1
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Bona N, Crossan GP. Fanconi anemia DNA crosslink repair factors protect against LINE-1 retrotransposition during mouse development. Nat Struct Mol Biol 2023; 30:1434-1445. [PMID: 37580626 PMCID: PMC10584689 DOI: 10.1038/s41594-023-01067-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 07/13/2023] [Indexed: 08/16/2023]
Abstract
Long interspersed nuclear element 1 (LINE-1) is the only autonomous retrotransposon in humans and new integrations are a major source of genetic variation between individuals. These events can also lead to de novo germline mutations, giving rise to heritable genetic diseases. Recently, a role for DNA repair in regulating these events has been identified. Here we find that Fanconi anemia (FA) DNA crosslink repair factors act in a common pathway to prevent retrotransposition. We purify recombinant SLX4-XPF-ERCC1, the crosslink repair incision complex, and find that it cleaves putative nucleic acid intermediates of retrotransposition. Mice deficient in upstream crosslink repair signaling (FANCA), a downstream component (FANCD2) or the nuclease XPF-ERCC1 show increased LINE-1 retrotransposition in vivo. Organisms limit retrotransposition through transcriptional silencing but this protection is attenuated during early development leaving the zygote vulnerable. We find that during this window of vulnerability, DNA crosslink repair acts as a failsafe to prevent retrotransposition. Together, our results indicate that the FA DNA crosslink repair pathway acts together to protect against mutation by restricting LINE-1 retrotransposition.
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2
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Parvin S, Akter J, Takenobu H, Katai Y, Satoh S, Okada R, Haruta M, Mukae K, Wada T, Ohira M, Ando K, Kamijo T. ATM depletion induces proteasomal degradation of FANCD2 and sensitizes neuroblastoma cells to PARP inhibitors. BMC Cancer 2023; 23:313. [PMID: 37020276 PMCID: PMC10077671 DOI: 10.1186/s12885-023-10772-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 03/26/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND Genomic alterations, including loss of function in chromosome band 11q22-23, are frequently observed in neuroblastoma, which is the most common extracranial childhood tumour. In neuroblastoma, ATM, a DNA damage response-associated gene located on 11q22-23, has been linked to tumorigenicity. Genetic changes in ATM are heterozygous in most tumours. However, it is unclear how ATM is associated with tumorigenesis and cancer aggressiveness. METHODS To elucidate its molecular mechanism of action, we established ATM-inactivated NGP and CHP-134 neuroblastoma cell lines using CRISPR/Cas9 genome editing. The knock out cells were rigorously characterized by analyzing proliferation, colony forming abilities and responses to PARP inhibitor (Olaparib). Western blot analyses were performed to detect different protein expression related to DNA repair pathway. ShRNA lentiviral vectors were used to knockdown ATM expression in SK-N-AS and SK-N-SH neuroblastoma cell lines. ATM knock out cells were stably transfected with FANCD2 expression plasmid to over-expressed the FANCD2. Moreover, knock out cells were treated with proteasome inhibitor MG132 to determine the protein stability of FANCD2. FANCD2, RAD51 and γH2AX protein expressions were determined by Immunofluorescence microscopy. RESULTS Haploinsufficient ATM resulted in increased proliferation (p < 0.01) and cell survival following PARP inhibitor (olaparib) treatment. However, complete ATM knockout decreased proliferation (p < 0.01) and promoted cell susceptibility to olaparib (p < 0.01). Complete loss of ATM suppressed the expression of DNA repair-associated molecules FANCD2 and RAD51 and induced DNA damage in neuroblastoma cells. A marked downregulation of FANCD2 expression was also observed in shRNA-mediated ATM-knockdown neuroblastoma cells. Inhibitor experiments demonstrated that the degradation of FANCD2 was regulated at the protein level through the ubiquitin-proteasome pathway. Reintroduction of FANCD2 expression is sufficient to reverse decreased proliferation mediated by ATM depletion. CONCLUSIONS Our study revealed the molecular mechanism underlying ATM heterozygosity in neuroblastomas and elucidated that ATM inactivation enhances the susceptibility of neuroblastoma cells to olaparib treatment. These findings might be useful in the treatment of high-risk NB patients showing ATM zygosity and aggressive cancer progression in future.
