence lifetime imaging (FLIM) for the advancement of studies of genomic structure including DNA compaction, replication as well as monitoring of gene expression. The proposed FLIM assay employs two independent mechanisms for DNA compaction sensing. One mechanism relies on the inverse quadratic relation between the fluorescence lifetimes of fluorescence probes incorporated into DNA and their local refractive index, variable due to DNA compaction density. Another mechanism is based on the Förster resonance energy transfer (FRET) process between the donor and the acceptor fluorophores, both incorporated into DNA. Both these proposed mechanisms were validated in cultured cells. The obtained data unravel a significant difference in compaction of the gene-rich and gene-poor pools of genomic DNA. We show that the gene-rich DNA is loosely compacted compared to the dense DNA domains devoid of active genes.
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Affiliation(s)
- Svitlana M Levchenko
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Artem Pliss
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, 14260-3000, USA
| | - Xiao Peng
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Paras N Prasad
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, 14260-3000, USA.
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China.
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5
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Takebayashi SI, Ryba T, Wimbish K, Hayakawa T, Sakaue M, Kuriya K, Takahashi S, Ogata S, Hiratani I, Okumura K, Okano M, Ogata M. The Temporal Order of DNA Replication Shaped by Mammalian DNA Methyltransferases. Cells 2021; 10:cells10020266. [PMID: 33572832 PMCID: PMC7911666 DOI: 10.3390/cells10020266] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/15/2021] [Accepted: 01/26/2021] [Indexed: 11/16/2022] Open
Abstract
Multiple epigenetic pathways underlie the temporal order of DNA replication (replication timing) in the contexts of development and disease. DNA methylation by DNA methyltransferases (Dnmts) and downstream chromatin reorganization and transcriptional changes are thought to impact DNA replication, yet this remains to be comprehensively tested. Using cell-based and genome-wide approaches to measure replication timing, we identified a number of genomic regions undergoing subtle but reproducible replication timing changes in various Dnmt-mutant mouse embryonic stem (ES) cell lines that included a cell line with a drug-inducible Dnmt3a2 expression system. Replication timing within pericentromeric heterochromatin (PH) was shown to be correlated with redistribution of H3K27me3 induced by DNA hypomethylation: Later replicating PH coincided with H3K27me3-enriched regions. In contrast, this relationship with H3K27me3 was not evident within chromosomal arm regions undergoing either early-to-late (EtoL) or late-to-early (LtoE) switching of replication timing upon loss of the Dnmts. Interestingly, Dnmt-sensitive transcriptional up- and downregulation frequently coincided with earlier and later shifts in replication timing of the chromosomal arm regions, respectively. Our study revealed the previously unrecognized complex and diverse effects of the Dnmts loss on the mammalian DNA replication landscape.
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Affiliation(s)
- Shin-ichiro Takebayashi
- Laboratory of Molecular and Cellular Biology, Graduate School of Bioresources, Mie University, Tsu, Mie 514-8507, Japan; (T.H.); (K.K.); (S.O.); (K.O.)
- Correspondence:
| | - Tyrone Ryba
- Division of Natural Sciences, New College of Florida, Sarasota, FL 34243, USA; (T.R.); (K.W.)
| | - Kelsey Wimbish
- Division of Natural Sciences, New College of Florida, Sarasota, FL 34243, USA; (T.R.); (K.W.)
| | - Takuya Hayakawa
- Laboratory of Molecular and Cellular Biology, Graduate School of Bioresources, Mie University, Tsu, Mie 514-8507, Japan; (T.H.); (K.K.); (S.O.); (K.O.)
| | - Morito Sakaue
- Department of Orthopaedic Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan;
| | - Kenji Kuriya
- Laboratory of Molecular and Cellular Biology, Graduate School of Bioresources, Mie University, Tsu, Mie 514-8507, Japan; (T.H.); (K.K.); (S.O.); (K.O.)
| | - Saori Takahashi
- Laboratory for Developmental Epigenetics, RIKEN BDR, Kobe, Hyogo 650-0047, Japan; (S.T.); (I.H.)
| | - Shin Ogata
- Laboratory of Molecular and Cellular Biology, Graduate School of Bioresources, Mie University, Tsu, Mie 514-8507, Japan; (T.H.); (K.K.); (S.O.); (K.O.)
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN BDR, Kobe, Hyogo 650-0047, Japan; (S.T.); (I.H.)
| | - Katsuzumi Okumura
- Laboratory of Molecular and Cellular Biology, Graduate School of Bioresources, Mie University, Tsu, Mie 514-8507, Japan; (T.H.); (K.K.); (S.O.); (K.O.)
| | - Masaki Okano
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan;
| | - Masato Ogata
- Department of Biochemistry and Proteomics, Graduate School of Medicine, Mie University, Tsu, Mie 514-8507, Japan;
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6
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Miura H, Takahashi S, Shibata T, Nagao K, Obuse C, Okumura K, Ogata M, Hiratani I, Takebayashi SI. Mapping replication timing domains genome wide in single mammalian cells with single-cell DNA replication sequencing. Nat Protoc 2020; 15:4058-4100. [PMID: 33230331 DOI: 10.1038/s41596-020-0378-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 07/02/2020] [Indexed: 01/03/2023]
Abstract
Replication timing (RT) domains are stable units of chromosome structure that are regulated in the context of development and disease. Conventional genome-wide RT mapping methods require many S-phase cells for either the effective enrichment of replicating DNA through bromodeoxyuridine (BrdU) immunoprecipitation or the determination of copy-number differences during S-phase, which precludes their application to non-abundant cell types and single cells. Here, we provide a simple, cost-effective, and robust protocol for single-cell DNA replication sequencing (scRepli-seq). The scRepli-seq methodology relies on whole-genome amplification (WGA) of genomic DNA (gDNA) from single S-phase cells and next-generation sequencing (NGS)-based determination of copy-number differences that arise between replicated and unreplicated DNA. Haplotype-resolved scRepli-seq, which distinguishes pairs of homologous chromosomes within a single cell, is feasible by using single-nucleotide polymorphism (SNP)/indel information. We also provide computational pipelines for quality control, normalization, and binarization of the scRepli-seq data. The experimental portion of this protocol (before sequencing) takes 3 d.
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Affiliation(s)
- Hisashi Miura
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Saori Takahashi
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Takahiro Shibata
- Department of Biochemistry and Proteomics, Graduate School of Medicine, Mie University, Tsu, Japan.,Laboratory of Molecular & Cellular Biology, Graduate School of Bioresources, Mie University, Tsu, Japan
| | - Koji Nagao
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Chikashi Obuse
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Katsuzumi Okumura
- Laboratory of Molecular & Cellular Biology, Graduate School of Bioresources, Mie University, Tsu, Japan
| | - Masato Ogata
- Department of Biochemistry and Proteomics, Graduate School of Medicine, Mie University, Tsu, Japan
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.
| | - Shin-Ichiro Takebayashi
- Department of Biochemistry and Proteomics, Graduate School of Medicine, Mie University, Tsu, Japan. .,Laboratory of Molecular & Cellular Biology, Graduate School of Bioresources, Mie University, Tsu, Japan.
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7
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Kužmová E, Zawada Z, Navrátil M, Günterová J, Kraus T. Flow cytometric determination of cell cycle progression via direct labeling of replicated DNA. Anal Biochem 2020; 614:114002. [PMID: 33159846 DOI: 10.1016/j.ab.2020.114002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/19/2020] [Accepted: 10/25/2020] [Indexed: 01/14/2023]
Abstract
The reported method allows for a simple and rapid monitoring of DNA replication and cell cycle progression in eukaryotic cells in vitro. The DNA of replicating cells is labeled by incorporation of a metabolically-active fluorescent (Cy3) deoxyuridine triphosphate derivative, which is delivered into the cells by a synthetic transporter (SNTT1). The cells are then fixed, stained with DAPI and analyzed by flow cytometry. Thus, this protocol obviates post-labeling steps, which are indispensable in currently used incorporation assays (BrdU, EdU). The applicability of the protocol is demonstrated in analyses of cell cycles of adherent (U-2 OS, HeLa S3, RAW 264.7, J774 A.1, Chem-1, U-87 MG) and suspension (CCRF-CEM, MOLT-4, THP-1, HL-60, JURKAT) cell cultures, including those affected by a DNA polymerase inhibitor (aphidicolin). Owing to a short incorporation time (5-60 min) and reduced number of steps, the protocol can be completed within 1-2 h with a minimal cell loss and with excellent reproducibility.
