101
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Wang Y, Khan A, Marks AB, Smith OK, Giri S, Lin YC, Creager R, MacAlpine DM, Prasanth KV, Aladjem MI, Prasanth SG. Temporal association of ORCA/LRWD1 to late-firing origins during G1 dictates heterochromatin replication and organization. Nucleic Acids Res 2017; 45:2490-2502. [PMID: 27924004 PMCID: PMC5389698 DOI: 10.1093/nar/gkw1211] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/23/2016] [Indexed: 12/19/2022] Open
Abstract
DNA replication requires the recruitment of a pre-replication complex facilitated by Origin Recognition Complex (ORC) onto the chromatin during G1 phase of the cell cycle. The ORC-associated protein (ORCA/LRWD1) stabilizes ORC on chromatin. Here, we evaluated the genome-wide distribution of ORCA using ChIP-seq during specific time points of G1. ORCA binding sites on the G1 chromatin are dynamic and temporally regulated. ORCA association to specific genomic sites decreases as the cells progressed towards S-phase. The majority of the ORCA-bound sites represent replication origins that also associate with the repressive chromatin marks H3K9me3 and methylated-CpGs, consistent with ORCA-bound origins initiating DNA replication late in S-phase. Further, ORCA directly associates with the repressive marks and interacts with the enzymes that catalyze these marks. Regions that associate with both ORCA and H3K9me3, exhibit diminished H3K9 methylation in ORCA-depleted cells, suggesting a role for ORCA in recruiting the H3K9me3 mark at certain genomic loci. Similarly, DNA methylation is altered at ORCA-occupied sites in cells lacking ORCA. Furthermore, repressive chromatin marks influence ORCA's binding on chromatin. We propose that ORCA coordinates with the histone and DNA methylation machinery to establish a repressive chromatin environment at a subset of origins, which primes them for late replication.
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Affiliation(s)
- Yating Wang
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Abid Khan
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Anna B Marks
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Owen K Smith
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Sumanprava Giri
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Yo-Chuen Lin
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Rachel Creager
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
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102
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Loss of Brap Results in Premature G1/S Phase Transition and Impeded Neural Progenitor Differentiation. Cell Rep 2017; 20:1148-1160. [DOI: 10.1016/j.celrep.2017.07.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 12/14/2016] [Accepted: 07/10/2017] [Indexed: 12/31/2022] Open
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103
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Abstract
Approximately half of high-grade serous epithelial ovarian cancers incur alterations in genes of homologous recombination (BRCA1, BRCA2, RAD51C, Fanconi anemia genes), and the rest incur alterations in other DNA repair pathways at high frequencies. Such cancer-specific gene alterations can confer selective sensitivity to DNA damaging agents such as cisplatin and carboplatin, topotecan, etoposide, doxorubicin, and gemcitabine. Originally presumed to inhibit DNA repair, PARP inhibitors that have recently been approved by the FDA for the treatment of advanced ovarian cancer also act as DNA damaging agents by inducing PARP-DNA complexes. These DNA damaging agents induce different types of DNA lesions that require various DNA repair genes for the repair, but commonly induce replication fork slowing or stalling, also referred to as replication stress. Replication stress activates DNA repair checkpoint proteins (ATR, CHK1), which prevent further DNA damage. Hence, targeting DNA repair genes or DNA repair checkpoint genes augments the anti-tumor activity of DNA damaging agents. This review describes the rational basis for using DNA repair and DNA repair checkpoint inhibitors as single agents. The review also presents the strategies combining these inhibitors with DNA damaging agents for ovarian cancer therapy based on specific gene alterations.
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104
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Devlin R, Marques CA, McCulloch R. Does DNA replication direct locus-specific recombination during host immune evasion by antigenic variation in the African trypanosome? Curr Genet 2017; 63:441-449. [PMID: 27822899 PMCID: PMC5422504 DOI: 10.1007/s00294-016-0662-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 12/14/2022]
Abstract
All pathogens must survive host immune attack and, amongst the survival strategies that have evolved, antigenic variation is a particularly widespread reaction to thwart adaptive immunity. Though the reactions that underlie antigenic variation are highly varied, recombination by gene conversion is a widespread approach to immune survival in bacterial and eukaryotic pathogens. In the African trypanosome, antigenic variation involves gene conversion-catalysed movement of a huge number of variant surface glycoprotein (VSG) genes into a few telomeric sites for VSG expression, amongst which only a single site is actively transcribed at one time. Genetic evidence indicates VSG gene conversion has co-opted the general genome maintenance reaction of homologous recombination, aligning the reaction strategy with targeted rearrangements found in many organisms. What is less clear is how gene conversion might be initiated within the locality of the VSG expression sites. Here, we discuss three emerging models for VSG switching initiation and ask how these compare with processes for adaptive genome change found in other organisms.
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Affiliation(s)
- Rebecca Devlin
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Catarina A Marques
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, UK
| | - Richard McCulloch
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK.
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105
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Agris PF, Narendran A, Sarachan K, Väre VYP, Eruysal E. The Importance of Being Modified: The Role of RNA Modifications in Translational Fidelity. Enzymes 2017; 41:1-50. [PMID: 28601219 DOI: 10.1016/bs.enz.2017.03.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The posttranscriptional modifications of tRNA's anticodon stem and loop (ASL) domain represent a third level, a third code, to the accuracy and efficiency of translating mRNA codons into the correct amino acid sequence of proteins. Modifications of tRNA's ASL domain are enzymatically synthesized and site specifically located at the anticodon wobble position-34 and 3'-adjacent to the anticodon at position-37. Degeneracy of the 64 Universal Genetic Codes and the limitation in the number of tRNA species require some tRNAs to decode more than one codon. The specific modification chemistries and their impact on the tRNA's ASL structure and dynamics enable one tRNA to decode cognate and "wobble codons" or to expand recognition to synonymous codons, all the while maintaining the translational reading frame. Some modified nucleosides' chemistries prestructure tRNA to read the two codons of a specific amino acid that shares a twofold degenerate codon box, and other chemistries allow a different tRNA to respond to all four codons of a fourfold degenerate codon box. Thus, tRNA ASL modifications are critical and mutations in genes for the modification enzymes and tRNA, the consequences of which is a lack of modification, lead to mistranslation and human disease. By optimizing tRNA anticodon chemistries, structure, and dynamics in all organisms, modifications ensure translational fidelity of mRNA transcripts.
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Affiliation(s)
- Paul F Agris
- The RNA Institute, State University of New York, Albany, NY, United States.
| | - Amithi Narendran
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Kathryn Sarachan
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Ville Y P Väre
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Emily Eruysal
- The RNA Institute, State University of New York, Albany, NY, United States
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106
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Anderson L, Gomes MR, daSilva LF, Pereira ADSA, Mourão MM, Romier C, Pierce R, Verjovski-Almeida S. Histone deacetylase inhibition modulates histone acetylation at gene promoter regions and affects genome-wide gene transcription in Schistosoma mansoni. PLoS Negl Trop Dis 2017; 11:e0005539. [PMID: 28406899 PMCID: PMC5404884 DOI: 10.1371/journal.pntd.0005539] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 04/25/2017] [Accepted: 03/30/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Schistosomiasis is a parasitic disease infecting hundreds of millions of people worldwide. Treatment depends on a single drug, praziquantel, which kills the Schistosoma spp. parasite only at the adult stage. HDAC inhibitors (HDACi) such as Trichostatin A (TSA) induce parasite mortality in vitro (schistosomula and adult worms), however the downstream effects of histone hyperacetylation on the parasite are not known. METHODOLOGY/PRINCIPAL FINDINGS TSA treatment of adult worms in vitro increased histone acetylation at H3K9ac and H3K14ac, which are transcription activation marks, not affecting the unrelated transcription repression mark H3K27me3. We investigated the effect of TSA HDACi on schistosomula gene expression at three different time points, finding a marked genome-wide change in the transcriptome profile. Gene transcription activity was correlated with changes on the chromatin acetylation mark at gene promoter regions. Moreover, combining expression data with ChIP-Seq public data for schistosomula, we found that differentially expressed genes having the H3K4me3 mark at their promoter region in general showed transcription activation upon HDACi treatment, compared with those without the mark, which showed transcription down-regulation. Affected genes are enriched for DNA replication processes, most of them being up-regulated. Twenty out of 22 genes encoding proteins involved in reducing reactive oxygen species accumulation were down-regulated. Dozens of genes encoding proteins with histone reader motifs were changed, including SmEED from the PRC2 complex. We targeted SmEZH2 methyltransferase PRC2 component with a new EZH2 inhibitor (GSK343) and showed a synergistic effect with TSA, significantly increasing schistosomula mortality. CONCLUSIONS/SIGNIFICANCE Genome-wide gene expression analyses have identified important pathways and cellular functions that were affected and may explain the schistosomicidal effect of TSA HDACi. The change in expression of dozens of histone reader genes involved in regulation of the epigenetic program in S. mansoni can be used as a starting point to look for possible novel schistosomicidal targets.
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Affiliation(s)
- Letícia Anderson
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
| | | | - Lucas Ferreira daSilva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
| | - Adriana da Silva Andrade Pereira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
| | - Marina M. Mourão
- Grupo de Helmintologia e Malacologia Médica, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Christophe Romier
- Département de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS, INSERM, Illkirch, France
| | - Raymond Pierce
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Sergio Verjovski-Almeida
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
- * E-mail:
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107
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Xie J, Wooten M, Tran V, Chen X. Breaking Symmetry - Asymmetric Histone Inheritance in Stem Cells. Trends Cell Biol 2017; 27:527-540. [PMID: 28268050 DOI: 10.1016/j.tcb.2017.02.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 01/27/2017] [Accepted: 02/01/2017] [Indexed: 01/17/2023]
Abstract
Asymmetric cell division (ACD) gives rise to two daughter cells with distinct fates. ACD is widely used during development and by many types of adult stem cells during tissue homeostasis and regeneration. ACD can be regulated by extrinsic cues, such as signaling molecules, as well as by intrinsic factors, such as organelles and cortex proteins. The recent discovery of asymmetric histone inheritance during stem cell ACD has revealed another intrinsic mechanism by which ACD produces two distinct daughters. In this review we discuss these findings in the context of cell-cycle regulation, as well as other studies of ACD, to begin understanding the underlying mechanisms and biological relevance of this phenomenon.