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Affiliation(s)
- Sultana Parvin
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
- Laboratory of Tumor Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, 338-8570, Japan
| | - Jesmin Akter
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
| | - Hisanori Takenobu
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
| | - Yutaka Katai
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
| | - Shunpei Satoh
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
| | - Ryu Okada
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
- Laboratory of Tumor Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, 338-8570, Japan
| | - Masayuki Haruta
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
| | - Kyosuke Mukae
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
| | - Tomoko Wada
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
| | - Miki Ohira
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
| | - Kiyohiro Ando
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
| | - Takehiko Kamijo
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan.
- Laboratory of Tumor Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, 338-8570, Japan.
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3
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Bayley R, Borel V, Moss RJ, Sweatman E, Ruis P, Ormrod A, Goula A, Mottram RMA, Stanage T, Hewitt G, Saponaro M, Stewart GS, Boulton SJ, Higgs MR. H3K4 methylation by SETD1A/BOD1L facilitates RIF1-dependent NHEJ. Mol Cell 2022; 82:1924-1939.e10. [PMID: 35439434 PMCID: PMC9616806 DOI: 10.1016/j.molcel.2022.03.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 12/14/2021] [Accepted: 03/23/2022] [Indexed: 12/14/2022]
Abstract
The 53BP1-RIF1-shieldin pathway maintains genome stability by suppressing nucleolytic degradation of DNA ends at double-strand breaks (DSBs). Although RIF1 interacts with damaged chromatin via phospho-53BP1 and facilitates recruitment of the shieldin complex to DSBs, it is unclear whether other regulatory cues contribute to this response. Here, we implicate methylation of histone H3 at lysine 4 by SETD1A-BOD1L in the recruitment of RIF1 to DSBs. Compromising SETD1A or BOD1L expression or deregulating H3K4 methylation allows uncontrolled resection of DNA ends, impairs end-joining of dysfunctional telomeres, and abrogates class switch recombination. Moreover, defects in RIF1 localization to DSBs are evident in patient cells bearing loss-of-function mutations in SETD1A. Loss of SETD1A-dependent RIF1 recruitment in BRCA1-deficient cells restores homologous recombination and leads to resistance to poly(ADP-ribose)polymerase inhibition, reinforcing the clinical relevance of these observations. Mechanistically, RIF1 binds directly to methylated H3K4, facilitating its recruitment to, or stabilization at, DSBs.
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Affiliation(s)
- Rachel Bayley
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Valerie Borel
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, Midland Road, London, UK
| | - Rhiannon J Moss
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ellie Sweatman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Philip Ruis
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, Midland Road, London, UK
| | - Alice Ormrod
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Amalia Goula
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Rachel M A Mottram
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Tyler Stanage
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, Midland Road, London, UK
| | - Graeme Hewitt
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, Midland Road, London, UK
| | - Marco Saponaro
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, Midland Road, London, UK.
| | - Martin R Higgs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK.
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4
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Wootton J, Soutoglou E. Chromatin and Nuclear Dynamics in the Maintenance of Replication Fork Integrity. Front Genet 2022; 12:773426. [PMID: 34970302 PMCID: PMC8712883 DOI: 10.3389/fgene.2021.773426] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Replication of the eukaryotic genome is a highly regulated process and stringent control is required to maintain genome integrity. In this review, we will discuss the many aspects of the chromatin and nuclear environment that play key roles in the regulation of both unperturbed and stressed replication. Firstly, the higher order organisation of the genome into A and B compartments, topologically associated domains (TADs) and sub-nuclear compartments has major implications in the control of replication timing. In addition, the local chromatin environment defined by non-canonical histone variants, histone post-translational modifications (PTMs) and enrichment of factors such as heterochromatin protein 1 (HP1) plays multiple roles in normal S phase progression and during the repair of replicative damage. Lastly, we will cover how the spatial organisation of stalled replication forks facilitates the resolution of replication stress.