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Affiliation(s)
- Erika Kužmová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nam. 2, CZ-16610, Prague 6, Czech Republic
| | - Zbigniew Zawada
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nam. 2, CZ-16610, Prague 6, Czech Republic; University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Michal Navrátil
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nam. 2, CZ-16610, Prague 6, Czech Republic
| | - Jana Günterová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nam. 2, CZ-16610, Prague 6, Czech Republic
| | - Tomáš Kraus
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nam. 2, CZ-16610, Prague 6, Czech Republic.
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8
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Krell K, Harijan D, Ganz D, Doll L, Wagenknecht HA. Postsynthetic Modifications of DNA and RNA by Means of Copper-Free Cycloadditions as Bioorthogonal Reactions. Bioconjug Chem 2020; 31:990-1011. [DOI: 10.1021/acs.bioconjchem.0c00072] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Katja Krell
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Dennis Harijan
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Dorothée Ganz
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Larissa Doll
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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9
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Chen G, Luo Y, Warncke K, Sun Y, Yu DS, Fu H, Behera M, Ramalingam SS, Doetsch PW, Duong DM, Lammers M, Curran WJ, Deng X. Acetylation regulates ribonucleotide reductase activity and cancer cell growth. Nat Commun 2019; 10:3213. [PMID: 31324785 PMCID: PMC6642173 DOI: 10.1038/s41467-019-11214-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 06/25/2019] [Indexed: 12/26/2022] Open
Abstract
Ribonucleotide reductase (RNR) catalyzes the de novo synthesis of deoxyribonucleoside diphosphates (dNDPs) to provide dNTP precursors for DNA synthesis. Here, we report that acetylation and deacetylation of the RRM2 subunit of RNR acts as a molecular switch that impacts RNR activity, dNTP synthesis, and DNA replication fork progression. Acetylation of RRM2 at K95 abrogates RNR activity by disrupting its homodimer assembly. RRM2 is directly acetylated by KAT7, and deacetylated by Sirt2, respectively. Sirt2, which level peak in S phase, sustains RNR activity at or above a threshold level required for dNTPs synthesis. We also find that radiation or camptothecin-induced DNA damage promotes RRM2 deacetylation by enhancing Sirt2-RRM2 interaction. Acetylation of RRM2 at K95 results in the reduction of the dNTP pool, DNA replication fork stalling, and the suppression of tumor cell growth in vitro and in vivo. This study therefore identifies acetylation as a regulatory mechanism governing RNR activity.
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Affiliation(s)
- Guo Chen
- Departments of Radiation Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, 1365C Clifton Road NE, Atlanta, GA, 30322, USA
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, 510632, Guangzhou, Guangdong, China
| | - Yin Luo
- Department of Pharmacology, Emory University School of Medicine and Winship Cancer Institute of Emory University, 1510 Clifton Rd. NE, Atlanta, GA, 30322, USA
| | - Kurt Warncke
- Department of Physics, Emory University, 400 Dowman Drive, Atlanta, GA, 30322, USA
| | - Youwei Sun
- Departments of Radiation Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, 1365C Clifton Road NE, Atlanta, GA, 30322, USA
| | - David S Yu
- Departments of Radiation Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, 1365C Clifton Road NE, Atlanta, GA, 30322, USA
| | - Haian Fu
- Department of Pharmacology, Emory University School of Medicine and Winship Cancer Institute of Emory University, 1510 Clifton Rd. NE, Atlanta, GA, 30322, USA
| | - Madhusmita Behera
- Department of Hematology and Medical Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, 1365C Clifton Road NE, Atlanta, GA, 30322, USA
| | - Suresh S Ramalingam
- Department of Hematology and Medical Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, 1365C Clifton Road NE, Atlanta, GA, 30322, USA
| | - Paul W Doetsch
- Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Rd. NE, Atlanta, GA, 30322, USA
| | - Michael Lammers
- Institute of Biochemistry, Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, Greifswald, 17487, Germany
| | - Walter J Curran
- Departments of Radiation Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, 1365C Clifton Road NE, Atlanta, GA, 30322, USA
| | - Xingming Deng
- Departments of Radiation Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, 1365C Clifton Road NE, Atlanta, GA, 30322, USA.
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10
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Gao X, Shu X, Song Y, Cao J, Gao M, Wang F, Wang Y, Sun JZ, Liu J, Tang BZ. Visualization and quantification of cellular RNA production and degradation using a combined fluorescence and mass spectrometry characterization assay. Chem Commun (Camb) 2019; 55:8321-8324. [DOI: 10.1039/c9cc03923f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combined fluorescence and mass spectrometry assay is developed to visualize and quantify cellular RNA production and degradation.
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11
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Ligasová A, Koberna K. DNA Replication: From Radioisotopes to Click Chemistry. Molecules 2018; 23:molecules23113007. [PMID: 30453631 PMCID: PMC6278288 DOI: 10.3390/molecules23113007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 12/14/2022] Open
Abstract
The replication of nuclear and mitochondrial DNA are basic processes assuring the doubling of the genetic information of eukaryotic cells. In research of the basic principles of DNA replication, and also in the studies focused on the cell cycle, an important role is played by artificially-prepared nucleoside and nucleotide analogues that serve as markers of newly synthesized DNA. These analogues are incorporated into the DNA during DNA replication, and are subsequently visualized. Several methods are used for their detection, including the highly popular click chemistry. This review aims to provide the readers with basic information about the various possibilities of the detection of replication activity using nucleoside and nucleotide analogues, and to show the strengths and weaknesses of those different detection systems, including click chemistry for microscopic studies.
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Affiliation(s)
- Anna Ligasová
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacký University in Olomouc, Hněvotínská 5, 779 00 Olomouc, Czech Republic.
| | - Karel Koberna
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacký University in Olomouc, Hněvotínská 5, 779 00 Olomouc, Czech Republic.
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12
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Stewart MP, Langer R, Jensen KF. Intracellular Delivery by Membrane Disruption: Mechanisms, Strategies, and Concepts. Chem Rev 2018; 118:7409-7531. [PMID: 30052023 PMCID: PMC6763210 DOI: 10.1021/acs.chemrev.7b00678] [Citation(s) in RCA: 382] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Intracellular delivery is a key step in biological research and has enabled decades of biomedical discoveries. It is also becoming increasingly important in industrial and medical applications ranging from biomanufacture to cell-based therapies. Here, we review techniques for membrane disruption-based intracellular delivery from 1911 until the present. These methods achieve rapid, direct, and universal delivery of almost any cargo molecule or material that can be dispersed in solution. We start by covering the motivations for intracellular delivery and the challenges associated with the different cargo types-small molecules, proteins/peptides, nucleic acids, synthetic nanomaterials, and large cargo. The review then presents a broad comparison of delivery strategies followed by an analysis of membrane disruption mechanisms and the biology of the cell response. We cover mechanical, electrical, thermal, optical, and chemical strategies of membrane disruption with a particular emphasis on their applications and challenges to implementation. Throughout, we highlight specific mechanisms of membrane disruption and suggest areas in need of further experimentation. We hope the concepts discussed in our review inspire scientists and engineers with further ideas to improve intracellular delivery.
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Affiliation(s)
- Martin P. Stewart
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
- The Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, USA
| | - Robert Langer
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
- The Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, USA
| | - Klavs F. Jensen
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
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13
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Zawada Z, Tatar A, Mocilac P, Buděšínský M, Kraus T. Transport of Nucleoside Triphosphates into Cells by Artificial Molecular Transporters. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801306] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Zbigniew Zawada
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Praha 6 Czech Republic
| | - Ameneh Tatar
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Praha 6 Czech Republic
| | - Pavle Mocilac
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Praha 6 Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Praha 6 Czech Republic
| | - Tomáš Kraus
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Praha 6 Czech Republic
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14
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Zawada Z, Tatar A, Mocilac P, Buděšínský M, Kraus T. Transport of Nucleoside Triphosphates into Cells by Artificial Molecular Transporters. Angew Chem Int Ed Engl 2018; 57:9891-9895. [PMID: 29578619 DOI: 10.1002/anie.201801306] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/14/2018] [Indexed: 01/18/2023]
Abstract
Chemically modified nucleoside triphosphates (NTPs) are widely exploited as unnatural metabolites in chemical biology and medicinal chemistry. Because anionic NTPs do not permeate cell membranes, their corresponding neutral precursors are employed in cell-based assays. These precursors become active metabolites after enzymatic conversion, which often proceeds insufficiently. Here we show that metabolically-active NTPs can be directly transported into eukaryotic cells and bacteria by the action of designed synthetic nucleoside triphosphate transporters (SNTTs). The transporter is composed of a receptor, which forms a non-covalent complex with a triphosphate anion, and a cell-penetrating agent, which translocates the complex across the plasma membrane. NTP is then released from the complex in the intracellular milieu and accumulates in nuclei and nucleoli in high concentration. The transport of NTPs proceeds rapidly (seconds to minutes) and selectively even in the presence of other organic anions. We demonstrate that this operationally simple and efficient means of transport of fluorescently labelled NTPs into cells can be used for metabolic labeling of DNA in live cells.