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Affiliation(s)
- Jing Xie
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Matthew Wooten
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Vuong Tran
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA; Current address: Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North Seattle, Seattle, WA 98109, USA
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.
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108
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Aladjem MI, Redon CE. Order from clutter: selective interactions at mammalian replication origins. Nat Rev Genet 2017; 18:101-116. [PMID: 27867195 PMCID: PMC6596300 DOI: 10.1038/nrg.2016.141] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mammalian chromosome duplication progresses in a precise order and is subject to constraints that are often relaxed in developmental disorders and malignancies. Molecular information about the regulation of DNA replication at the chromatin level is lacking because protein complexes that initiate replication seem to bind chromatin indiscriminately. High-throughput sequencing and mathematical modelling have yielded detailed genome-wide replication initiation maps. Combining these maps and models with functional genetic analyses suggests that distinct DNA-protein interactions at subgroups of replication initiation sites (replication origins) modulate the ubiquitous replication machinery and supports an emerging model that delineates how indiscriminate DNA-binding patterns translate into a consistent, organized replication programme.
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Affiliation(s)
- Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, Maryland 20892, USA
| | - Christophe E Redon
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, Maryland 20892, USA
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109
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Risks at the DNA Replication Fork: Effects upon Carcinogenesis and Tumor Heterogeneity. Genes (Basel) 2017; 8:genes8010046. [PMID: 28117753 PMCID: PMC5295039 DOI: 10.3390/genes8010046] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/09/2017] [Accepted: 01/17/2017] [Indexed: 12/27/2022] Open
Abstract
The ability of all organisms to copy their genetic information via DNA replication is a prerequisite for cell division and a biological imperative of life. In multicellular organisms, however, mutations arising from DNA replication errors in the germline and somatic cells are the basis of genetic diseases and cancer, respectively. Within human tumors, replication errors additionally contribute to mutator phenotypes and tumor heterogeneity, which are major confounding factors for cancer therapeutics. Successful DNA replication involves the coordination of many large-scale, complex cellular processes. In this review, we focus on the roles that defects in enzymes that normally act at the replication fork and dysregulation of enzymes that inappropriately damage single-stranded DNA at the fork play in causing mutations that contribute to carcinogenesis. We focus on tumor data and experimental evidence that error-prone variants of replicative polymerases promote carcinogenesis and on research indicating that the primary target mutated by APOBEC (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like) cytidine deaminases is ssDNA present at the replication fork. Furthermore, we discuss evidence from model systems that indicate replication stress and other cancer-associated metabolic changes may modulate mutagenic enzymatic activities at the replication fork.
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110
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Raspelli E, Falbo L, Costanzo V. Xenopus egg extract to study regulation of genome-wide and locus-specific DNA replication. Genesis 2017; 55. [PMID: 28095613 DOI: 10.1002/dvg.22996] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 11/10/2016] [Accepted: 11/10/2016] [Indexed: 11/10/2022]
Abstract
Faithful DNA replication, coupled with accurate repair of DNA damage, is essential to maintain genome stability and relies on different DNA metabolism genes. Many of these genes are involved in the assembly of replication origins, in the coordination of DNA repair to protect replication forks progression in the presence of DNA damage and in the replication of repetitive chromatin regions. Some DNA metabolism genes are essential in higher eukaryotes, suggesting the existence of specialized mechanisms of repair and replication in organisms with complex genomes. The impact on cell survival of many of these genes has so far precluded in depth molecular analysis of their function. The cell-free Xenopus laevis egg extract represents an ideal system to overcome survival issues and to facilitate the biochemical study of replication-associated functions of essential proteins in vertebrate organisms. Here, we will discuss how Xenopus egg extracts have been used to study cellular and molecular processes, such as DNA replication and DNA repair. In particular, we will focus on innovative imaging and proteomic-based experimental approaches to characterize the molecular function of a number of essential DNA metabolism factors involved in the duplication of complex vertebrate genomes.
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Affiliation(s)
- Erica Raspelli
- DNA metabolism laboratory, IFOM, The FIRC institute for Molecular Oncology, Milan, Italy
| | - Lucia Falbo
- DNA metabolism laboratory, IFOM, The FIRC institute for Molecular Oncology, Milan, Italy
| | - Vincenzo Costanzo
- DNA metabolism laboratory, IFOM, The FIRC institute for Molecular Oncology, Milan, Italy
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111
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Takahashi S, Motooka S, Kawasaki S, Kurita H, Mizuno T, Matsuura SI, Hanaoka F, Mizuno A, Oshige M, Katsura S. Direct single-molecule observations of DNA unwinding by SV40 large tumor antigen under a negative DNA supercoil state. J Biomol Struct Dyn 2017; 36:32-44. [PMID: 27928933 DOI: 10.1080/07391102.2016.1269689] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Superhelices, which are induced by the twisting and coiling of double-helical DNA in chromosomes, are thought to affect transcription, replication, and other DNA metabolic processes. In this study, we report the effects of negative supercoiling on the unwinding activity of simian virus 40 large tumor antigen (SV40 TAg) at a single-molecular level. The supercoiling density of linear DNA templates was controlled using magnetic tweezers and monitored using a fluorescent microscope in a flow cell. SV40 TAg-mediated DNA unwinding under relaxed and negative supercoil states was analyzed by the direct observation of both single- and double-stranded regions of single DNA molecules. Increased negative superhelicity stimulated SV40 TAg-mediated DNA unwinding more strongly than a relaxed state; furthermore, negative superhelicity was associated with an increased probability of SV40 TAg-mediated DNA unwinding. These results suggest that negative superhelicity helps to regulate the initiation of DNA replication.
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Affiliation(s)
- Shunsuke Takahashi
- a Department of Environmental Engineering Science, Graduate School of Science and Technology , Gunma University , Kiryu , Japan.,f Japan Society for the Promotion of Science
| | - Shinya Motooka
- a Department of Environmental Engineering Science, Graduate School of Science and Technology , Gunma University , Kiryu , Japan
| | - Shohei Kawasaki
- a Department of Environmental Engineering Science, Graduate School of Science and Technology , Gunma University , Kiryu , Japan
| | - Hirofumi Kurita
- b Department of Environmental and Life Sciences, Graduate School of Engineering , Toyohashi University of Technology , Toyohashi , Japan
| | - Takeshi Mizuno
- c Cellular Dynamics Laboratory , RIKEN, Wako , Saitama , Japan
| | - Shun-Ichi Matsuura
- d Research Institute for Chemical Process Technology , National Institute of Advanced Industrial Science and Technology (AIST) , Sendai , Japan
| | - Fumio Hanaoka
- e Faculty of Science, Institute for Biomolecular Science , Gakushuin University , Tokyo , Japan
| | - Akira Mizuno
- b Department of Environmental and Life Sciences, Graduate School of Engineering , Toyohashi University of Technology , Toyohashi , Japan
| | - Masahiko Oshige
- a Department of Environmental Engineering Science, Graduate School of Science and Technology , Gunma University , Kiryu , Japan
| | - Shinji Katsura
- a Department of Environmental Engineering Science, Graduate School of Science and Technology , Gunma University , Kiryu , Japan
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112
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TRF2 recruits ORC through TRFH domain dimerization. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:191-201. [DOI: 10.1016/j.bbamcr.2016.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 09/23/2016] [Accepted: 11/07/2016] [Indexed: 12/23/2022]
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113
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Pozo PN, Cook JG. Regulation and Function of Cdt1; A Key Factor in Cell Proliferation and Genome Stability. Genes (Basel) 2016; 8:genes8010002. [PMID: 28025526 PMCID: PMC5294997 DOI: 10.3390/genes8010002] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 12/13/2016] [Accepted: 12/14/2016] [Indexed: 12/30/2022] Open
Abstract
Successful cell proliferation requires efficient and precise genome duplication followed by accurate chromosome segregation. The Cdc10-dependent transcript 1 protein (Cdt1) is required for the first step in DNA replication, and in human cells Cdt1 is also required during mitosis. Tight cell cycle controls over Cdt1 abundance and activity are critical to normal development and genome stability. We review here recent advances in elucidating Cdt1 molecular functions in both origin licensing and kinetochore–microtubule attachment, and we describe the current understanding of human Cdt1 regulation.
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Affiliation(s)
- Pedro N Pozo
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Jeanette Gowen Cook
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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114
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Swuec P, Costa A. DNA replication and inter-strand crosslink repair: Symmetric activation of dimeric nanomachines? Biophys Chem 2016; 225:15-19. [PMID: 27989548 DOI: 10.1016/j.bpc.2016.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 10/28/2016] [Accepted: 11/01/2016] [Indexed: 10/20/2022]
Abstract
Eukaryotic DNA replication initiation and the Fanconi anemia pathway of interstrand crosslink repair both revolve around the recruitment of a set of DNA-processing factors onto a dimeric protein complex, which functions as a loading platform (MCM and FANCI-FANCD2 respectively). Here we compare and contrast the two systems, identifying a set of unresolved mechanistic questions. How is the dimeric loading platform assembled on the DNA? How can equivalent covalent modification of both factors in a dimer be achieved? Are multicomponent DNA-interacting machines built symmetrically around their dimeric loading platform? Recent biochemical reconstitution studies are starting to shed light on these issues.
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Affiliation(s)
- Paolo Swuec
- Macromolecular Machines Laboratory, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Alessandro Costa
- Macromolecular Machines Laboratory, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK.