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Affiliation(s)
- Jack Wootton
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Evi Soutoglou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
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5
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Chatzidoukaki O, Stratigi K, Goulielmaki E, Niotis G, Akalestou-Clocher A, Gkirtzimanaki K, Zafeiropoulos A, Altmüller J, Topalis P, Garinis GA. R-loops trigger the release of cytoplasmic ssDNAs leading to chronic inflammation upon DNA damage. SCIENCE ADVANCES 2021; 7:eabj5769. [PMID: 34797720 PMCID: PMC8604417 DOI: 10.1126/sciadv.abj5769] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
How DNA damage leads to chronic inflammation and tissue degeneration with aging remains to be fully resolved. Here, we show that DNA damage leads to cellular senescence, fibrosis, loss-of-tissue architecture, and chronic pancreatitis in mice with an inborn defect in the excision repair cross complementation group 1 (Ercc1) gene. We find that DNA damage-driven R-loops causally contribute to the active release and buildup of single-stranded DNAs (ssDNAs) in the cytoplasm of cells triggering a viral-like immune response in progeroid and naturally aged pancreata. To reduce the proinflammatory load, we developed an extracellular vesicle (EV)-based strategy to deliver recombinant S1 or ribonuclease H nucleases in inflamed Ercc1−/− pancreatic cells. Treatment of Ercc1−/− animals with the EV-delivered nuclease cargo eliminates DNA damage-induced R-loops and cytoplasmic ssDNAs alleviating chronic inflammation. Thus, DNA damage-driven ssDNAs causally contribute to tissue degeneration, Ercc1−/− paving the way for novel rationalized intervention strategies against age-related chronic inflammation.
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Affiliation(s)
- Ourania Chatzidoukaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, GR70013 Heraklion, Crete, Greece
- Medical School, University of Crete, Heraklion, Crete, Greece
| | - Kalliopi Stratigi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, GR70013 Heraklion, Crete, Greece
| | - Evi Goulielmaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, GR70013 Heraklion, Crete, Greece
| | - George Niotis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, GR70013 Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Alexia Akalestou-Clocher
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, GR70013 Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Katerina Gkirtzimanaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, GR70013 Heraklion, Crete, Greece
| | | | - Janine Altmüller
- Cologne Center for Genomics (CCG), Institute for Genetics, University of Cologne, 50931 Cologne, Germany
| | - Pantelis Topalis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, GR70013 Heraklion, Crete, Greece
| | - George A. Garinis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, GR70013 Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Corresponding author.
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6
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Raghunandan M, Yeo JE, Walter R, Saito K, Harvey AJ, Ittershagen S, Lee EA, Yang J, Hoatlin ME, Bielinsky AK, Hendrickson EA, Schärer O, Sobeck A. Functional cross talk between the Fanconi anemia and ATRX/DAXX histone chaperone pathways promotes replication fork recovery. Hum Mol Genet 2021; 29:1083-1095. [PMID: 31628488 DOI: 10.1093/hmg/ddz250] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/24/2019] [Accepted: 10/03/2019] [Indexed: 12/31/2022] Open
Abstract
Fanconi anemia (FA) is a chromosome instability syndrome characterized by increased cancer predisposition. Specifically, the FA pathway functions to protect genome stability during DNA replication. The central FA pathway protein, FANCD2, locates to stalled replication forks and recruits homologous recombination (HR) factors such as CtBP interacting protein (CtIP) to promote replication fork restart while suppressing new origin firing. Here, we identify alpha-thalassemia retardation syndrome X-linked (ATRX) as a novel physical and functional interaction partner of FANCD2. ATRX is a chromatin remodeler that forms a complex with Death domain-associated protein 6 (DAXX) to deposit the histone variant H3.3 into specific genomic regions. Intriguingly, ATRX was recently implicated in replication fork recovery; however, the underlying mechanism(s) remained incompletely understood. Our findings demonstrate that ATRX forms a constitutive protein complex with FANCD2 and protects FANCD2 from proteasomal degradation. ATRX and FANCD2 localize to stalled replication forks where they cooperate to recruit CtIP and promote MRE11 exonuclease-dependent fork restart while suppressing the firing of new replication origins. Remarkably, replication restart requires the concerted histone H3 chaperone activities of ATRX/DAXX and FANCD2, demonstrating that coordinated histone H3 variant deposition is a crucial event during the reinitiation of replicative DNA synthesis. Lastly, ATRX also cooperates with FANCD2 to promote the HR-dependent repair of directly induced DNA double-stranded breaks. We propose that ATRX is a novel functional partner of FANCD2 to promote histone deposition-dependent HR mechanisms in S-phase.