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Affiliation(s)
- Zbigniew Zawada
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic
| | - Ameneh Tatar
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic
| | - Pavle Mocilac
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic
| | - Tomáš Kraus
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic
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15
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Transcriptional mutagenesis mediated by 8-oxoG induces translational errors in mammalian cells. Proc Natl Acad Sci U S A 2018; 115:4218-4222. [PMID: 29610342 DOI: 10.1073/pnas.1718363115] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Reactive oxygen species formed within the mammalian cell can produce 8-oxo-7,8-dihydroguanine (8-oxoG) in mRNA, which can cause base mispairing during gene expression. Here we found that administration of 8-oxoGTP in MTH1-knockdown cells results in increased 8-oxoG content in mRNA. Under this condition, an amber mutation of the reporter luciferase is suppressed. Using second-generation sequencing techniques, we found that U-to-G changes at preassigned sites of the luciferase transcript increased when 8-oxoGTP was supplied. In addition, an increased level of 8-oxoG content in RNA induced the accumulation of aggregable amyloid β peptides in cells expressing amyloid precursor protein. Our findings indicate that 8-oxoG accumulation in mRNA can alter protein synthesis in mammalian cells. Further work is required to assess the significance of these findings under normal physiological conditions.
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16
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Ligasová A, Konečný P, Frydrych I, Koberna K. Cell cycle profiling by image and flow cytometry: The optimised protocol for the detection of replicational activity using 5-Bromo-2'-deoxyuridine, low concentration of hydrochloric acid and exonuclease III. PLoS One 2017; 12:e0175880. [PMID: 28426799 PMCID: PMC5398562 DOI: 10.1371/journal.pone.0175880] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/31/2017] [Indexed: 11/19/2022] Open
Abstract
The approach for the detection of replicational activity in cells using 5-bromo-2'-deoxyuridine, a low concentration of hydrochloric acid and exonuclease III is presented in the study. The described method was optimised with the aim to provide a fast and robust tool for the detection of DNA synthesis with minimal impact on the cellular structures using image and flow cytometry. The approach is based on the introduction of breaks into the DNA by the low concentration of hydrochloric acid followed by the subsequent enzymatic extension of these breaks using exonuclease III. Our data showed that the method has only a minimal effect on the tested protein localisations and is applicable both for formaldehyde- and ethanol-fixed cells. The approach partially also preserves the fluorescence of the fluorescent proteins in the HeLa cells expressing Fluorescent Ubiquitin Cell Cycle Indicator. In the case of the short labelling pulses that disabled the use of 5-ethynyl-2'-deoxyuridine because of the low specific signal, the described method provided a bright signal enabling reliable recognition of replicating cells. The optimized protocol was also successfully tested for the detection of trifluridine, the nucleoside used as an antiviral drug and in combination with tipiracil also for the treatment of some types of cancer.
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Affiliation(s)
- Anna Ligasová
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University in Olomouc, Olomouc, Czech Republic
- * E-mail: (AL); (KK)
| | - Petr Konečný
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University in Olomouc, Olomouc, Czech Republic
| | - Ivo Frydrych
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University in Olomouc, Olomouc, Czech Republic
| | - Karel Koberna
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University in Olomouc, Olomouc, Czech Republic
- * E-mail: (AL); (KK)
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17
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Ligasová A, Liboska R, Friedecký D, Mičová K, Adam T, Oždian T, Rosenberg I, Koberna K. Dr Jekyll and Mr Hyde: a strange case of 5-ethynyl-2'-deoxyuridine and 5-ethynyl-2'-deoxycytidine. Open Biol 2016; 6:150172. [PMID: 26740587 PMCID: PMC4736823 DOI: 10.1098/rsob.150172] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
5-Ethynyl-2′-deoxyuridine (EdU) and 5-ethynyl-2′-deoxycytidine (EdC) are mainly used as markers of cellular replicational activity. Although EdU is employed as a replicational marker more frequently than EdC, its cytotoxicity is commonly much higher than the toxicity of EdC. To reveal the reason of the lower cytotoxicity of EdC, we performed a DNA analysis of five EdC-treated human cell lines. Surprisingly, not a single one of the tested cell lines contained a detectable amount of EdC in their DNA. Instead, the DNA of all the cell lines contained EdU. The content of incorporated EdU differed in particular cells and EdC-related cytotoxicity was directly proportional to the content of EdU. The results of experiments with the targeted inhibition of the cytidine deaminase (CDD) and dCMP deaminase activities indicated that the dominant role in the conversion pathway of EdC to EdUTP is played by CDD in HeLa cells. Our results also showed that the deamination itself was not able to effectively prevent the conversion of EdC to EdCTP, the conversion of EdC to EdCTP occurs with much lesser effectivity than the conversion of EdU to EdUTP and the EdCTP is not effectively recognized by the replication complex as a substrate for the synthesis of nuclear DNA.
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Affiliation(s)
- Anna Ligasová
- Institute of Molecular and Translational Medicine, Palacký University in Olomouc, Olomouc 77900, Czech Republic
| | - Radek Liboska
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, v.v.i., Prague 16610, Czech Republic
| | - David Friedecký
- Institute of Molecular and Translational Medicine, Palacký University in Olomouc, Olomouc 77900, Czech Republic
| | - Kateřina Mičová
- Institute of Molecular and Translational Medicine, Palacký University in Olomouc, Olomouc 77900, Czech Republic
| | - Tomáš Adam
- Institute of Molecular and Translational Medicine, Palacký University in Olomouc, Olomouc 77900, Czech Republic
| | - Tomáš Oždian
- Institute of Molecular and Translational Medicine, Palacký University in Olomouc, Olomouc 77900, Czech Republic
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, v.v.i., Prague 16610, Czech Republic
| | - Karel Koberna
- Institute of Molecular and Translational Medicine, Palacký University in Olomouc, Olomouc 77900, Czech Republic
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18
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Kim N, Duncan GA, Hanes J, Suk JS. Barriers to inhaled gene therapy of obstructive lung diseases: A review. J Control Release 2016; 240:465-488. [PMID: 27196742 DOI: 10.1016/j.jconrel.2016.05.031] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 12/29/2022]
Abstract
Knowledge of genetic origins of obstructive lung diseases has made inhaled gene therapy an attractive alternative to the current standards of care that are limited to managing disease symptoms. Initial lung gene therapy clinical trials occurred in the early 1990s following the discovery of the genetic defect responsible for cystic fibrosis (CF), a monogenic disorder. However, despite over two decades of intensive effort, gene therapy has yet to help patients with CF or any other obstructive lung disease. The slow progress is due in part to poor understanding of the biological barriers to inhaled gene therapy. Encouragingly, clinical trials have shown that inhaled gene therapy with various viral vectors and non-viral gene vectors is well tolerated by patients, and continued research has provided valuable lessons and resources that may lead to future success of this therapeutic strategy. In this review, we first introduce representative obstructive lung diseases and examine limitations of currently available therapeutic options. We then review key components for successful execution of inhaled gene therapy, including gene delivery systems, primary physiological barriers and strategies to overcome them, and advances in preclinical disease models with which the most promising systems may be identified for human clinical trials.
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Affiliation(s)
- Namho Kim
- The Center for Nanomedicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Gregg A Duncan
- The Center for Nanomedicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Justin Hanes
- The Center for Nanomedicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Environmental and Health Sciences, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neurosurgery, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jung Soo Suk
- The Center for Nanomedicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.