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115
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Ohsaki E, Ueda K. A chimeric protein composed of NuMA fused to the DNA binding domain of LANA is sufficient for the ori-P-dependent DNA replication. Virology 2016; 500:190-197. [PMID: 27829174 DOI: 10.1016/j.virol.2016.10.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/20/2016] [Accepted: 10/31/2016] [Indexed: 01/25/2023]
Abstract
The Kaposi's sarcoma-associated herpesvirus (KSHV) genome is stably maintained in KSHV-infected PEL cell lines during cell division. We previously showed that accumulation of LANA in the nuclear matrix fraction could be important for the latent DNA replication, and that the functional significance of LANA should be its recruitment of ori-P to the nuclear matrix. Here, we investigated whether the forced localization of the LANA-DNA binding domain (DBD) to the nuclear matrix facilitated ori-P-containing plasmid replication. We demonstrated that chimeric proteins constructed by fusion of LANA DBD with the nuclear mitotic apparatus protein (NuMA), which is one of the components of the nuclear matrix, could bind with ori-P and enhance replication of an ori-P-containing plasmid, compared with that in the presence of DBD alone. These results further suggested that the ori-P recruitment to the nuclear matrix through the binding with DBD is important for latent viral DNA replication.
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Affiliation(s)
- Eriko Ohsaki
- Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Keiji Ueda
- Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Osaka, Japan.
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116
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Lacroix J, Pélofy S, Blatché C, Pillaire MJ, Huet S, Chapuis C, Hoffmann JS, Bancaud A. Analysis of DNA Replication by Optical Mapping in Nanochannels. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:5963-5970. [PMID: 27624455 DOI: 10.1002/smll.201503795] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 06/21/2016] [Indexed: 06/06/2023]
Abstract
DNA replication is essential to maintain genome integrity in S phase of the cell division cycle. Accumulation of stalled replication forks is a major source of genetic instability, and likely constitutes a key driver of tumorigenesis. The mechanisms of regulation of replication fork progression have therefore been extensively investigated, in particular with DNA combing, an optical mapping technique that allows the stretching of single molecules and the mapping of active region for DNA synthesis by fluorescence microscopy. DNA linearization in nanochannels has been successfully used to probe genomic information patterns along single chromosomes, and has been proposed to be a competitive alternative to DNA combing. Yet this conjecture remains to be confirmed experimentally. Here, two complementary techniques are established to detect the genomic distribution of tracks of newly synthesized DNA in human cells by optical mapping in nanochannels. Their respective advantages and limitations are compared, and applied them to detect deregulations of the replication program induced by the antitumor drug hydroxyurea. The developments here thus broaden the field of applications accessible to nanofluidic technologies, and can be used in the future as part for molecular diagnostics in the context of high throughput cancer drug screening.
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Affiliation(s)
- Joris Lacroix
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
| | - Sandrine Pélofy
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
| | - Charline Blatché
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
| | - Marie-Jeanne Pillaire
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
- Equipe "Labellisée LA LIGUE CONTRE LE CANCER 2013" - Laboratoire d'Excellence Toulouse Cancer LABEX TOUCAN - Cancer Research Center of Toulouse, Inserm U1037, CNRS ERL5294, 2 Avenue Hubert Curien, CS 53717, 31037, Toulouse, France
| | - Sébastien Huet
- CNRS, UMR 6061, Institut Génétique et Développement de Rennes, F-35043, Rennes, France
- Université Rennes 1, UEB, UMR 6290, Faculté de Médecine, F-35043, Rennes, France
| | - Catherine Chapuis
- CNRS, UMR 6061, Institut Génétique et Développement de Rennes, F-35043, Rennes, France
- Université Rennes 1, UEB, UMR 6290, Faculté de Médecine, F-35043, Rennes, France
| | - Jean-Sébastien Hoffmann
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
- Equipe "Labellisée LA LIGUE CONTRE LE CANCER 2013" - Laboratoire d'Excellence Toulouse Cancer LABEX TOUCAN - Cancer Research Center of Toulouse, Inserm U1037, CNRS ERL5294, 2 Avenue Hubert Curien, CS 53717, 31037, Toulouse, France
| | - Aurélien Bancaud
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
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117
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The Replicative Consequences of Papillomavirus E2 Protein Binding to the Origin Replication Factor ORC2. PLoS Pathog 2016; 12:e1005934. [PMID: 27701460 PMCID: PMC5049798 DOI: 10.1371/journal.ppat.1005934] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/13/2016] [Indexed: 12/20/2022] Open
Abstract
The origin recognition complex (ORC) coordinates a series of events that lead to initiation of DNA strand duplication. As a nuclear double stranded DNA plasmid, the papillomavirus (PV) genome resembles a mini-chromosome in infected cells. To initiate its replication, the viral E2 protein binds to and recruits the E1 DNA helicase at the viral origin. PV genome replication program exhibits three stages: initial amplification from a single genome upon infection to a few copies per cell, a cell cycle linked maintenance phase, and a differentiation dependent late stage where the genome is amplified to thousands of copies. Involvement of ORC or other pre-replication complex (pre-RC) factors has not been described. We report that human PV (HPV) and bovine PV (BPV-1) E2 proteins bind to ORC2, however, ORC2 was not detected at the viral origin. Depletion of ORC2 enhanced PV replication in a transient replication model and in keratinocytes stably maintaining viral episomes, while there was no effect on copy number in a cell line with integrated HPV genomes. Consistent with this, occupancy of E1 and E2 at the viral origin increased following ORC2 silencing. These data imply that ORC2 is not necessary for activation of the PV origin by E1 and E2 but instead suppresses E2 replicative function. Furthermore, we observed that over-expression of HPV E2 decreased ORC2 occupation at two known mammalian origins of replication, suggesting that E2 restricts pre-ORC assembly that could otherwise compete for host replication complexes necessary for viral genome amplification. We infer that the ORC2 complex with E2 restricts viral replication in the maintenance phase of the viral replication program and that elevated levels of E2 that occur during the differentiation dependent amplification stage subvert ORC loading and hence DNA synthesis at cellular origins. Papillomavirus genome replication occurs during three distinct stages that are linked to the differentiation state of the infected epithelium. The viral proteins E1 and E2 recognize the viral origin and initiate a process that attracts host DNA replication factors. The origin recognition complex (ORC) coordinates initiation of chromosome duplication. While ORC2 binds to the E2 protein, its depletion does not impair PV genome replication. Instead, depletion of ORC2 stimulates viral replication, while over-expression of E2 protein decreases ORC2 occupancy at mammalian origins. We propose that the relative abundance of E2 and ORC2 in complex regulates viral and cellular origin licensing.
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118
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Identification of Pif1 helicases with novel accessory domains in various amoebae. Mol Phylogenet Evol 2016; 103:64-74. [DOI: 10.1016/j.ympev.2016.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 06/06/2016] [Accepted: 07/12/2016] [Indexed: 11/19/2022]
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119
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Feng W, Michaels SD. Accessing the Inaccessible: The Organization, Transcription, Replication, and Repair of Heterochromatin in Plants. Annu Rev Genet 2016; 49:439-59. [PMID: 26631514 DOI: 10.1146/annurev-genet-112414-055048] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Eukaryotic genomes often contain large quantities of potentially deleterious sequences, such as transposons. One strategy for mitigating this risk is to package such sequences into so-called constitutive heterochromatin, where the dense chromatin environment is thought to inhibit transcription by excluding transcription factors and RNA polymerase. This type of model makes it tempting to think of heterochromatin as an inert region that is isolated from the rest of the nucleus. Recent work on heterochromatin, however, reveals that it is a dynamic environment. Despite its dense packaging, heterochromatin must remain accessible for a host of processes, including DNA replication and repair, and, paradoxically, transcription. In plants, transcripts produced by specialized RNA polymerases are used to target regions of the genome for silencing via DNA methylation. Thus, the maintenance of heterochromatin requires a careful balancing act of access and exclusion, which is achieved through the action of a host of interrelated pathways.
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Affiliation(s)
- Wei Feng
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305;
| | - Scott D Michaels
- Department of Biology, Indiana University, Bloomington, Indiana 47405;
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120
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Inevitability and containment of replication errors for eukaryotic genome lengths spanning megabase to gigabase. Proc Natl Acad Sci U S A 2016; 113:E5765-74. [PMID: 27630194 PMCID: PMC5047159 DOI: 10.1073/pnas.1603241113] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The replication of DNA is initiated at particular sites on the genome called replication origins (ROs). Understanding the constraints that regulate the distribution of ROs across different organisms is fundamental for quantifying the degree of replication errors and their downstream consequences. Using a simple probabilistic model, we generate a set of predictions on the extreme sensitivity of error rates to the distribution of ROs, and how this distribution must therefore be tuned for genomes of vastly different sizes. As genome size changes from megabases to gigabases, we predict that regularity of RO spacing is lost, that large gaps between ROs dominate error rates but are heavily constrained by the mean stalling distance of replication forks, and that, for genomes spanning ∼100 megabases to ∼10 gigabases, errors become increasingly inevitable but their number remains very small (three or less). Our theory predicts that the number of errors becomes significantly higher for genome sizes greater than ∼10 gigabases. We test these predictions against datasets in yeast, Arabidopsis, Drosophila, and human, and also through direct experimentation on two different human cell lines. Agreement of theoretical predictions with experiment and datasets is found in all cases, resulting in a picture of great simplicity, whereby the density and positioning of ROs explain the replication error rates for the entire range of eukaryotes for which data are available. The theory highlights three domains of error rates: negligible (yeast), tolerable (metazoan), and high (some plants), with the human genome at the extreme end of the middle domain.