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Affiliation(s)
- Maya Raghunandan
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Jung Eun Yeo
- Center for Genomic Integrity (CGI), Institute for Basic Science (IBS), Ulsan, Republic of Korea
| | - Ryan Walter
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Kai Saito
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Adam J Harvey
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Stacie Ittershagen
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Eun-A Lee
- Center for Genomic Integrity (CGI), Institute for Basic Science (IBS), Ulsan, Republic of Korea
| | - Jihyeon Yang
- Center for Genomic Integrity (CGI), Institute for Basic Science (IBS), Ulsan, Republic of Korea
| | - Maureen E Hoatlin
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Anja K Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Orlando Schärer
- Center for Genomic Integrity (CGI), Institute for Basic Science (IBS), Ulsan, Republic of Korea.,School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Alexandra Sobeck
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
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7
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Pires E, Sharma N, Selemenakis P, Wu B, Huang Y, Alimbetov DS, Zhao W, Wiese C. RAD51AP1 mediates RAD51 activity through nucleosome interaction. J Biol Chem 2021; 297:100844. [PMID: 34058198 PMCID: PMC8233230 DOI: 10.1016/j.jbc.2021.100844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 10/31/2022] Open
Abstract
RAD51-associated protein 1 (RAD51AP1) is a key protein in the homologous recombination (HR) DNA repair pathway. Loss of RAD51AP1 leads to defective HR, genome instability, and telomere erosion. RAD51AP1 physically interacts with the RAD51 recombinase and promotes RAD51-mediated capture of donor DNA, synaptic complex assembly, and displacement-loop formation when tested with nucleosome-free DNA substrates. In cells, however, DNA is packaged into chromatin, posing an additional barrier to the complexities of the HR reaction. In this study, we show that RAD51AP1 binds to nucleosome core particles (NCPs), the minimum basic unit of chromatin in which approximately two superhelical turns of 147 bp double-stranded DNA are wrapped around one histone octamer with no free DNA ends remaining. We identified a C-terminal region in RAD51AP1, including its previously mapped DNA-binding domain, as critical for mediating the association between RAD51AP1 and both the NCP and the histone octamer. Using in vitro surrogate assays of HR activity, we show that RAD51AP1 is capable of promoting duplex DNA capture and initiating joint-molecule formation with the NCP and chromatinized template DNA, respectively. Together, our results suggest that RAD51AP1 directly assists in the RAD51-mediated search for donor DNA in chromatin. We present a model, in which RAD51AP1 anchors the DNA template through affinity for its nucleosomes to the RAD51-ssDNA nucleoprotein filament.
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Affiliation(s)
- Elena Pires
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, USA; Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, Colorado, USA
| | - Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Platon Selemenakis
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, USA; Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, Colorado, USA
| | - Bo Wu
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Yuxin Huang
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Dauren S Alimbetov
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Claudia Wiese
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, USA.
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8
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Tye S, Ronson GE, Morris JR. A fork in the road: Where homologous recombination and stalled replication fork protection part ways. Semin Cell Dev Biol 2021; 113:14-26. [PMID: 32653304 PMCID: PMC8082280 DOI: 10.1016/j.semcdb.2020.07.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/06/2020] [Accepted: 07/06/2020] [Indexed: 12/14/2022]
Abstract
In response to replication hindrances, DNA replication forks frequently stall and are remodelled into a four-way junction. In such a structure the annealed nascent strand is thought to resemble a DNA double-strand break and remodelled forks are vulnerable to nuclease attack by MRE11 and DNA2. Proteins that promote the recruitment, loading and stabilisation of RAD51 onto single-stranded DNA for homology search and strand exchange in homologous recombination (HR) repair and inter-strand cross-link repair also act to set up RAD51-mediated protection of nascent DNA at stalled replication forks. However, despite the similarities of these pathways, several lines of evidence indicate that fork protection is not simply analogous to the RAD51 loading step of HR. Protection of stalled forks not only requires separate functions of a number of recombination proteins, but also utilises nucleases important for the resection steps of HR in alternative ways. Here we discuss how fork protection arises and how its differences with HR give insights into the differing contexts of these two pathways.
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Affiliation(s)
- Stephanie Tye
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
| | - George E Ronson
- University of Birmingham, College of Medical Dental Schools, Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Joanna R Morris
- University of Birmingham, College of Medical Dental Schools, Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK.