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19
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Kuriya K, Higashiyama E, Avşar-Ban E, Tamaru Y, Ogata S, Takebayashi SI, Ogata M, Okumura K. Direct Visualization of DNA Replication Dynamics in Zebrafish Cells. Zebrafish 2015; 12:432-9. [PMID: 26540100 DOI: 10.1089/zeb.2015.1151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Spatiotemporal regulation of DNA replication in the S-phase nucleus has been extensively studied in mammalian cells because it is tightly coupled with the regulation of other nuclear processes such as transcription. However, little is known about the replication dynamics in nonmammalian cells. Here, we analyzed the DNA replication processes of zebrafish (Danio rerio) cells through the direct visualization of replicating DNA in the nucleus and on DNA fiber molecules isolated from the nucleus. We found that zebrafish chromosomal DNA at the nuclear interior was replicated first, followed by replication of DNA at the nuclear periphery, which is reminiscent of the spatiotemporal regulation of mammalian DNA replication. However, the relative duration of interior DNA replication in zebrafish cells was longer compared to mammalian cells, possibly reflecting zebrafish-specific genomic organization. The rate of replication fork progression and ori-to-ori distance measured by the DNA combing technique were ∼ 1.4 kb/min and 100 kb, respectively, which are comparable to those in mammalian cells. To our knowledge, this is a first report that measures replication dynamics in zebrafish cells.
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Affiliation(s)
- Kenji Kuriya
- 1 Laboratory of Molecular and Cellular Biology, Department of Life Sciences, Graduate School of Bioresources, Mie University , Tsu, Japan
| | - Eriko Higashiyama
- 1 Laboratory of Molecular and Cellular Biology, Department of Life Sciences, Graduate School of Bioresources, Mie University , Tsu, Japan
| | - Eriko Avşar-Ban
- 2 Laboratory for the Utilization of Aquatic Bioresources, Department of Life Sciences, Graduate School of Bioresources, Mie University , Tsu, Japan
| | - Yutaka Tamaru
- 2 Laboratory for the Utilization of Aquatic Bioresources, Department of Life Sciences, Graduate School of Bioresources, Mie University , Tsu, Japan
| | - Shin Ogata
- 1 Laboratory of Molecular and Cellular Biology, Department of Life Sciences, Graduate School of Bioresources, Mie University , Tsu, Japan
| | - Shin-ichiro Takebayashi
- 3 Department of Biochemistry and Proteomics, Graduate School of Medicine, Mie University , Tsu, Japan
| | - Masato Ogata
- 3 Department of Biochemistry and Proteomics, Graduate School of Medicine, Mie University , Tsu, Japan
| | - Katsuzumi Okumura
- 1 Laboratory of Molecular and Cellular Biology, Department of Life Sciences, Graduate School of Bioresources, Mie University , Tsu, Japan
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20
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Roberts TC, Hart JR, Kaikkonen MU, Weinberg MS, Vogt PK, Morris KV. Quantification of nascent transcription by bromouridine immunocapture nuclear run-on RT-qPCR. Nat Protoc 2015; 10:1198-211. [PMID: 26182239 PMCID: PMC4790731 DOI: 10.1038/nprot.2015.076] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nuclear run-on (NRO) is a method that measures transcriptional activity via the quantification of biochemically labeled nascent RNA molecules derived from nuclear isolates. Widespread use of this technique has been limited because of its technical difficulty relative to steady-state total mRNA analyses. Here we describe a detailed protocol for the quantification of transcriptional activity in human cell cultures. Nuclei are first isolated and NRO transcription is performed in the presence of bromouridine. Labeled nascent transcripts are purified by immunoprecipitation, and transcript levels are determined by reverse-transcription quantitative PCR (RT-qPCR). Data are then analyzed using standard techniques described elsewhere. This method is rapid (the protocol can be completed in 2 d) and cost-effective, exhibits negligible detection of background noise from unlabeled transcripts, requires no radioactive materials and can be performed from as few as 500,000 nuclei. It also takes advantage of the high sensitivity, specificity and dynamic range of RT-qPCR.
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Affiliation(s)
- Thomas C. Roberts
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX, United Kingdom
- Sanford-Burnham Medical Research Institute, Development, Aging and Regeneration Program, 10901 N. Torrey pines Road, La Jolla, CA, 92037, USA
| | - Jonathan R. Hart
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Minna U. Kaikkonen
- University of Eastern Finland, A.I. Virtanen institute, Department of Biotechnology and Molecular Medicine, P.O.B. 1627, 70211 Kuopio, Finland
| | - Marc S. Weinberg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
- Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, WITS 2050, South Africa
| | - Peter K. Vogt
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Kevin V. Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
- School of Biotechnology and Biomedical Sciences, University of New South Wales, NSW 2052, Australia
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21
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Ligasová A, Liboska R, Rosenberg I, Koberna K. The Fingerprint of Anti-Bromodeoxyuridine Antibodies and Its Use for the Assessment of Their Affinity to 5-Bromo-2'-Deoxyuridine in Cellular DNA under Various Conditions. PLoS One 2015; 10:e0132393. [PMID: 26161977 PMCID: PMC4498590 DOI: 10.1371/journal.pone.0132393] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 06/13/2015] [Indexed: 01/31/2023] Open
Abstract
We have developed a simple system for the analysis of the affinity of anti-bromodeoxyuridine antibodies. The system is based on the anchored oligonucleotides containing 5-bromo-2'-deoxyuridine (BrdU) at three different positions. It allows a reliable estimation of the reactivity of particular clones of monoclonal anti-bromodeoxyuridine antibodies with BrdU in fixed and permeabilized cells. Using oligonucleotide probes and four different protocols for the detection of BrdU incorporated in cellular DNA, we identified two antibody clones that evinced sufficient reactivity to BrdU in all the tested protocols. One of these clones exhibited higher reactivity to 5-iodo-2'-deoxyuridine (IdU) than to BrdU. It allowed us to increase the sensitivity of the used protocols without a negative effect on the cell physiology as the cytotoxicity of IdU was comparable with BrdU and negligible when compared to 5-ethynyl-2'-deoxyuridine. The combination of IdU and the improved protocol for oxidative degradation of DNA provided a sensitive and reliable approach for the situations when the low degradation of DNA and high BrdU signal is a priority.
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Affiliation(s)
- Anna Ligasová
- Institute of Molecular and Translational Medicine, Faculty of Medicine, Palacký University, Olomouc, Czech Republic
- * E-mail:
| | - Radek Liboska
- Oligonucleotide group, Institute of Organic Chemistry and Biochemistry CAS, v.v.i., Prague, Czech Republic
| | - Ivan Rosenberg
- Oligonucleotide group, Institute of Organic Chemistry and Biochemistry CAS, v.v.i., Prague, Czech Republic
| | - Karel Koberna
- Institute of Molecular and Translational Medicine, Faculty of Medicine, Palacký University, Olomouc, Czech Republic
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22
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Sugaya K, Ishihara Y, Inoue S. Analysis of a temperature-sensitive mutation in Uba1: Effects of the click reaction on subsequent immunolabeling of proteins involved in DNA replication. FEBS Open Bio 2015; 5:167-74. [PMID: 25834782 PMCID: PMC4359972 DOI: 10.1016/j.fob.2015.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 02/26/2015] [Accepted: 02/26/2015] [Indexed: 11/28/2022] Open
Abstract
The click reaction inhibits the indirect immunolabeling of Cdt1. The click reaction allows for the detection of PCNA with nascent DNA. Cdt1 appears to remain close to replication sites in the ts-mutant of Uba1. Impaired ubiquitination caused by the defect of Uba1 affects DNA replication only slowly.
In our previous study, a Met-to-Ile substitution at amino acid 256 in the catalytic domain of Uba1 was determined in temperature-sensitive CHO-K1 mutant tsTM3 cells, which exhibited chromosomal instability and cell-cycle arrest in the S to G2 phases with decreased DNA synthesis at the nonpermissive temperature, 39 °C. Mutant cells were also characterized by a significant decrease of Uba1 in the nucleus with decreased ubiquitination activity at 39 °C. Defects of ubiquitination activity in the nucleus resulted in an inappropriate balance between Cdt1 and geminin, a licensing factor of DNA replication and its inhibitor. In the present study, we found that the Cu(I)-catalyzed [3 + 2] cycloaddition (click) reaction inhibits the subsequent indirect immunolabeling of Cdt1 but allows for the detection of PCNA with nascent DNA. Using a procedure without the click reaction, we also demonstrated that Cdt1 remained close to active replication sites in tsTM3 cells at the nonpermissive temperature. Analysis of genome replication by DNA fiber spreading revealed that DNA synthesis continues for at least 10 h after incubation at 39 °C, suggesting that impaired ubiquitination in the nucleus, caused by the defect of Uba1, affected DNA replication only after a long delay.