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121
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Kylie K, Romero J, Lindamulage IK, Knockleby J, Lee H. Dynamic regulation of histone H3K9 is linked to the switch between replication and transcription at the Dbf4 origin-promoter locus. Cell Cycle 2016; 15:2321-35. [PMID: 27341472 PMCID: PMC5004705 DOI: 10.1080/15384101.2016.1201254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/20/2016] [Accepted: 06/08/2016] [Indexed: 02/07/2023] Open
Abstract
The co-regulation of DNA replication and gene transcription is still poorly understood. To gain a better understanding of this important control mechanism, we examined the DNA replication and transcription using the Dbf4 origin-promoter and Dbf4 pseudogene models. We found that origin firing and Dbf4 transcription activity were inversely regulated in a cell cycle-dependent manner. We also found that proteins critical for the regulation of replication (ORC, MCM), transcription (SP1, TFIIB), and cohesin (Smc1, Smc3) and Mediator functions (Med1, Med12) interact with specific sites within and the surrounding regions of the Dbf4 locus in a cell cycle-dependent manner. As expected, replication initiation occurred within a nucleosome-depleted region, and nucleosomes flanked the 2 replication initiation zones. Further, the histone H3 in this region was distinctly acetylated or trimethylated on lysine 9 in a cell cycle-dependent fluctuation pattern: H3K9ac was most prevalent when the Dbf4 transcription level was highest whereas the H3K9me3 level was greatest during and just after replication. The KDM4A histone demethylase, which is responsible for the H3K9me3 modification, was enriched at the Dbf4 origin in a manner coinciding with H3K9me3. Finally, HP1γ, a protein known to interact with H3K9me3 in the heterochromatin was also found enriched at the origin during DNA replication, indicating that H3K9me3 may be required for the regulation of replication at both heterochromatin and euchromatin regions. Taken together, our data show that mammalian cells employ an extremely sophisticated and multilayered co-regulation mechanism for replication and transcription in a highly coordinated manner.
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Affiliation(s)
- Kathleen Kylie
- Tumour Biology Group, Health Sciences North Research Institute, Sudbury, Ontario, Canada
| | - Julia Romero
- Tumour Biology Group, Health Sciences North Research Institute, Sudbury, Ontario, Canada
| | | | - James Knockleby
- Tumour Biology Group, Health Sciences North Research Institute, Sudbury, Ontario, Canada
| | - Hoyun Lee
- Tumour Biology Group, Health Sciences North Research Institute, Sudbury, Ontario, Canada
- Department of Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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122
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Gerhardt J, Bhalla AD, Butler JS, Puckett JW, Dervan PB, Rosenwaks Z, Napierala M. Stalled DNA Replication Forks at the Endogenous GAA Repeats Drive Repeat Expansion in Friedreich's Ataxia Cells. Cell Rep 2016; 16:1218-1227. [PMID: 27425605 PMCID: PMC5028224 DOI: 10.1016/j.celrep.2016.06.075] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/31/2016] [Accepted: 06/17/2016] [Indexed: 10/21/2022] Open
Abstract
Friedreich's ataxia (FRDA) is caused by the expansion of GAA repeats located in the Frataxin (FXN) gene. The GAA repeats continue to expand in FRDA patients, aggravating symptoms and contributing to disease progression. The mechanism leading to repeat expansion and decreased FXN transcription remains unclear. Using single-molecule analysis of replicated DNA, we detected that expanded GAA repeats present a substantial obstacle for the replication machinery at the FXN locus in FRDA cells. Furthermore, aberrant origin activation and lack of a proper stress response to rescue the stalled forks in FRDA cells cause an increase in 3'-5' progressing forks, which could enhance repeat expansion and hinder FXN transcription by head-on collision with RNA polymerases. Treatment of FRDA cells with GAA-specific polyamides rescues DNA replication fork stalling and alleviates expansion of the GAA repeats, implicating DNA triplexes as a replication impediment and suggesting that fork stalling might be a therapeutic target for FRDA.
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Affiliation(s)
- Jeannine Gerhardt
- Center for Reproductive Medicine, Weill Cornell Medical College, New York, NY 10065, USA.
| | - Angela D Bhalla
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama, Birmingham, AL 35294, USA
| | - Jill Sergesketter Butler
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama, Birmingham, AL 35294, USA
| | - James W Puckett
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Peter B Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zev Rosenwaks
- Center for Reproductive Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Marek Napierala
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama, Birmingham, AL 35294, USA; Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61 704, Poland.
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123
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Lombraña R, Álvarez A, Fernández-Justel JM, Almeida R, Poza-Carrión C, Gomes F, Calzada A, Requena JM, Gómez M. Transcriptionally Driven DNA Replication Program of the Human Parasite Leishmania major. Cell Rep 2016; 16:1774-1786. [PMID: 27477279 DOI: 10.1016/j.celrep.2016.07.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 05/26/2016] [Accepted: 07/01/2016] [Indexed: 01/04/2023] Open
Abstract
Faithful inheritance of eukaryotic genomes requires the orchestrated activation of multiple DNA replication origins (ORIs). Although origin firing is mechanistically conserved, how origins are specified and selected for activation varies across different model systems. Here, we provide a complete analysis of the nucleosomal landscape and replication program of the human parasite Leishmania major, building on a better evolutionary understanding of replication organization in Eukarya. We found that active transcription is a driving force for the nucleosomal organization of the L. major genome and that both the spatial and the temporal program of DNA replication can be explained as associated to RNA polymerase kinetics. This simple scenario likely provides flexibility and robustness to deal with the environmental changes that impose alterations in the genetic programs during parasitic life cycle stages. Our findings also suggest that coupling replication initiation to transcription elongation could be an ancient solution used by eukaryotic cells for origin maintenance.
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Affiliation(s)
- Rodrigo Lombraña
- Functional Organization of the Genome Group, Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Alba Álvarez
- Functional Organization of the Genome Group, Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - José Miguel Fernández-Justel
- Functional Organization of the Genome Group, Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Ricardo Almeida
- Functional Organization of the Genome Group, Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - César Poza-Carrión
- Functional Organization of the Genome Group, Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Fábia Gomes
- Centro Nacional de Biotecnología (CSIC), Darwin 3, 28049 Madrid, Spain
| | - Arturo Calzada
- Centro Nacional de Biotecnología (CSIC), Darwin 3, 28049 Madrid, Spain
| | - José María Requena
- Functional Organization of the Genome Group, Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - María Gómez
- Functional Organization of the Genome Group, Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain.
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124
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Zhang B, Wu WQ, Liu NN, Duan XL, Li M, Dou SX, Hou XM, Xi XG. G-quadruplex and G-rich sequence stimulate Pif1p-catalyzed downstream duplex DNA unwinding through reducing waiting time at ss/dsDNA junction. Nucleic Acids Res 2016; 44:8385-94. [PMID: 27471032 PMCID: PMC5041479 DOI: 10.1093/nar/gkw669] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 07/19/2016] [Indexed: 01/04/2023] Open
Abstract
Alternative DNA structures that deviate from B-form double-stranded DNA such as G-quadruplex (G4) DNA can be formed by G-rich sequences that are widely distributed throughout the human genome. We have previously shown that Pif1p not only unfolds G4, but also unwinds the downstream duplex DNA in a G4-stimulated manner. In the present study, we further characterized the G4-stimulated duplex DNA unwinding phenomenon by means of single-molecule fluorescence resonance energy transfer. It was found that Pif1p did not unwind the partial duplex DNA immediately after unfolding the upstream G4 structure, but rather, it would dwell at the ss/dsDNA junction with a 'waiting time'. Further studies revealed that the waiting time was in fact related to a protein dimerization process that was sensitive to ssDNA sequence and would become rapid if the sequence is G-rich. Furthermore, we identified that the G-rich sequence, as the G4 structure, equally stimulates duplex DNA unwinding. The present work sheds new light on the molecular mechanism by which G4-unwinding helicase Pif1p resolves physiological G4/duplex DNA structures in cells.
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Affiliation(s)
- Bo Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wen-Qiang Wu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Na-Nv Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiao-Lei Duan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, Centre National de la Recherche Scientifique, 61 Avenue du Président Wilson, 94235 Cachan, France
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125
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Stevanoni M, Palumbo E, Russo A. The Replication of Frataxin Gene Is Assured by Activation of Dormant Origins in the Presence of a GAA-Repeat Expansion. PLoS Genet 2016; 12:e1006201. [PMID: 27447727 PMCID: PMC4957762 DOI: 10.1371/journal.pgen.1006201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 06/27/2016] [Indexed: 12/17/2022] Open
Abstract
It is well known that DNA replication affects the stability of several trinucleotide repeats, but whether replication profiles of human loci carrying an expanded repeat differ from those of normal alleles is poorly understood in the endogenous context. We investigated this issue using cell lines from Friedreich's ataxia patients, homozygous for a GAA-repeat expansion in intron 1 of the Frataxin gene. By interphase, FISH we found that in comparison to the normal Frataxin sequence the replication of expanded alleles is slowed or delayed. According to molecular combing, origins never fired within the normal Frataxin allele. In contrast, in mutant alleles dormant origins are recruited within the gene, causing a switch of the prevalent fork direction through the expanded repeat. Furthermore, a global modification of the replication profile, involving origin choice and a differential distribution of unidirectional forks, was observed in the surrounding 850 kb region. These data provide a wide-view of the interplay of events occurring during replication of genes carrying an expanded repeat.