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9
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Tan W, van Twest S, Leis A, Bythell-Douglas R, Murphy VJ, Sharp M, Parker MW, Crismani W, Deans AJ. Monoubiquitination by the human Fanconi anemia core complex clamps FANCI:FANCD2 on DNA in filamentous arrays. eLife 2020; 9:e54128. [PMID: 32167469 PMCID: PMC7156235 DOI: 10.7554/elife.54128] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/12/2020] [Indexed: 12/24/2022] Open
Abstract
FANCI:FANCD2 monoubiquitination is a critical event for replication fork stabilization by the Fanconi anemia (FA) DNA repair pathway. It has been proposed that at stalled replication forks, monoubiquitinated-FANCD2 serves to recruit DNA repair proteins that contain ubiquitin-binding motifs. Here, we have reconstituted the FA pathway in vitro to study functional consequences of FANCI:FANCD2 monoubiquitination. We report that monoubiquitination does not promote any specific exogenous protein:protein interactions, but instead stabilizes FANCI:FANCD2 heterodimers on dsDNA. This clamping requires monoubiquitination of only the FANCD2 subunit. We further show using electron microscopy that purified monoubiquitinated FANCI:FANCD2 forms filament-like arrays on long dsDNA. Our results reveal how monoubiquitinated FANCI:FANCD2, defective in many cancer types and all cases of FA, is activated upon DNA binding.
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Affiliation(s)
- Winnie Tan
- Genome Stability Unit, St. Vincent’s Institute of Medical ResearchFitzroyAustralia
- Department of Medicine (St. Vincent’s Health), The University of MelbourneMelbourneAustralia
| | - Sylvie van Twest
- Genome Stability Unit, St. Vincent’s Institute of Medical ResearchFitzroyAustralia
| | - Andrew Leis
- Bio21 Institute, University of MelbourneParkvilleAustralia
| | | | - Vincent J Murphy
- Genome Stability Unit, St. Vincent’s Institute of Medical ResearchFitzroyAustralia
| | - Michael Sharp
- Genome Stability Unit, St. Vincent’s Institute of Medical ResearchFitzroyAustralia
| | - Michael W Parker
- Bio21 Institute, University of MelbourneParkvilleAustralia
- Structural Biology Unit, St. Vincent’s Institute of Medical ResearchFitzroyAustralia
| | - Wayne Crismani
- Genome Stability Unit, St. Vincent’s Institute of Medical ResearchFitzroyAustralia
- Department of Medicine (St. Vincent’s Health), The University of MelbourneMelbourneAustralia
| | - Andrew J Deans
- Genome Stability Unit, St. Vincent’s Institute of Medical ResearchFitzroyAustralia
- Department of Medicine (St. Vincent’s Health), The University of MelbourneMelbourneAustralia
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10
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Tissue-infiltrating macrophages mediate an exosome-based metabolic reprogramming upon DNA damage. Nat Commun 2020; 11:42. [PMID: 31896748 PMCID: PMC6940362 DOI: 10.1038/s41467-019-13894-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/04/2019] [Indexed: 12/26/2022] Open
Abstract
DNA damage and metabolic disorders are intimately linked with premature disease onset but the underlying mechanisms remain poorly understood. Here, we show that persistent DNA damage accumulation in tissue-infiltrating macrophages carrying an ERCC1-XPF DNA repair defect (Er1F/−) triggers Golgi dispersal, dilation of endoplasmic reticulum, autophagy and exosome biogenesis leading to the secretion of extracellular vesicles (EVs) in vivo and ex vivo. Macrophage-derived EVs accumulate in Er1F/− animal sera and are secreted in macrophage media after DNA damage. The Er1F/− EV cargo is taken up by recipient cells leading to an increase in insulin-independent glucose transporter levels, enhanced cellular glucose uptake, higher cellular oxygen consumption rate and greater tolerance to glucose challenge in mice. We find that high glucose in EV-targeted cells triggers pro-inflammatory stimuli via mTOR activation. This, in turn, establishes chronic inflammation and tissue pathology in mice with important ramifications for DNA repair-deficient, progeroid syndromes and aging. DNA damage is associated with metabolic disorders, but the mechanism in unclear. Here, the authors show that persistent DNA damage induced by lack of the endonuclease XPF-ERCC1 triggers extracellular vesicle biogenesis in tissue infiltrating macrophages, and that vesicle uptake stimulates glucose uptake in recipient cells, leading to increased inflammation.