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Key Words
- BrdU, 5-bromo-2′-deoxyuridine
- Chromosome instability
- CldU, 5-chloro-2′-deoxyuridine
- Click chemistry
- DIG-dUTP, digoxigenin-dUTP
- E1, ubiquitin activating enzyme
- E2, ubiquitin conjugating enzyme
- E3, ubiquitin ligase
- EdU, 5-ethynyl-2′-deoxyuridine
- IdU, 5-iodo-2′-deoxyuridine
- MCM7, mini-chromosome maintenance protein 7
- PCNA, proliferating cell nuclear antigen
- PFA, paraformaldehyde
- Replication
- Temperature-sensitive mutation
- Ubiquitination
- ts, temperature-sensitive
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Affiliation(s)
- Kimihiko Sugaya
- Research Center for Radiation Protection and Fukushima Project Headquarters, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Yoshie Ishihara
- Research Center for Radiation Protection and Fukushima Project Headquarters, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Sonoe Inoue
- Research Center for Radiation Protection and Fukushima Project Headquarters, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
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23
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Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components. Nat Cell Biol 2014; 16:281-93. [PMID: 24561620 DOI: 10.1038/ncb2918] [Citation(s) in RCA: 263] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 01/15/2014] [Indexed: 02/07/2023]
Abstract
To maintain genome function and stability, DNA sequence and its organization into chromatin must be duplicated during cell division. Understanding how entire chromosomes are copied remains a major challenge. Here, we use nascent chromatin capture (NCC) to profile chromatin proteome dynamics during replication in human cells. NCC relies on biotin-dUTP labelling of replicating DNA, affinity purification and quantitative proteomics. Comparing nascent chromatin with mature post-replicative chromatin, we provide association dynamics for 3,995 proteins. The replication machinery and 485 chromatin factors such as CAF-1, DNMT1 and SUV39h1 are enriched in nascent chromatin, whereas 170 factors including histone H1, DNMT3, MBD1-3 and PRC1 show delayed association. This correlates with H4K5K12diAc removal and H3K9me1 accumulation, whereas H3K27me3 and H3K9me3 remain unchanged. Finally, we combine NCC enrichment with experimentally derived chromatin probabilities to predict a function in nascent chromatin for 93 uncharacterized proteins, and identify FAM111A as a replication factor required for PCNA loading. Together, this provides an extensive resource to understand genome and epigenome maintenance.
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24
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Luebben SW, Shima N, Kawabata T. Methods for the detection of genome instability derived from replication stress in primary mouse embryonic fibroblasts. Methods Mol Biol 2014; 1194:341-352. [PMID: 25064113 DOI: 10.1007/978-1-4939-1215-5_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Replication stress, with its subsequent genome instability, is a hallmark of cancer from its earliest stages of development. Here, we describe assays that are sufficiently sensitive to detect intrinsic replicative stress and its consequences in primary mouse embryonic fibroblasts. First, we explain the non-denatured DNA fiber assay, a powerful tool to directly measure DNA replication kinetics via the dual-labeling of active replication forks. Then, we describe the cytokinesis-block micronucleus assay, which can be combined with detection of 53BP1 nuclear bodies to measure the levels of replication-associated genome instability carried over into G1 phase of the cell cycle.
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Affiliation(s)
- Spencer W Luebben
- Department of Genetics, Cell Biology and Development, University of Minnesota, 6-160 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
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25
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5-Ethynylcytidine as a new agent for detecting RNA synthesis in live cells by “click” chemistry. Anal Biochem 2013; 434:128-35. [DOI: 10.1016/j.ab.2012.11.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 11/22/2012] [Accepted: 11/27/2012] [Indexed: 11/23/2022]
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26
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Atomic scissors: a new method of tracking the 5-bromo-2'-deoxyuridine-labeled DNA in situ. PLoS One 2012; 7:e52584. [PMID: 23300711 PMCID: PMC3530445 DOI: 10.1371/journal.pone.0052584] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 11/20/2012] [Indexed: 01/06/2023] Open
Abstract
A new method of the light microscopy detection of BrdU-labeled DNA in situ is described. It is based on the oxidative attack at the deoxyribose moiety by copper(I) in the presence of oxygen, which leads to the abstraction of hydrogen atom from deoxyribose culminating in the elimination of the nucleobase, scission of the nucleic-acid strand and formation of frequent gaps. The gaps allow the reaction of the antibodies with the commonly used markers of replication (e.g. 5-bromo-2′-deoxyuridine), which are otherwise masked. The method developed makes it possible to detect nuclear and mitochondrial DNA replication efficiently. In most cases, it does not inhibit effective protein detections and in addition enables simultaneous localization of newly-synthesized RNA. The alternative presently-used methods result in protein denaturation and/or extensive DNA cleavage followed by the DNA-bound proteins peeling off.
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27
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Pliss A, Zhao L, Ohulchanskyy TY, Qu J, Prasad PN. Fluorescence lifetime of fluorescent proteins as an intracellular environment probe sensing the cell cycle progression. ACS Chem Biol 2012; 7:1385-92. [PMID: 22594453 DOI: 10.1021/cb300065w] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The fluorescence lifetime of fluorescent proteins is affected by the concentration of solutes in a medium, in inverse correlation with local refractive index. In this paper, we introduce the concept of using this dependence to probe cellular molecular environment and its transformation during cellular processes. We employ the fluorescence lifetime of Green Fluorescent Protein and tdTomato Fluorescent Protein expressed in cultured cells and probe the changes in the local molecular environment during the cell cycle progression. We report that the longest fluorescence lifetimes occurred during mitosis. Following the cell division, the fluorescence lifetimes of these proteins were rapidly shortened. Furthermore the fluorescence lifetime of tdTomato in the nucleoplasm gradually increased throughout the span of S-phase and remained constantly long until the end of interphase. We interpret the observed fluorescence lifetime changes to be derived from changes in concentration of macromolecular solutes in the cell interior throughout cell cycle progression.
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Affiliation(s)
- Artem Pliss
- Institute for Lasers, Photonics
and Biophotonics, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Lingling Zhao
- Institute for Lasers, Photonics
and Biophotonics, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Tymish Y. Ohulchanskyy
- Institute for Lasers, Photonics
and Biophotonics, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Junle Qu
- Key Laboratory of Optoelectronic
Devices and Systems of Ministry of Education and Guangdong Province,
Institute of Optoelectronics, Shenzhen University, 3688 Nanhai Road, Shenzhen, Guangdong Province 518060, PR China
| | - Paras N. Prasad
- Institute for Lasers, Photonics
and Biophotonics, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
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Yamazaki S, Ishii A, Kanoh Y, Oda M, Nishito Y, Masai H. Rif1 regulates the replication timing domains on the human genome. EMBO J 2012; 31:3667-77. [PMID: 22850674 DOI: 10.1038/emboj.2012.180] [Citation(s) in RCA: 182] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 06/13/2012] [Indexed: 11/09/2022] Open
Abstract
DNA replication is spatially and temporally regulated during S-phase. DNA replication timing is established in early-G1-phase at a point referred to as timing decision point. However, how the genome-wide replication timing domains are established is unknown. Here, we show that Rif1 (Rap1-interacting-factor-1), originally identified as a telomere-binding factor in yeast, is a critical determinant of the replication timing programme in human cells. Depletion of Rif1 results in specific loss of mid-S replication foci profiles, stimulation of initiation events in early-S-phase and changes in long-range replication timing domain structures. Analyses of replication timing show replication of sequences normally replicating early is delayed, whereas that normally replicating late is advanced, suggesting that replication timing regulation is abrogated in the absence of Rif1. Rif1 tightly binds to nuclear-insoluble structures at late-M-to-early-G1 and regulates chromatin-loop sizes. Furthermore, Rif1 colocalizes specifically with the mid-S replication foci. Thus, Rif1 establishes the mid-S replication domains that are restrained from being activated at early-S-phase. Our results indicate that Rif1 plays crucial roles in determining the replication timing domain structures in human cells through regulating higher-order chromatin architecture.