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Affiliation(s)
| | - Elisa Palumbo
- Department of Biology, University of Padova, Padova, Italy
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126
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Panneerselvam J, Shen Y, Che R, Fei P. Fanconi Anemia Group D2 Protein Participates in Replication Origin Firing. Chemotherapy 2016; 5. [PMID: 27738567 DOI: 10.4172/2167-7700.1000206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- J Panneerselvam
- University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, Hawai'i 96813, USA
| | - Y Shen
- University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, Hawai'i 96813, USA
| | - R Che
- University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, Hawai'i 96813, USA; Graduate Program of Molecular Biosciences and Bio-engineering, University of Hawaii, HI, USA
| | - P Fei
- University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, Hawai'i 96813, USA; Graduate Program of Molecular Biosciences and Bio-engineering, University of Hawaii, HI, USA
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127
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Zhang Y, Huang L, Fu H, Smith OK, Lin CM, Utani K, Rao M, Reinhold WC, Redon CE, Ryan M, Kim R, You Y, Hanna H, Boisclair Y, Long Q, Aladjem MI. A replicator-specific binding protein essential for site-specific initiation of DNA replication in mammalian cells. Nat Commun 2016; 7:11748. [PMID: 27272143 PMCID: PMC4899857 DOI: 10.1038/ncomms11748] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/26/2016] [Indexed: 12/28/2022] Open
Abstract
Mammalian chromosome replication starts from distinct sites; however, the principles governing initiation site selection are unclear because proteins essential for DNA replication do not exhibit sequence-specific DNA binding. Here we identify a replication-initiation determinant (RepID) protein that binds a subset of replication-initiation sites. A large fraction of RepID-binding sites share a common G-rich motif and exhibit elevated replication initiation. RepID is required for initiation of DNA replication from RepID-bound replication origins, including the origin at the human beta-globin (HBB) locus. At HBB, RepID is involved in an interaction between the replication origin (Rep-P) and the locus control region. RepID-depleted murine embryonic fibroblasts exhibit abnormal replication fork progression and fewer replication-initiation events. These observations are consistent with a model, suggesting that RepID facilitates replication initiation at a distinct group of human replication origins. Origins of mammalian DNA replication are poorly characterised because they lack an Identifiable consensus sequence. Here the authors identify RepID, a protein that binds to a subset of G-rich replication origins and facilitates initiation from those origins.
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Affiliation(s)
- Ya Zhang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Liang Huang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Haiqing Fu
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Owen K Smith
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Chii Mei Lin
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Koichi Utani
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mishal Rao
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Christophe E Redon
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Michael Ryan
- In Silico Solutions, Fairfax, Virginia 22033, USA
| | - RyangGuk Kim
- In Silico Solutions, Fairfax, Virginia 22033, USA
| | - Yang You
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Harlington Hanna
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yves Boisclair
- Department of Animal Science, Cornell University, Ithaca, New York 14853-4801, USA
| | - Qiaoming Long
- Department of Animal Science, Cornell University, Ithaca, New York 14853-4801, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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128
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Boskovic J, Bragado-Nilsson E, Saligram Prabhakar B, Yefimenko I, Martínez-Gago J, Muñoz S, Méndez J, Montoya G. Molecular architecture of the recombinant human MCM2-7 helicase in complex with nucleotides and DNA. Cell Cycle 2016; 15:2431-40. [PMID: 27249176 DOI: 10.1080/15384101.2016.1191712] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
DNA replication is a key biological process that involves different protein complexes whose assembly is rigorously regulated in a successive order. One of these complexes is a replicative hexameric helicase, the MCM complex, which is essential for the initiation and elongation phases of replication. After the assembly of a double heterohexameric MCM2-7 complex at replication origins in G1, the 2 heterohexamers separate from each other and associate with Cdc45 and GINS proteins in a CMG complex that is capable of unwinding dsDNA during S phase. Here, we have reconstituted and characterized the purified human MCM2-7 (hMCM2-7) hexameric complex by co-expression of its 6 different subunits in insect cells. The conformational variability of the complex has been analyzed by single particle electron microscopy in the presence of different nucleotide analogs and DNA. The interaction with nucleotide stabilizes the complex while DNA introduces conformational changes in the hexamer inducing a cylindrical shape. Our studies suggest that the assembly of GINS and Cdc45 to the hMCM2-7 hexamer would favor conformational changes on the hexamer bound to ssDNA shifting the cylindrical shape of the complex into a right-handed spiral conformation as observed in the CMG complex bound to DNA.
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Affiliation(s)
- Jasminka Boskovic
- a Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group , c/Melchor Fdez. Almagro 3, Madrid , Spain
| | - Elisabeth Bragado-Nilsson
- b Protein Structure & Function Programme, Novo Nordisk Foundation Centre for Protein Research, Faculty of Heath and Medical Sciences, University of Copenhagen , Denmark
| | - Bhargrav Saligram Prabhakar
- b Protein Structure & Function Programme, Novo Nordisk Foundation Centre for Protein Research, Faculty of Heath and Medical Sciences, University of Copenhagen , Denmark
| | - Igor Yefimenko
- a Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group , c/Melchor Fdez. Almagro 3, Madrid , Spain
| | - Jaime Martínez-Gago
- a Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group , c/Melchor Fdez. Almagro 3, Madrid , Spain
| | - Sergio Muñoz
- c DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO) , Madrid , Spain
| | - Juan Méndez
- c DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO) , Madrid , Spain
| | - Guillermo Montoya
- b Protein Structure & Function Programme, Novo Nordisk Foundation Centre for Protein Research, Faculty of Heath and Medical Sciences, University of Copenhagen , Denmark
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129
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The Histone Variant H3.3 Is Enriched at Drosophila Amplicon Origins but Does Not Mark Them for Activation. G3-GENES GENOMES GENETICS 2016; 6:1661-71. [PMID: 27172191 PMCID: PMC4889662 DOI: 10.1534/g3.116.028068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Eukaryotic DNA replication begins from multiple origins. The origin recognition complex (ORC) binds origin DNA and scaffolds assembly of a prereplicative complex (pre-RC), which is subsequently activated to initiate DNA replication. In multicellular eukaryotes, origins do not share a strict DNA consensus sequence, and their activity changes in concert with chromatin status during development, but mechanisms are ill-defined. Previous genome-wide analyses in Drosophila and other organisms have revealed a correlation between ORC binding sites and the histone variant H3.3. This correlation suggests that H3.3 may designate origin sites, but this idea has remained untested. To address this question, we examined the enrichment and function of H3.3 at the origins responsible for developmental gene amplification in the somatic follicle cells of the Drosophila ovary. We found that H3.3 is abundant at these amplicon origins. H3.3 levels remained high when replication initiation was blocked, indicating that H3.3 is abundant at the origins before activation of the pre-RC. H3.3 was also enriched at the origins during early oogenesis, raising the possibility that H3.3 bookmarks sites for later amplification. However, flies null mutant for both of the H3.3 genes in Drosophila did not have overt defects in developmental gene amplification or genomic replication, suggesting that H3.3 is not essential for the assembly or activation of the pre-RC at origins. Instead, our results imply that the correlation between H3.3 and ORC sites reflects other chromatin attributes that are important for origin function.
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130
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Petrakis TG, Komseli ES, Papaioannou M, Vougas K, Polyzos A, Myrianthopoulos V, Mikros E, Trougakos IP, Thanos D, Branzei D, Townsend P, Gorgoulis VG. Exploring and exploiting the systemic effects of deregulated replication licensing. Semin Cancer Biol 2016; 37-38:3-15. [PMID: 26707000 DOI: 10.1016/j.semcancer.2015.12.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/10/2015] [Accepted: 12/15/2015] [Indexed: 02/07/2023]
Abstract
Maintenance and accurate propagation of the genetic material are key features for physiological development and wellbeing. The replication licensing machinery is crucial for replication precision as it ensures that replication takes place once per cell cycle. Thus, the expression status of the components comprising the replication licensing apparatus is tightly regulated to avoid re-replication; a form of replication stress that leads to genomic instability, a hallmark of cancer. In the present review we discuss the mechanistic basis of replication licensing deregulation, which leads to systemic effects, exemplified by its role in carcinogenesis and a variety of genetic syndromes. In addition, new insights demonstrate that above a particular threshold, the replication licensing factor Cdc6 acts as global transcriptional regulator, outlining new lines of exploration. The role of the putative replication licensing factor ChlR1/DDX11, mutated in the Warsaw Breakage Syndrome, in cancer is also considered. Finally, future perspectives focused on the potential therapeutic advantage by targeting replication licensing factors, and particularly Cdc6, are discussed.
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Affiliation(s)
- Theodoros G Petrakis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, University of Athens, Athens, Greece
| | - Eirini-Stavroula Komseli
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, University of Athens, Athens, Greece
| | - Marilena Papaioannou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, University of Athens, Athens, Greece
| | - Kostas Vougas
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | | | | | - Emmanuel Mikros
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Athens, Athens, Greece
| | - Ioannis P Trougakos
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens, Greece
| | - Dimitris Thanos
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Dana Branzei
- FIRC (Fondazione Italiana per la Ricerca sul Cancro) Institute of Molecular Oncology (IFOM), Milan, Italy
| | - Paul Townsend
- Faculty Institute of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Vassilis G Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, University of Athens, Athens, Greece; Biomedical Research Foundation of the Academy of Athens, Athens, Greece; Faculty Institute of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.
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131
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Nguyen BCQ, Tawata S. The Chemistry and Biological Activities of Mimosine: A Review. Phytother Res 2016; 30:1230-42. [PMID: 27213712 DOI: 10.1002/ptr.5636] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/05/2016] [Accepted: 04/12/2016] [Indexed: 12/14/2022]
Abstract
Mimosine [β-[N-(3-hydroxy-4-oxypyridyl)]-α-aminopropionic acid] is a non-protein amino acid found in the members of Mimosoideae family. There are a considerable number of reports available on the chemistry, methods for estimation, biosynthesis, regulation, and degradation of this secondary metabolite. On the other hand, over the past years of active research, mimosine has been found to have various biological activities such as anti-cancer, antiinflammation, anti-fibrosis, anti-influenza, anti-virus, herbicidal and insecticidal activities, and others. Mimosine is a leading compound of interest for use in the development of RAC/CDC42-activated kinase 1 (PAK1)-specific inhibitors for the treatment of various diseases/disorders, because PAK1 is not essential for the growth of normal cells. Interestingly, the new roles of mimosine in malignant glioma treatment, regenerative dentistry, and phytoremediation are being emerged. These identified properties indicate an exciting future for this amino acid. The present review is focused on the chemistry and recognized biological activities of mimosine in an attempt to draw a link between these two characteristics. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Binh Cao Quan Nguyen
- Department of Bioscience and Biotechnology, The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, 890-0065, Japan.,PAK Research Center, Okinawa, 903-0213, Japan
| | - Shinkichi Tawata
- PAK Research Center, Okinawa, 903-0213, Japan.,Department of Bioscience and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Senbaru 1, Nishihara-cho, Okinawa, 903-0213, Japan
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132
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Lowe M, Hostager R, Kikyo N. Preservation of Epigenetic Memory During DNA Replication. ACTA ACUST UNITED AC 2016; 1. [PMID: 27158681 DOI: 10.15406/jsrt.2015.01.00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Faithful duplication of a cell's epigenetic state during DNA replication is essential for the maintenance of a cell's lineage. One of the key mechanisms is the recruitment of several critical chromatin modifying enzymes to the replication fork by proliferating cell nuclear antigen (PCNA). Another mechanism is mediated by the dual function of some histone modifying enzymes as both "reader" and "writer" of the same modification. This capacity allows for parental histones to act as a seed to copy the modification onto nearby newly synthesized histones. In contrast to the vast quantity of research into the maintenance of epigenetic memory, little is known about how the recruitment of these maintenance enzymes changes during stem cell differentiation. This question is especially pertinent due to the recent emphasis on cell reprogramming for regenerative medicine.