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11
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Dubois EL, Guitton-Sert L, Béliveau M, Parmar K, Chagraoui J, Vignard J, Pauty J, Caron MC, Coulombe Y, Buisson R, Jacquet K, Gamblin C, Gao Y, Laprise P, Lebel M, Sauvageau G, D d'Andrea A, Masson JY. A Fanci knockout mouse model reveals common and distinct functions for FANCI and FANCD2. Nucleic Acids Res 2019; 47:7532-7547. [PMID: 31219578 PMCID: PMC6698648 DOI: 10.1093/nar/gkz514] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 05/22/2019] [Accepted: 06/05/2019] [Indexed: 12/12/2022] Open
Abstract
Fanconi Anemia (FA) clinical phenotypes are heterogenous and rely on a mutation in one of the 22 FANC genes (FANCA-W) involved in a common interstrand DNA crosslink-repair pathway. A critical step in the activation of FA pathway is the monoubiquitination of FANCD2 and its binding partner FANCI. To better address the clinical phenotype associated with FANCI and the epistatic relationship with FANCD2, we created the first conditional inactivation model for FANCI in mouse. Fanci −/− mice displayed typical FA features such as delayed development in utero, microphtalmia, cellular sensitivity to mitomycin C, occasional limb abnormalities and hematological deficiencies. Interestingly, the deletion of Fanci leads to a strong meiotic phenotype and severe hypogonadism. FANCI was localized in spermatocytes and spermatids and in the nucleus of oocytes. Both FANCI and FANCD2 proteins co-localized with RPA along meiotic chromosomes, albeit at different levels. Consistent with a role in meiotic recombination, FANCI interacted with RAD51 and stimulated D-loop formation, unlike FANCD2. The double knockout Fanci−/− Fancd2−/− also showed epistatic relationship for hematological defects while being not epistatic with respect to generating viable mice in crosses of double heterozygotes. Collectively, this study highlights common and distinct functions of FANCI and FANCD2 during mouse development, meiotic recombination and hematopoiesis.
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Affiliation(s)
- Emilie L Dubois
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Laure Guitton-Sert
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Mariline Béliveau
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Kalindi Parmar
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jalila Chagraoui
- Laboratory of Molecular Genetics of Hematopoietic Stem Cells, Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, H3C 3J7, Canada
| | - Julien Vignard
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Joris Pauty
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Marie-Christine Caron
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Yan Coulombe
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Rémi Buisson
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
| | - Karine Jacquet
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Clémence Gamblin
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Yuandi Gao
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Patrick Laprise
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Michel Lebel
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Guy Sauvageau
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
| | - Alan D d'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jean-Yves Masson
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada.,FRQS chair in genome stability
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12
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Okamoto Y, Iwasaki WM, Kugou K, Takahashi KK, Oda A, Sato K, Kobayashi W, Kawai H, Sakasai R, Takaori-Kondo A, Yamamoto T, Kanemaki MT, Taoka M, Isobe T, Kurumizaka H, Innan H, Ohta K, Ishiai M, Takata M. Replication stress induces accumulation of FANCD2 at central region of large fragile genes. Nucleic Acids Res 2019; 46:2932-2944. [PMID: 29394375 PMCID: PMC5888676 DOI: 10.1093/nar/gky058] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/20/2018] [Indexed: 12/20/2022] Open
Abstract
During mild replication stress provoked by low dose aphidicolin (APH) treatment, the key Fanconi anemia protein FANCD2 accumulates on common fragile sites, observed as sister foci, and protects genome stability. To gain further insights into FANCD2 function and its regulatory mechanisms, we examined the genome-wide chromatin localization of FANCD2 in this setting by ChIP-seq analysis. We found that FANCD2 mostly accumulates in the central regions of a set of large transcribed genes that were extensively overlapped with known CFS. Consistent with previous studies, we found that this FANCD2 retention is R-loop-dependent. However, FANCD2 monoubiquitination and RPA foci formation were still induced in cells depleted of R-loops. Interestingly, we detected increased Proximal Ligation Assay dots between FANCD2 and R-loops following APH treatment, which was suppressed by transcriptional inhibition. Collectively, our data suggested that R-loops are required to retain FANCD2 in chromatin at the middle intronic region of large genes, while the replication stress-induced upstream events leading to the FA pathway activation are not triggered by R-loops.