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Affiliation(s)
- Satoshi Yamazaki
- Genome Dynamics Project, Department of Genome Medicine, Tokyo, Japan
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29
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Stephens AS, Day CJ, Tiralongo J. Optimized Conditions for the Delivery of Small Membrane Impermeable Compounds into Human Cells Using Hypotonic Shift. Cell 2012. [DOI: 10.4236/cellbio.2012.12005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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30
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Lowered nudix type 5 (NUDT5) expression leads to cell cycle retardation in HeLa cells. Mol Cell Biochem 2011; 363:377-84. [PMID: 22200976 DOI: 10.1007/s11010-011-1190-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 12/13/2011] [Indexed: 10/14/2022]
Abstract
The molecule 8-oxo-7,8-dihydroguanine (8-oxoGua), an oxidized form of guanine, can pair with adenine or cytosine during nucleic acid synthesis. Moreover, RNA containing 8-oxoGua causes translational errors, thus leading to the production of abnormal proteins. Human NUDT5, a MutT-related protein, catalyzes the hydrolysis of 8-oxoGDP to 8-oxoGMP, thereby preventing misincorporation of 8-oxoGua into RNA. To investigate the biological roles of NUDT5 in mammalian cells, we established cell lines with decreased level of NUDT5 expression. In NUDT5 inhibited cells, the RNA oxidation was not significantly higher than that of normal cells. However, the cell cycle G1 phase was significantly delayed, and cell numbers in both S and G2/M phases were reduced, indicating that cell proliferation was hampered by NUDT5 suppression. Key proteins for preventing the G1-S transition, including p53, p16, and Rb were increased, while the Rb phosphorylation was decreased. These results suggested that the NUDT5 protein may play significant roles in regulating the G1-S transition in mammalian cells.
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31
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Growth inhibition and chromosomal instability of cultured marsupial (opossum) cells after treatment with DNA polymerase α inhibitor. Biosci Biotechnol Biochem 2011; 75:1349-53. [PMID: 21737927 DOI: 10.1271/bbb.110112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The DNA replication mechanism has been well established for eutherian mammals (placental mammals such as humans, mice, and cattle), but not, to date, for metatherian mammals (marsupials such as kangaroos, koalas, and opossums). In this study, we found that dehydroaltenusin, a selective inhibitor of mammalian (eutherian) DNA polymerase α, clearly suppressed the growth of metatherian (opossum and rat kangaroo) cultured cells. In cultured opossum (OK) cells, dehydroaltenusin also suppressed the progression of DNA replication. These results suggest that dehydroaltenusin inhibits metatherian as well as eutherian DNA replication. Dehydroaltenusin treatment of OK cells engendered fluctuations in the numbers of chromosomes in the OK cells as well as inhibition of cell growth and DNA replication. This suggests that partial inhibition of DNA replication by dehydroaltenusin causes chromosomal instability in cultured cells.
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32
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Ligasová A, Koberna K. In situ reverse transcription: the magic of strength and anonymity. Nucleic Acids Res 2010; 38:e167. [PMID: 20627869 PMCID: PMC2938209 DOI: 10.1093/nar/gkq619] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In this study, we describe an approach that enables a highly specific, effective and fast detection of polyadenylated RNA sequences in situ at the light and electron microscopy levels. The method developed is based on the incorporation of 5-bromo-2′-deoxyuridine into the growing cDNA strand by means of the reverse transcriptase. We have shown that unlike the previously used deoxyuridine tagged with biotin or digoxigenin, 5-bromo-2′-deoxyuridine is ‘invisible’ in the DNA–DNA duplex but easily detectable in the DNA–RNA duplex. This feature is an important pre-requisite for the correct interpretation of the data obtained, as our results strongly indicate that reverse transcriptase uses DNA breaks as primers efficiently. We have also shown that the replacement of deoxythymidine by 5-bromo-2′-deoxyuridine considerably stabilizes the growing DNA–RNA duplex, thus enabling the one-step detection of polyadenylated RNA in structurally well-preserved cells. The method developed provides a highly specific signal with the signal/noise ratio higher than 130 for permeabilized cells and 25 for conventional acrylic resin sections under the conditions used. When the high pressure freezing technique followed by the freeze substitution is employed for the cell's preparation, the ratio is higher than 80.
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Affiliation(s)
- Anna Ligasová
- Laboratory of Cell Biology, Institute of Experimental Medicine, v.v.i., AS CR, Vídenská 1083, 142 20 Prague 4, Czech Republic.
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33
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Kamiya H, Goto H, Kanda G, Yamada Y, Harashima H. Transgene expression efficiency from plasmid DNA delivered as a complex with histone H3. Int J Pharm 2010; 392:249-53. [DOI: 10.1016/j.ijpharm.2010.03.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Revised: 03/08/2010] [Accepted: 03/11/2010] [Indexed: 10/19/2022]
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34
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Hasegawa M, Iwai S, Kuraoka I. A non-isotopic assay uses bromouridine and RNA synthesis to detect DNA damage responses. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2010; 699:62-6. [DOI: 10.1016/j.mrgentox.2010.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Revised: 02/20/2010] [Accepted: 04/07/2010] [Indexed: 10/19/2022]
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35
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Lee YH, Peng CA. Effect of hypotonic stress on retroviral transduction. Biochem Biophys Res Commun 2009; 390:1367-71. [DOI: 10.1016/j.bbrc.2009.10.161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 10/29/2009] [Indexed: 11/25/2022]
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36
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Satou K, Hori M, Kawai K, Kasai H, Harashima H, Kamiya H. Involvement of specialized DNA polymerases in mutagenesis by 8-hydroxy-dGTP in human cells. DNA Repair (Amst) 2009; 8:637-42. [PMID: 19179121 DOI: 10.1016/j.dnarep.2008.12.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Revised: 12/16/2008] [Accepted: 12/17/2008] [Indexed: 11/17/2022]
Abstract
The mutagenicity of an oxidized form of dGTP, 8-hydroxy-2'-deoxyguanosine 5'-triphosphate (8-OH-dGTP), was examined using human 293T cells. Shuttle plasmid DNA containing the supF gene was first transfected into the cells, and then 8-OH-dGTP was introduced by means of osmotic pressure. The DNAs replicated in the cells were recovered and then transfected into Escherichia coli. 8-OH-dGTP induced A:T-->C:G substitution mutations in the cells. The knock-downs of DNA polymerases eta and zeta, and REV1 by siRNAs reduced the A:T-->C:G substitution mutations, suggesting that these DNA polymerases are involved in the misincorporation of 8-OH-dGTP opposite A in human cells. In contrast, the knock-down of DNA polymerase iota did not affect the 8-OH-dGTP-induced mutations. The decrease in the induced mutation frequency was more evident by double knock-downs of DNA pols eta plus zeta and REV1 plus DNA pol zeta (but not by that of DNA pol eta plus REV1), suggesting that REV1-DNA pol eta and DNA pol zeta work in different steps. These results indicate that specialized DNA polymerases are involved in the mutagenesis induced by the oxidized dGTP.
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Affiliation(s)
- Kazuya Satou
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
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37
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Thiry M, Lamaye F, Thelen N, Chatron-Colliet A, Lalun N, Bobichon H, Ploton D. A protocol for studying the kinetics of RNA within cultured cells: application to ribosomal RNA. Nat Protoc 2009; 3:1997-2004. [PMID: 19180082 DOI: 10.1038/nprot.2008.198] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This protocol describes a nonisotopic method for high-resolution investigation of the kinetics of RNA within the cell. This involves the incorporation of bromouridine-5'-triphosphate into RNA of living cells by lipofection followed by immunocytological detection of BrRNAs. The use of the same antibody identified either with fluorescence or with gold particles revealed the three-dimensional organization of sites containing labeled RNAs or their precise localization by using confocal and ultrastructural microscopy, respectively. Comparison of three-dimensional reconstruction obtained from the series of optical sections and ultrathin sections was extremely fruitful to describe topological and spatial dynamics of RNAs from their synthesis site inside the nucleus to the cytoplasm. Combined with immunolocalization of proteins involved in different nuclear activities and with highly resolved three-dimensional visualizations of the labelings, this method should also provide a significant contribution to our understanding of the functional, volumic organization of the cell nucleus. The entire protocol can be completed in approximately 10 d.