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Affiliation(s)
- Matthew Lowe
- Department of Genetics, Cell Biology and Developmental Biology, University of Minnesota, USA
| | - Reilly Hostager
- Department of Genetics, Cell Biology and Developmental Biology, University of Minnesota, USA
| | - Nobuaki Kikyo
- Department of Genetics, Cell Biology and Developmental Biology, University of Minnesota, USA
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133
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Löb D, Lengert N, Chagin VO, Reinhart M, Casas-Delucchi CS, Cardoso MC, Drossel B. 3D replicon distributions arise from stochastic initiation and domino-like DNA replication progression. Nat Commun 2016; 7:11207. [PMID: 27052359 PMCID: PMC4829661 DOI: 10.1038/ncomms11207] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 03/02/2016] [Indexed: 01/02/2023] Open
Abstract
DNA replication dynamics in cells from higher eukaryotes follows very complex but highly efficient mechanisms. However, the principles behind initiation of potential replication origins and emergence of typical patterns of nuclear replication sites remain unclear. Here, we propose a comprehensive model of DNA replication in human cells that is based on stochastic, proximity-induced replication initiation. Critical model features are: spontaneous stochastic firing of individual origins in euchromatin and facultative heterochromatin, inhibition of firing at distances below the size of chromatin loops and a domino-like effect by which replication forks induce firing of nearby origins. The model reproduces the empirical temporal and chromatin-related properties of DNA replication in human cells. We advance the one-dimensional DNA replication model to a spatial model by taking into account chromatin folding in the nucleus, and we are able to reproduce the spatial and temporal characteristics of the replication foci distribution throughout S-phase.
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Affiliation(s)
- D. Löb
- Department of Physics, Institute for Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - N. Lengert
- Department of Physics, Institute for Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - V. O. Chagin
- Laboratory of Chromosome Stability, Institute of Cytology, St Petersburg 194064, Russia
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - M. Reinhart
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - C. S. Casas-Delucchi
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - M. C. Cardoso
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - B. Drossel
- Department of Physics, Institute for Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
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134
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Benatti P, Belluti S, Miotto B, Neusiedler J, Dolfini D, Drac M, Basile V, Schwob E, Mantovani R, Blow JJ, Imbriano C. Direct non transcriptional role of NF-Y in DNA replication. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1863:673-85. [PMID: 26732297 DOI: 10.1016/j.bbamcr.2015.12.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/06/2015] [Accepted: 12/23/2015] [Indexed: 11/30/2022]
Abstract
NF-Y is a heterotrimeric transcription factor, which plays a pioneer role in the transcriptional control of promoters containing the CCAAT-box, among which genes involved in cell cycle regulation, apoptosis and DNA damage response. The knock-down of the sequence-specific subunit NF-YA triggers defects in S-phase progression, which lead to apoptotic cell death. Here, we report that NF-Y has a critical function in DNA replication progression, independent from its transcriptional activity. NF-YA colocalizes with early DNA replication factories, its depletion affects the loading of replisome proteins to DNA, among which Cdc45, and delays the passage from early to middle-late S phase. Molecular combing experiments are consistent with a role for NF-Y in the control of fork progression. Finally, we unambiguously demonstrate a direct non-transcriptional role of NF-Y in the overall efficiency of DNA replication, specifically in the DNA elongation process, using a Xenopus cell-free system. Our findings broaden the activity of NF-Y on a DNA metabolism other than transcription, supporting the existence of specific TFs required for proper and efficient DNA replication.
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Affiliation(s)
- Paolo Benatti
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, via Campi 213/D, 41125 Modena, Italy
| | - Silvia Belluti
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, via Campi 213/D, 41125 Modena, Italy; College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Benoit Miotto
- INSERM, U1016, Institut Cochin, Paris, France; CNRS, UMR8104, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Julia Neusiedler
- College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
| | - Marjorie Drac
- Institute of Molecular Genetics, CNRS UMR5535 & Université Montpellier, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Valentina Basile
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, via Campi 213/D, 41125 Modena, Italy
| | - Etienne Schwob
- Institute of Molecular Genetics, CNRS UMR5535 & Université Montpellier, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
| | - J Julian Blow
- College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Carol Imbriano
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, via Campi 213/D, 41125 Modena, Italy.
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135
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Yun J, Song SH, Kang JY, Park J, Kim HP, Han SW, Kim TY. Reduced cohesin destabilizes high-level gene amplification by disrupting pre-replication complex bindings in human cancers with chromosomal instability. Nucleic Acids Res 2016; 44:558-72. [PMID: 26420833 PMCID: PMC4737181 DOI: 10.1093/nar/gkv933] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 08/09/2015] [Accepted: 09/08/2015] [Indexed: 01/03/2023] Open
Abstract
Gene amplification is a hallmark of cancer with chromosomal instability although the underlying mechanism by which altered copy numbers are maintained is largely unclear. Cohesin, involved in sister chromatid cohesion, DNA repair, cell cycle progression and transcriptional regulation of key developmental genes, is frequently overexpressed in human cancer. Here we show that cohesin-dependent change in DNA replication controls the copy numbers of amplified genes in cancer cells with chromosomal instability. We found that the down-regulation of elevated cohesin leads to copy number-associated gene expression changes without disturbing chromosomal segregation. Highly amplified genes form typical long-range chromatin interactions, which are stabilized by enriched cohesin. The spatial proximities among cohesin binding sites within amplified genes are decreased by RAD21-knockdown, resulting in the rapid decline of amplified gene expression. After several passages, cohesin depletion inhibits DNA replication initiation by reducing the recruitment of pre-replication complexes such as minichromosome maintenance subunits 7 (MCM7), DNA polymerase α, and CDC45 at replication origins near the amplified regions, and as a result, decreases the DNA copy numbers of highly amplified genes. Collectively, our data demonstrate that cohesin-mediated chromatin organization and DNA replication are important for stabilizing gene amplification in cancer cells with chromosomal instability.
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Affiliation(s)
- Jiyeon Yun
- Cancer Research Institute, Seoul National University, Seoul 110-799, Republic of Korea Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 110-799, Republic of Korea
| | - Sang-Hyun Song
- Cancer Research Institute, Seoul National University, Seoul 110-799, Republic of Korea
| | - Jee-Youn Kang
- Cancer Research Institute, Seoul National University, Seoul 110-799, Republic of Korea Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 110-799, Republic of Korea
| | - Jinah Park
- Cancer Research Institute, Seoul National University, Seoul 110-799, Republic of Korea
| | - Hwang-Phill Kim
- Cancer Research Institute, Seoul National University, Seoul 110-799, Republic of Korea Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 110-799, Republic of Korea
| | - Sae-Won Han
- Cancer Research Institute, Seoul National University, Seoul 110-799, Republic of Korea Department of Internal Medicine, Seoul National University Hospital, Seoul 110-744, Republic of Korea
| | - Tae-You Kim
- Cancer Research Institute, Seoul National University, Seoul 110-799, Republic of Korea Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 110-799, Republic of Korea Department of Internal Medicine, Seoul National University Hospital, Seoul 110-744, Republic of Korea
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136
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Molecular Combing of Single DNA Molecules on the 10 Megabase Scale. Sci Rep 2016; 6:19636. [PMID: 26781994 PMCID: PMC4726065 DOI: 10.1038/srep19636] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/14/2015] [Indexed: 02/06/2023] Open
Abstract
DNA combing allows the investigation of DNA replication on genomic single DNA molecules, but the lengths that can be analysed have been restricted to molecules of 200-500 kb. We have improved the DNA combing procedure so that DNA molecules can be analysed up to the length of entire chromosomes in fission yeast and up to 12 Mb fragments in human cells. Combing multi-Mb-scale DNA molecules revealed previously undetected origin clusters in fission yeast and shows that in human cells replication origins fire stochastically forming clusters of fired origins with an average size of 370 kb. We estimate that a single human cell forms around 3200 clusters at mid S-phase and fires approximately 100,000 origins to complete genome duplication. The procedure presented here will be adaptable to other organisms and experimental conditions.
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137
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Abstract
Although deoxyribonuclease I (DNase I) was used to probe the structure of the nucleosome in the 1960s and 1970s, in the current high-throughput sequencing era, DNase I has mainly been used to study genomic regions devoid of nucleosomes. Here, we reveal for the first time that DNase I can be used to precisely map the (translational) positions of in vivo nucleosomes genome-wide. Specifically, exploiting a distinctive DNase I cleavage profile within nucleosome-associated DNA—including a signature 10.3 base pair oscillation that corresponds to accessibility of the minor groove as DNA winds around the nucleosome—we develop a Bayes-factor–based method that can be used to map nucleosome positions along the genome. Compared to methods that require genetically modified histones, our DNase-based approach is easily applied in any organism, which we demonstrate by producing maps in yeast and human. Compared to micrococcal nuclease (MNase)-based methods that map nucleosomes based on cuts in linker regions, we utilize DNase I cuts both outside and within nucleosomal DNA; the oscillatory nature of the DNase I cleavage profile within nucleosomal DNA enables us to identify translational positioning details not apparent in MNase digestion of linker DNA. Because the oscillatory pattern corresponds to nucleosome rotational positioning, it also reveals the rotational context of transcription factor (TF) binding sites. We show that potential binding sites within nucleosome-associated DNA are often centered preferentially on an exposed major or minor groove. This preferential localization may modulate TF interaction with nucleosome-associated DNA as TFs search for binding sites.