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Affiliation(s)
- Yusuke Okamoto
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan.,Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Watal M Iwasaki
- SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Kazuto Kugou
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Arisa Oda
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Koichi Sato
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Wataru Kobayashi
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Hidehiko Kawai
- Department of Molecular Radiobiology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Ryo Sakasai
- Department of Biochemistry I, School of Medicine, Kanazawa Medical University, Ishikawa, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan
| | - Masato T Kanemaki
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka, Japan.,Department of Genetics, SOKENDAI, Shizuoka, Japan
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Hideki Innan
- SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Masamichi Ishiai
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan
| | - Minoru Takata
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan
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13
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FANCD2 Binding to H4K20me2 via a Methyl-Binding Domain Is Essential for Efficient DNA Cross-Link Repair. Mol Cell Biol 2019; 39:MCB.00194-19. [PMID: 31085681 DOI: 10.1128/mcb.00194-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/06/2019] [Indexed: 01/02/2023] Open
Abstract
Fanconi anemia (FA) is an inherited disease characterized by bone marrow failure and increased cancer risk. FA is caused by mutation of any 1 of 22 genes, and the FA proteins function cooperatively to repair DNA interstrand cross-links (ICLs). A central step in the activation of the FA pathway is the monoubiquitination of the FANCD2 and FANCI proteins, which occurs within chromatin. How FANCD2 and FANCI are anchored to chromatin remains unknown. In this study, we identify and characterize a FANCD2 histone-binding domain (HBD) and embedded methyl-lysine-binding domain (MBD) and demonstrate binding specificity for H4K20me2. Disruption of the HBD/MBD compromises FANCD2 chromatin binding and nuclear focus formation and its ability to promote error-free DNA interstrand cross-link repair, leading to increased error-prone repair and genome instability. Our study functionally describes the first FA protein chromatin reader domain and establishes an important link between this human genetic disease and chromatin plasticity.
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14
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Begum S, Goula A, Bayley R, Higgs MR. On your marks, get SET(D1A): the race to protect stalled replication forks. Mol Cell Oncol 2018; 5:e1511209. [PMID: 30525090 PMCID: PMC6276854 DOI: 10.1080/23723556.2018.1511209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 08/01/2018] [Accepted: 08/09/2018] [Indexed: 11/25/2022]
Abstract
We recently identified that methylation of lysine 4 of histone H3 (H3K4) by SETD1A (SET domain containing 1A) maintains genome stability by protecting newly-replicated DNA from degradation. Mechanistically, SETD1A-dependent histone methylation regulates nucleosome mobilisation by FANCD2 (FA complementation group D2), a crucial step in maintaining genome integrity with important implications in chemo-sensitivity.
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Affiliation(s)
- Shabana Begum
- Lysine Methylation and DNA Damage Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Amalia Goula
- Lysine Methylation and DNA Damage Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Rachel Bayley
- Lysine Methylation and DNA Damage Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Martin R Higgs
- Lysine Methylation and DNA Damage Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
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15
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Histone Methylation by SETD1A Protects Nascent DNA through the Nucleosome Chaperone Activity of FANCD2. Mol Cell 2018; 71:25-41.e6. [PMID: 29937342 PMCID: PMC6039718 DOI: 10.1016/j.molcel.2018.05.018] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/20/2018] [Accepted: 05/15/2018] [Indexed: 12/20/2022]
Abstract