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Affiliation(s)
- Marc Thiry
- Laboratoire de biologie cellulaire et tissulaire, Université de Liège, Institut d'anatomie (Bât L3), 20 rue de Pitteurs, 4020 Liège, Belgique.
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38
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Isokane M, Hieda M, Hirakawa S, Shudou M, Nakashiro K, Hashimoto K, Hamakawa H, Higashiyama S. Plasma-membrane-anchored growth factor pro-amphiregulin binds A-type lamin and regulates global transcription. J Cell Sci 2009; 121:3608-18. [PMID: 18946024 DOI: 10.1242/jcs.031443] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Amphiregulin (AR), a member of the EGF family, is synthesized as a type I transmembrane protein precursor (proAR) and expressed on the cell surface. Shedding of proAR yields a transmembrane-cytoplasmic fragment (AR-CTF), as well as a soluble AR. Here we demonstrate that the proAR-shedding stimuli trigger endocytosis of both AR-CTF and un-shed proAR. ProAR translocates from the plasma membrane to the inner nuclear membrane, whereas AR-CTF is translocated to the lysosome via retrograde membrane trafficking. Nuclear envelope localization of proAR involves truncation of the C-terminus, which subsequently activates the ER-retrieval signal. The truncated form of proAR interacts with A-type lamin and is retained at the inner nuclear membrane. Heterochromatin formation is then induced and global transcription is transiently suppressed. This study gives new insight into epigenetic chromatin organization in mammalian cells: a plasma-membrane-anchored growth factor is targeted to the inner nuclear membrane where it participates in dynamic chromatin organization and control of transcription.
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Affiliation(s)
- Mayumi Isokane
- Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
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39
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Ligasová A, Raska I, Koberna K. Organization of human replicon: singles or zipping couples? J Struct Biol 2008; 165:204-13. [PMID: 19063972 PMCID: PMC2670984 DOI: 10.1016/j.jsb.2008.11.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Revised: 11/07/2008] [Accepted: 11/10/2008] [Indexed: 01/18/2023]
Abstract
According to a general paradigm, proper DNA duplication from each replication origin is ensured by two protein complexes termed replisomes. In prokaryotes and in budding yeast Saccharomyces cerevisiae, these two replisomes seem to be associated with one another until DNA replication initiated from the origin has finished. This arrangement results in the formation of the loop of newly synthesized DNA. However, arrangement of replisomes in other eukaryotic organisms including vertebrate cells is largely unknown. Here, we used in vivo labeling of DNA segments in combination with the electron microscopy tomography to describe the organization of replisomes in human HeLa cells. The experiments were devised in order to distinguish between a model of independent replisomes and a model of replisome couples. The comparative analysis of short segments of replicons labeled in pulse-chase experiments of various length shows that replisomes in HeLa cells are organized into the couples during DNA replication. Moreover, our data enabled to suggest a new model of the organization of replicated DNA. According to this model, replisome couples produce loop with the associated arms in the form of four tightly associated 30 nm fibers.
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Affiliation(s)
- Anna Ligasová
- Laboratory of Cell Biology, Institute of Experimental Medicine, v.v.i., Academy of Sciences of the Czech Republic, Vídenská 1083, 14200 Prague 4, Czech Republic.
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40
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Effect of dehydroaltenusin-C12 derivative, a selective DNA polymerase alpha inhibitor, on DNA replication in cultured cells. Molecules 2008; 13:2948-61. [PMID: 19043348 PMCID: PMC6245447 DOI: 10.3390/molecules13122948] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Revised: 11/19/2008] [Accepted: 11/29/2008] [Indexed: 11/17/2022] Open
Abstract
Dehydroaltenusin is a selective inhibitor of mammalian DNA polymerase α (pol α) from a fungus (Alternaria tennuis). We have designed, synthesized, and characterized a derivative of dehydroaltenusin conjugated with a C12-alkyl side chain (dehydroaltenusin-C12 [C12]). C12 was the strongest pol α inhibitor in vitro. We introduced C12 into NIH3T3 cells with the help of a hypotonic shift, that is, a transient exposure of cultured cells in hypotonic buffer with small molecules which can not penetrate cells. The cells that took in C12 by hypotonic shift showed cell growth inhibition. At a low concentration (5 μM), DNA replication was inhibited and several large replication protein A (RPA) foci, which is different from dUTP foci. Furthermore, when C12 was incubated with aphidicolin, RPA foci were not observed in cells. Finally, these findings suggest that C12 inhibited DNA replication through pol α inhibition, and generated single-stranded DNA, resulted in uncoupling of the leading strand and lagging strand synthesis. These findings suggest that C12 could be more interesting as a molecule probe or anticancer agent than aphidicolin. C12 might provide novel markers for the development of antiproliferative drugs.
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41
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Exploring RNA transcription and turnover in vivo by using click chemistry. Proc Natl Acad Sci U S A 2008; 105:15779-84. [PMID: 18840688 DOI: 10.1073/pnas.0808480105] [Citation(s) in RCA: 500] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We describe a chemical method to detect RNA synthesis in cells, based on the biosynthetic incorporation of the uridine analog 5-ethynyluridine (EU) into newly transcribed RNA, on average once every 35 uridine residues in total RNA. EU-labeled cellular RNA is detected quickly and with high sensitivity by using a copper (I)-catalyzed cycloaddition reaction (often referred to as "click" chemistry) with fluorescent azides, followed by microscopic imaging. We demonstrate the use of this method in cultured cells, in which we examine the turnover of bulk RNA after EU pulses of varying lengths. We also use EU to assay transcription rates of various tissues in whole animals, both on sections and by whole-mount staining. We find that total transcription rates vary greatly among different tissues and among different cell types within organs.
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42
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Hyper-phosphorylated retinoblastoma protein suppresses telomere elongation. Biosci Biotechnol Biochem 2008; 72:630-5. [PMID: 18256459 DOI: 10.1271/bbb.70715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Immortalized cell lines maintain telomeres by the expression of telomerase or by a mechanism designated alternative lengthening of telomeres (ALT). Although DNA polymerase alpha (pol-alpha) is reported to be required for telomere maintenance, the critical role of pol-alpha in telomere maintenance has not been firmly determined. We examined the role of retinoblastoma protein (pRb) and pol-alpha in the regulation of telomere length, using telomere-fiber FISH. Telomere length varied dependent on the intracellular abundance of pol-alpha or pRb in HeLa cells. A proportion of hyper-phosphorylated pRb (ppRb) molecules localized to sites of telomeric DNA replication in HeLa cells. Pol-alpha might thus contribute to telomere maintenance, and might be regulated by ppRb.
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43
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44
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The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature 2007; 450:908-12. [PMID: 17994007 DOI: 10.1038/nature06397] [Citation(s) in RCA: 902] [Impact Index Per Article: 53.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 10/22/2007] [Indexed: 12/21/2022]
Abstract
DNA methyltransferase (cytosine-5) 1 (Dnmt1) is the principal enzyme responsible for maintenance of CpG methylation and is essential for the regulation of gene expression, silencing of parasitic DNA elements, genomic imprinting and embryogenesis. Dnmt1 is needed in S phase to methylate newly replicated CpGs occurring opposite methylated ones on the mother strand of the DNA, which is essential for the epigenetic inheritance of methylation patterns in the genome. Despite an intrinsic affinity of Dnmt1 for such hemi-methylated DNA, the molecular mechanisms that ensure the correct loading of Dnmt1 onto newly replicated DNA in vivo are not understood. The Np95 (also known as Uhrf1 and ICBP90) protein binds methylated CpG through its SET and RING finger-associated (SRA) domain. Here we show that localization of mouse Np95 to replicating heterochromatin is dependent on the presence of hemi-methylated DNA. Np95 forms complexes with Dnmt1 and mediates the loading of Dnmt1 to replicating heterochromatic regions. By using Np95-deficient embryonic stem cells and embryos, we show that Np95 is essential in vivo to maintain global and local DNA methylation and to repress transcription of retrotransposons and imprinted genes. The link between hemi-methylated DNA, Np95 and Dnmt1 thus establishes key steps of the mechanism for epigenetic inheritance of DNA methylation.