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138
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Hutchins JRA, Aze A, Coulombe P, Méchali M. Characteristics of Metazoan DNA Replication Origins. DNA REPLICATION, RECOMBINATION, AND REPAIR 2016. [PMCID: PMC7120227 DOI: 10.1007/978-4-431-55873-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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139
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Sanuki Y, Kubota Y, Kanemaki MT, Takahashi TS, Mimura S, Takisawa H. RecQ4 promotes the conversion of the pre-initiation complex at a site-specific origin for DNA unwinding in Xenopus egg extracts. Cell Cycle 2015; 14:1010-23. [PMID: 25602506 DOI: 10.1080/15384101.2015.1007003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Eukaryotic DNA replication is initiated through stepwise assembly of evolutionarily conserved replication proteins onto replication origins, but how the origin DNA is unwound during the assembly process remains elusive. Here, we established a site-specific origin on a plasmid DNA, using in vitro replication systems derived from Xenopus egg extracts. We found that the pre-replicative complex (pre-RC) was preferentially assembled in the vicinity of GAL4 DNA-binding sites of the plasmid, depending on the binding of Cdc6 fused with a GAL4 DNA-binding domain in Cdc6-depleted extracts. Subsequent addition of nucleoplasmic S-phase extracts to the GAL4-dependent pre-RC promoted initiation of DNA replication from the origin, and components of the pre-initiation complex (pre-IC) and the replisome were recruited to the origin concomitant with origin unwinding. In this replication system, RecQ4 is dispensable for both recruitment of Cdc45 onto the origin and stable binding of Cdc45 and GINS to the pre-RC assembled plasmid. However, both origin binding of DNA polymerase α and unwinding of DNA were diminished upon depletion of RecQ4 from the extracts. These results suggest that RecQ4 plays an important role in the conversion of pre-ICs into active replisomes requiring the unwinding of origin DNA in vertebrates.
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Affiliation(s)
- Yosuke Sanuki
- a Department of Biological Sciences; Graduate School of Science ; Osaka University ; Toyonaka , Osaka , Japan
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140
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Hesketh EL, Knight JRP, Wilson RHC, Chong JPJ, Coverley D. Transient association of MCM complex proteins with the nuclear matrix during initiation of mammalian DNA replication. Cell Cycle 2015; 14:333-41. [PMID: 25659032 DOI: 10.4161/15384101.2014.980647] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The minichromosome maintenance complex (MCM2-7) is the putative DNA helicase in eukaryotes, and essential for DNA replication. By applying serial extractions to mammalian cells synchronized by release from quiescence, we reveal dynamic changes to the sub-nuclear compartmentalization of MCM2 as cells pass through late G1 and early S phase, identifying a brief window when MCM2 becomes transiently attached to the nuclear-matrix. The data distinguish 3 states that correspond to loose association with chromatin prior to DNA replication, transient highly stable binding to the nuclear-matrix coincident with initiation, and a post-initiation phase when MCM2 remains tightly associated with chromatin but not the nuclear-matrix. The data suggests that functional MCM complex loading takes place at the nuclear-matrix.
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Affiliation(s)
- Emma L Hesketh
- a Department of Biology ; University of York ; York , UK
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141
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Duxin JP, Walter JC. What is the DNA repair defect underlying Fanconi anemia? Curr Opin Cell Biol 2015; 37:49-60. [PMID: 26512453 PMCID: PMC4688103 DOI: 10.1016/j.ceb.2015.09.002] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 09/15/2015] [Indexed: 12/14/2022]
Abstract
Fanconi anemia (FA) is a rare human genetic disease characterized by bone marrow failure, cancer predisposition, and genomic instability. It has been known for many years that FA patient-derived cells are exquisitely sensitive to DNA interstrand cross-linking agents such as cisplatin and mitomycin C. On this basis, it was widely assumed that failure to repair endogenous interstrand cross-links (ICLs) causes FA, although the endogenous mutagen that generates these lesions remained elusive. Recent genetic evidence now suggests that endogenous aldehydes are the driving force behind FA. Importantly, aldehydes cause a variety of DNA lesions, including ICLs and DNA protein cross-links (DPCs), re-kindling the debate about which DNA lesions cause FA. In this review, we discuss new developments in our understanding of DPC and ICL repair, and how these findings bear on the question of which DNA lesion underlies FA.
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Affiliation(s)
- Julien P Duxin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute.
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142
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Feng Y, Vlassis A, Roques C, Lalonde ME, González-Aguilera C, Lambert JP, Lee SB, Zhao X, Alabert C, Johansen JV, Paquet E, Yang XJ, Gingras AC, Côté J, Groth A. BRPF3-HBO1 regulates replication origin activation and histone H3K14 acetylation. EMBO J 2015; 35:176-92. [PMID: 26620551 DOI: 10.15252/embj.201591293] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 11/03/2015] [Indexed: 12/23/2022] Open
Abstract
During DNA replication, thousands of replication origins are activated across the genome. Chromatin architecture contributes to origin specification and usage, yet it remains unclear which chromatin features impact on DNA replication. Here, we perform a RNAi screen for chromatin regulators implicated in replication control by measuring RPA accumulation upon replication stress. We identify six factors required for normal rates of DNA replication and characterize a function of the bromodomain and PHD finger-containing protein 3 (BRPF3) in replication initiation. BRPF3 forms a complex with HBO1 that specifically acetylates histone H3K14, and genomewide analysis shows high enrichment of BRPF3, HBO1 and H3K14ac at ORC1-binding sites and replication origins found in the vicinity of TSSs. Consistent with this, BRPF3 is necessary for H3K14ac at selected origins and efficient origin activation. CDC45 recruitment, but not MCM2-7 loading, is impaired in BRPF3-depleted cells, identifying a BRPF3-dependent function of HBO1 in origin activation that is complementary to its role in licencing. We thus propose that BRPF3-HBO1 acetylation of histone H3K14 around TSS facilitates efficient activation of nearby replication origins.
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Affiliation(s)
- Yunpeng Feng
- Biotech Research and Innovation Centre (BRIC) and Center for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Arsenios Vlassis
- Biotech Research and Innovation Centre (BRIC) and Center for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Céline Roques
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Axis-CHU de Québec Research Center, Quebec City, QC, Canada
| | - Marie-Eve Lalonde
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Axis-CHU de Québec Research Center, Quebec City, QC, Canada
| | - Cristina González-Aguilera
- Biotech Research and Innovation Centre (BRIC) and Center for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | | | - Sung-Bau Lee
- Biotech Research and Innovation Centre (BRIC) and Center for Epigenetics, University of Copenhagen, Copenhagen, Denmark Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Xiaobei Zhao
- Bioinformatics Centre Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Constance Alabert
- Biotech Research and Innovation Centre (BRIC) and Center for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Jens V Johansen
- Biotech Research and Innovation Centre (BRIC) and Center for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Eric Paquet
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Axis-CHU de Québec Research Center, Quebec City, QC, Canada
| | - Xiang-Jiao Yang
- Department of Medicine, McGill University Health Center, Montréal, QC, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Axis-CHU de Québec Research Center, Quebec City, QC, Canada
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC) and Center for Epigenetics, University of Copenhagen, Copenhagen, Denmark
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143
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Sidhu K, Kumar V. c-ETS transcription factors play an essential role in the licensing of human MCM4 origin of replication. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1319-28. [DOI: 10.1016/j.bbagrm.2015.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 08/26/2015] [Accepted: 09/08/2015] [Indexed: 11/30/2022]
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144
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Graindorge D, Martineau S, Machon C, Arnoux P, Guitton J, Francesconi S, Frochot C, Sage E, Girard PM. Singlet Oxygen-Mediated Oxidation during UVA Radiation Alters the Dynamic of Genomic DNA Replication. PLoS One 2015; 10:e0140645. [PMID: 26485711 PMCID: PMC4618472 DOI: 10.1371/journal.pone.0140645] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 09/29/2015] [Indexed: 02/07/2023] Open
Abstract
UVA radiation (320–400 nm) is a major environmental agent that can exert its deleterious action on living organisms through absorption of the UVA photons by endogenous or exogenous photosensitizers. This leads to the production of reactive oxygen species (ROS), such as singlet oxygen (1O2) and hydrogen peroxide (H2O2), which in turn can modify reversibly or irreversibly biomolecules, such as lipids, proteins and nucleic acids. We have previously reported that UVA-induced ROS strongly inhibit DNA replication in a dose-dependent manner, but independently of the cell cycle checkpoints activation. Here, we report that the production of 1O2 by UVA radiation leads to a transient inhibition of replication fork velocity, a transient decrease in the dNTP pool, a quickly reversible GSH-dependent oxidation of the RRM1 subunit of ribonucleotide reductase and sustained inhibition of origin firing. The time of recovery post irradiation for each of these events can last from few minutes (reduction of oxidized RRM1) to several hours (replication fork velocity and origin firing). The quenching of 1O2 by sodium azide prevents the delay of DNA replication, the decrease in the dNTP pool and the oxidation of RRM1, while inhibition of Chk1 does not prevent the inhibition of origin firing. Although the molecular mechanism remains elusive, our data demonstrate that the dynamic of replication is altered by UVA photosensitization of vitamins via the production of singlet oxygen.
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Affiliation(s)
- Dany Graindorge
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
- Curie Institute, PSL Research University, Orsay, France
| | - Sylvain Martineau
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
- Curie Institute, PSL Research University, Orsay, France
| | - Christelle Machon
- Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Laboratoire de biochimie-toxicologie, Pierre Bénite, France
- Laboratoire de chimie analytique, Université Lyon 1, ISPBL, Faculté de pharmacie, Lyon, France
| | - Philippe Arnoux
- Université de Lorraine, Laboratoire Réactions et Génie des Procédés (LRGP), Nancy, France
- CNRS, UMR7274, Nancy, France
| | - Jérôme Guitton
- Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Laboratoire de biochimie-toxicologie, Pierre Bénite, France
- Laboratoire de Toxicologie, Université Lyon 1, ISPBL, Faculté de pharmacie, Lyon, France
| | - Stefania Francesconi
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
- Curie Institute, PSL Research University, Orsay, France
| | - Céline Frochot
- Université de Lorraine, Laboratoire Réactions et Génie des Procédés (LRGP), Nancy, France
- CNRS, UMR7274, Nancy, France
| | - Evelyne Sage
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
- Curie Institute, PSL Research University, Orsay, France
| | - Pierre-Marie Girard
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
- Curie Institute, PSL Research University, Orsay, France
- * E-mail:
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145
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Alvarez S, Díaz M, Flach J, Rodriguez-Acebes S, López-Contreras AJ, Martínez D, Cañamero M, Fernández-Capetillo O, Isern J, Passegué E, Méndez J. Replication stress caused by low MCM expression limits fetal erythropoiesis and hematopoietic stem cell functionality. Nat Commun 2015; 6:8548. [PMID: 26456157 PMCID: PMC4608254 DOI: 10.1038/ncomms9548] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 09/04/2015] [Indexed: 01/04/2023] Open
Abstract
Replicative stress during embryonic development influences ageing and predisposition to disease in adults. A protective mechanism against replicative stress is provided by the licensing of thousands of origins in G1 that are not necessarily activated in the subsequent S-phase. These ‘dormant' origins provide a backup in the presence of stalled forks and may confer flexibility to the replication program in specific cell types during differentiation, a role that has remained unexplored. Here we show, using a mouse strain with hypomorphic expression of the origin licensing factor mini-chromosome maintenance (MCM)3 that limiting origin licensing in vivo affects the functionality of hematopoietic stem cells and the differentiation of rapidly-dividing erythrocyte precursors. Mcm3-deficient erythroblasts display aberrant DNA replication patterns and fail to complete maturation, causing lethal anemia. Our results indicate that hematopoietic progenitors are particularly sensitive to replication stress, and full origin licensing ensures their correct differentiation and functionality. What causes hematopoietic stem cell loss of functionality? Here, Alvarez et al. show that loss of origin licensing factor MCM3 induces replicative stress (RS), causing aberrant erythrocyte maturation, but mice strains with higher tolerance to RS can overcome this defect.
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Affiliation(s)
- Silvia Alvarez
- DNA Replication Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Marcos Díaz
- DNA Replication Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Johanna Flach
- The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, 94143 California, USA
| | - Sara Rodriguez-Acebes
- DNA Replication Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Andrés J López-Contreras
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Dolores Martínez
- Flow Cytometry Unit, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Marta Cañamero
- Compared Pathology Unit, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Oscar Fernández-Capetillo
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Joan Isern
- Spanish National Cardiovascular Research Center (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Emmanuelle Passegué
- The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, 94143 California, USA
| | - Juan Méndez
- DNA Replication Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
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146
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Activation of a dormant replication origin is essential for Haloferax mediterranei lacking the primary origins. Nat Commun 2015; 6:8321. [PMID: 26374389 PMCID: PMC4595724 DOI: 10.1038/ncomms9321] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 08/11/2015] [Indexed: 01/21/2023] Open
Abstract
The use of multiple origins for chromosome replication has been demonstrated in archaea. Similar to the dormant origins in eukaryotes, some potential origins in archaea appear to be inactive during genome replication. We have comprehensively explored the origin utilization in Haloferax mediterranei. Here we report three active chromosomal origins by genome-wide replication profiling, and demonstrate that when these three origins are deleted, a dormant origin becomes activated. Notably, this dormant origin cannot be further deleted when the other origins are already absent and vice versa. Interestingly, a potential origin that appears to stay dormant in its native host H. volcanii lacking the main active origins becomes activated and competent for replication of the entire chromosome when integrated into the chromosome of origin-deleted H. mediterranei. These results indicate that origin-dependent replication is strictly required for H. mediterranei and that dormant replication origins in archaea can be activated if needed.
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147
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Abstract
DNA replication begins with the assembly of pre-replication complexes (pre-RCs) at thousands of DNA replication origins during the G1 phase of the cell cycle. At the G1-S-phase transition, pre-RCs are converted into pre-initiation complexes, in which the replicative helicase is activated, leading to DNA unwinding and initiation of DNA synthesis. However, only a subset of origins are activated during any S phase. Recent insights into the mechanisms underlying this choice reveal how flexibility in origin usage and temporal activation are linked to chromosome structure and organization, cell growth and differentiation, and replication stress.
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148
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Liu J, Zimmer K, Rusch DB, Paranjape N, Podicheti R, Tang H, Calvi BR. DNA sequence templates adjacent nucleosome and ORC sites at gene amplification origins in Drosophila. Nucleic Acids Res 2015; 43:8746-61. [PMID: 26227968 PMCID: PMC4605296 DOI: 10.1093/nar/gkv766] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/16/2015] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic origins of DNA replication are bound by the origin recognition complex (ORC), which scaffolds assembly of a pre-replicative complex (pre-RC) that is then activated to initiate replication. Both pre-RC assembly and activation are strongly influenced by developmental changes to the epigenome, but molecular mechanisms remain incompletely defined. We have been examining the activation of origins responsible for developmental gene amplification in Drosophila. At a specific time in oogenesis, somatic follicle cells transition from genomic replication to a locus-specific replication from six amplicon origins. Previous evidence indicated that these amplicon origins are activated by nucleosome acetylation, but how this affects origin chromatin is unknown. Here, we examine nucleosome position in follicle cells using micrococcal nuclease digestion with Ilumina sequencing. The results indicate that ORC binding sites and other essential origin sequences are nucleosome-depleted regions (NDRs). Nucleosome position at the amplicons was highly similar among developmental stages during which ORC is or is not bound, indicating that being an NDR is not sufficient to specify ORC binding. Importantly, the data suggest that nucleosomes and ORC have opposite preferences for DNA sequence and structure. We propose that nucleosome hyperacetylation promotes pre-RC assembly onto adjacent DNA sequences that are disfavored by nucleosomes but favored by ORC.
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Affiliation(s)
- Jun Liu
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Kurt Zimmer
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Neha Paranjape
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Ram Podicheti
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Haixu Tang
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Brian R Calvi
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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149
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Abstract
This brief introduction is followed by a published version of my Nobel Laureate lecture, re-published herein with the kind permission of the Nobel Foundation. Much has happened since my original research, for which that prize was awarded. Hence, I am pleased to offer a few thoughts about the future of my research and its possible impact on humankind.Although the original work on nuclear transfer and reprogramming was done over half a century ago, advances continue to be made. In particular the Takahashi and Yamanaka induced pluripotent stem cells (iPS) procedure has opened up the field of cell replacement to a great extent. Now, more recently, further advances make this whole field come closer to actual usefulness for humans. Recently, in the UK, the government approved the use of mitochondrial replacement therapy to avoid the problems associated with genetically defective mitochondria in certain women. Although the House of Commons (members of Parliament) and the House of Lords had to debate and discuss whether to allow this kind of human therapy, I was very pleased to find that both bodies approved this procedure. This means that a patient can choose to make use of the procedure; it does not in any way force an individual to have a procedure that they are not comfortable with. In my view, this is a great advance in respect to giving patients a choice about the treatment they receive. I am told that the UK is the first country in the world to approve mitochondrial replacement therapy.Now that the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPr) technology is being widely used and works well, one can foresee that there will be those who wish to use this technology to make genetic changes to humans. For example, if a human has a gene that makes it susceptible to infection or any other disorder, the removal of that gene might give such a person immunity from that disease. If this gene deletion is done within the germ line, the genetic change will be inherited. However, one can imagine that various people will strongly object and say that this technology should not be allowed. I would very much hope that various regulatory bodies, governments, etc. will allow the choice to remain with the individual. I can see no argument for such bodies to make a law that removes any choice whatsoever by an individual.
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150
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Sequeira-Mendes J, Gutierrez C. Links between genome replication and chromatin landscapes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:38-51. [PMID: 25847096 DOI: 10.1111/tpj.12847] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 03/27/2015] [Accepted: 04/01/2015] [Indexed: 05/07/2023]
Abstract
Post-embryonic organogenesis in plants requires the continuous production of cells in the organ primordia, their expansion and a coordinated exit to differentiation. Genome replication is one of the most important processes that occur during the cell cycle, as the maintenance of genomic integrity is of primary relevance for development. As it is chromatin that must be duplicated, a strict coordination occurs between DNA replication, the deposition of new histones, and the introduction of histone modifications and variants. In turn, the chromatin landscape affects several stages during genome replication. Thus, chromatin accessibility is crucial for the initial stages and to specify the location of DNA replication origins with different chromatin signatures. The chromatin landscape also determines the timing of activation during the S phase. Genome replication must occur fully, but only once during each cell cycle. The re-replication avoidance mechanisms rely primarily on restricting the availability of certain replication factors; however, the presence of specific histone modifications are also revealed as contributing to the mechanisms that avoid re-replication, in particular for heterochromatin replication. We provide here an update of genome replication mostly focused on data from Arabidopsis, and the advances that genomic approaches are likely to provide in the coming years. The data available, both in plants and animals, point to the relevance of the chromatin landscape in genome replication, and require a critical evaluation of the existing views about the nature of replication origins, the mechanisms of origin specification and the relevance of epigenetic modifications for genome replication.
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Affiliation(s)
- Joana Sequeira-Mendes
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049, Madrid, Spain
| | - Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049, Madrid, Spain
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