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45
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Vecchio L, Solimando L, Biggiogera M, Fakan S. Use of halogenated precursors for simultaneous DNA and RNA detection by means of immunoelectron and immunofluorescence microscopy. J Histochem Cytochem 2007; 56:45-55. [PMID: 17938284 DOI: 10.1369/jhc.7a7225.2007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We have developed a novel approach for in situ labeling and detection of nucleic acids in cultured cells. It is based on in vivo incorporation of chlorouridine (ClU) or iododeoxyuridine (IdU) into Chinese hamster ovary cells with the aim of labeling RNA and DNA, respectively. The halogenated nucleotides are immunolabeled on ultrathin sections with anti-bromodeoxyuridine (BrdU) monoclonal antibodies that specifically react with either IdU or ClU. Furthermore, we combined ClU and IdU incubation to label simultaneously RNA and DNA in the same cell. Both were visualized by means of anti-BrdU antibodies exhibiting strong affinity for one of the two halogenated epitopes. Confocal imaging of interphase nuclei and electron microscopic analysis showed evidence of a partial colocalization of newly synthesized DNA and RNA inside the cell nucleus. RNase and DNase digestion of ultrathin sections after formaldehyde fixation and acrylic resin embedding confirmed the specificity of incorporation. Consequently, this method allows us to differentially label DNA and RNA on the same section. Using short pulses with the precursors, we could show that newly synthesized DNA and RNA both preferentially occur within the perichromatin region at the border of condensed chromatin domains.
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Affiliation(s)
- Lorella Vecchio
- Centre of Electron Microscopy, University of Lausanne, Rue du Bugnon 27, CH 1005 Lausanne, Switzerland
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46
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Takebayashi SI, Tamura T, Matsuoka C, Okano M. Major and essential role for the DNA methylation mark in mouse embryogenesis and stable association of DNMT1 with newly replicated regions. Mol Cell Biol 2007; 27:8243-58. [PMID: 17893328 PMCID: PMC2169176 DOI: 10.1128/mcb.00899-07] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA methyltransferase 1 (DNMT1) plays an important role in the inheritance of genomic DNA methylation, which is coupled to the DNA replication process. Early embryonic lethality in DNMT1-null mutant (Dnmt1(c)) mice indicates that DNA methylation is essential for mammalian development. DNMT1, however, interacts with a number of transcriptional regulators and has a transcriptional repressor activity independent of its catalytic activity. To examine the roles of the catalytic activity of DNMT1 in vivo, we generated a Dnmt1(ps) allele that expresses a point-mutated protein that lacks catalytic activity (DNMT1-C1229S). Dnmt1(ps) mutant mice showed developmental arrest shortly after gastrulation, near-complete loss of DNA methylation, and an altered distribution of repressive chromatin markers in the nuclei; these phenotypes are quite similar to those of the Dnmt1(c) mutant. The mutant DNMT1 protein failed to associate with replication foci in Dnmt1(ps) cells. Reconstitution experiments and replication labeling in Dnmt1-/- Dnmt3a-/- Dnmt3b-/- (i.e., unmethylated) embryonic stem cells revealed that preexisting DNA methylation is a major determinant for the cell cycle-dependent localization of DNMT1. The C-terminal catalytic domain of DNMT1 inhibited its stable association with unmethylated chromatin. Our results reveal essential roles for the DNA methylation mark in mammalian development and in DNMT1 localization.
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Affiliation(s)
- Shin-ichiro Takebayashi
- Laboratory for Mammalian Epigenetic Studies, Center for Developmental Biology, RIKEN, 2-2-3, Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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47
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Mazumder A, Shivashankar GV. Gold-nanoparticle-assisted laser perturbation of chromatin assembly reveals unusual aspects of nuclear architecture within living cells. Biophys J 2007; 93:2209-16. [PMID: 17496030 PMCID: PMC1959558 DOI: 10.1529/biophysj.106.102202] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Chromatin organization within the nucleus is a vital regulator of genome function, yet its mechanical coupling to the nuclear architecture has remained elusive. To directly investigate this coupling, we locally modulated chromatin structure in living cells using nanoparticle-based laser perturbation. Unusual differences in the response of the cell nucleus were observed depending on the nuclear region that was perturbed--the heterochromatin, the euchromatin, and the nuclear envelope. This response varied under different conditions of cellular perturbations such as ATP depletion, apoptosis, and inhibition of histone deacetylases. Our studies implicate heterochromatin organization in imparting mechanical stability to the cell nucleus and suggest that nuclear size and shape are the result of interplay between nuclear and cytoplasmic anchors.
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Affiliation(s)
- Aprotim Mazumder
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India
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48
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Sugimura K, Takebayashi SI, Ogata S, Taguchi H, Okumura K. Non-denaturing fluorescence in situ hybridization to find replication origins in a specific genome region on the DNA fiber. Biosci Biotechnol Biochem 2007; 71:627-32. [PMID: 17284819 DOI: 10.1271/bbb.60662] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorescence in situ hybridization (FISH) is a useful method of determining the replication timing of specific genomic loci in mammals and of delineating replicon structures on DNA fibers in combination with in vivo replication labeling. In the case of simultaneous detection of a FISH probe and replicated forks, however, the DNA fibers are damaged by the DNA denaturation step for FISH detection, and the resulting fragmented fluorescence signals prevent analysis at high resolution. Here we found that hybridization of the probe to the genomic DNA was possible even under non-denaturing condition, but only at the time its genomic region replicated. Using the method designated non-denaturing FISH, we determined the replication timing of a specific BAC clone and the standard clones, and found that at least one replication origin exists within the genomic region covered by its BAC clone as an example.
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Affiliation(s)
- Kazuto Sugimura
- Laboratory of Molecular and Cellular Biology, Graduate School of Bioresources, Mie University, Tsu, Mie, Japan
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Yasukawa T, Sugimura K, Fukuda M, Yamazaki K, Kitajima S, Okumura K, Aso T. Functional characterization of a mammalian transcription factor, Elongin A. Biochem Biophys Res Commun 2006; 352:237-43. [PMID: 17112477 DOI: 10.1016/j.bbrc.2006.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Accepted: 11/06/2006] [Indexed: 11/17/2022]
Abstract
Elongin A is the transcriptionally active subunit of the Elongin complex that strongly stimulates the rate of elongation by RNA polymerase II (pol II) by suppressing the transient pausing of the polymerase at many sites along the DNA template. We have recently shown that Elongin A-deficient mice are embryonic lethal, and mouse embryonic fibroblasts (MEFs) derived from Elongin A(-/-) embryos display not only increased apoptosis but also senescence-like phenotypes accompanied by the activation of p53. To further understand the function of Elongin A in vivo, we have carried out the structure-function analysis of Elongin A and identified sequences critical to its nuclear localization and direct interaction with pol II. Moreover, we have analyzed the replication fork movement in wild-type and Elongin A(-/-) MEFs, and shown the possibility that the genomic instability observed in Elongin A(-/-) MEFs might be caused by the replication fork collapse due to Elongin A deficiency.
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Affiliation(s)
- Takashi Yasukawa
- Department of Functional Genomics, Kochi Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783-8505, Japan
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Bhattacharya D, Mazumder A, Miriam SA, Shivashankar GV. EGFP-tagged core and linker histones diffuse via distinct mechanisms within living cells. Biophys J 2006; 91:2326-36. [PMID: 16815908 PMCID: PMC1557551 DOI: 10.1529/biophysj.105.079343] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Accepted: 06/09/2006] [Indexed: 11/18/2022] Open
Abstract
The effect of chromatin organization on EGFP-tagged histone protein dynamics within the cell nucleus has been probed using fluorescence correlation and recovery measurements on single living HeLa cells. Our studies reveal that free fraction of core-particle histones exist as multimers within the cell nucleus whereas the linker histones exist in monomeric forms. The multimeric state of core histones is found to be invariant across mammalian and polytene chromosomes and this is ATP dependent. In contrast, the dynamics of the linker histones exhibits two distinct diffusion timescales corresponding to its transient binding and unbinding to chromatin governed by the tail domain residues. Under conditions of chromatin condensation induced by apoptosis, the free multimeric fraction of core histones is found to become immobile, while the monomeric linker histone mobility is partially reduced. In addition, we observe differences in nuclear colocalization of linker and core particle histones. These results are validated through Brownian dynamics simulation of core and linker histone mobility. Our findings provide a framework to understand the coupling between the state of chromatin assembly and histone protein dynamics that is central to accessing regulatory sites on the genome.
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