Components of the Fanconi anemia and homologous recombination pathways play a vital role in protecting newly replicated DNA from uncontrolled nucleolytic degradation, safeguarding genome stability. Here we report that histone methylation by the lysine methyltransferase SETD1A is crucial for protecting stalled replication forks from deleterious resection. Depletion of SETD1A sensitizes cells to replication stress and leads to uncontrolled DNA2-dependent resection of damaged replication forks. The ability of SETD1A to prevent degradation of these structures is mediated by its ability to catalyze methylation on Lys4 of histone H3 (H3K4) at replication forks, which enhances FANCD2-dependent histone chaperone activity. Suppressing H3K4 methylation or expression of a chaperone-defective FANCD2 mutant leads to loss of RAD51 nucleofilament stability and severe nucleolytic degradation of replication forks. Our work identifies epigenetic modification and histone mobility as critical regulatory mechanisms in maintaining genome stability by restraining nucleases from irreparably damaging stalled replication forks. Methylation of H3K4 by SETD1A maintains genome stability during replication stress SETD1A and H3K4 methylation stabilize RAD51 nucleofilaments to protect nascent DNA SETD1A-dependent H3K4 methylation enhances FANCD2-dependent histone remodeling Histone mobility stabilizes RAD51 nucleofilaments to inhibit fork degradation
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16
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Kim HM, Beese-Sims SE, Colaiácovo MP. Fanconi Anemia FANCM/FNCM-1 and FANCD2/FCD-2 Are Required for Maintaining Histone Methylation Levels and Interact with the Histone Demethylase LSD1/SPR-5 in Caenorhabditis elegans. Genetics 2018; 209:409-423. [PMID: 29588287 PMCID: PMC5972417 DOI: 10.1534/genetics.118.300823] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 03/22/2018] [Indexed: 11/18/2022] Open
Abstract
The histone demethylase LSD1 was originally discovered by removing methyl groups from di- and monomethylated histone H3 lysine 4 (H3K4me2/1). Several studies suggest that LSD1 plays roles in meiosis as well as in the epigenetic regulation of fertility given that, in its absence, there is evidence of a progressive accumulation of H3K4me2 and increased sterility through generations. In addition to the progressive sterility phenotype observed in the mutants, growing evidence for the importance of histone methylation in the regulation of DNA damage repair has attracted more attention to the field in recent years. However, we are still far from understanding the mechanisms by which histone methylation is involved in DNA damage repair, and only a few studies have focused on the roles of histone demethylases in germline maintenance. Here, we show that the histone demethylase LSD1/CeSPR-5 interacts with the Fanconi anemia (FA) protein FANCM/CeFNCM-1 using biochemical, cytological, and genetic analyses. LSD1/CeSPR-5 is required for replication stress-induced S phase-checkpoint activation, and its absence suppresses the embryonic lethality and larval arrest observed in fncm-1 mutants. FANCM/CeFNCM-1 relocalizes upon hydroxyurea exposure and colocalizes with FANCD2/CeFCD-2 and LSD1/CeSPR-5, suggesting coordination between this histone demethylase and FA components to resolve replication stress. Surprisingly, the FA pathway is required for H3K4me2 maintenance, regardless of the presence of replication stress. Our study reveals a connection between FA and epigenetic maintenance and therefore provides new mechanistic insight into the regulation of histone methylation in DNA repair.
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Affiliation(s)
- Hyun-Min Kim
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
- School of Pharmaceutical Science and Technology, Tianjin University, 300072, China
| | - Sara E Beese-Sims
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
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17
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Zhang Y, Chang JF, Sun J, Chen L, Yang XM, Tang HY, Jing YY, Kang X, He ZM, Wu JY, Wei HM, Wang DL, Xu RG, Zhu RB, Shen Y, Zeng SY, Wang C, Liu KN, Zhang Y, Mao ZY, Jiang CZ, Sun FL. Histone H3K27 methylation is required for NHEJ and genome stability by modulating the dynamics of FANCD2 on chromatin. J Cell Sci 2018; 131:jcs.215525. [PMID: 29760279 DOI: 10.1242/jcs.215525] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/24/2018] [Indexed: 12/13/2022] Open
Abstract
Dysregulation of homeostatic balance in di- and tri-methyl H3K27 levels or that caused by mis-sense mutations of histone H3 (H3K27M) was reported to be associated with various types of cancers. In this study, we found that reduction in H3K27me2/3 caused by H3.1K27M, a mutation of H3 variants found in DIPG patients, dramatically attenuated the presence of 53BP1 foci and NHEJ repair capability in HDF cells. H3.1K27M cells showed increased rates of genomic insertions/deletions (In/Dels) and copy number variations (CNVs), as well as augmented p53-dependent apoptotic cells. We further showed that both hypo-H3K27me2/3 and H3.1K27M interacted with FANCD2, a central player to orchestrate DNA repair pathway choice. H3.1K27M triggered an accumulation of FANCD2 on chromatin, supporting the interaction between H3.1K27M and FANCD2. Most interestingly, knock-down of FANCD2 in H3.1K27M cells recovered the number of 53BP1 foci, NHEJ efficiency and apoptosis rate. Although these findings in HDF cells may differ from the case of endogenous H3.1K27M mutant regulation in the specific tumor context of DIPG, our results suggest a new model by which H3K27me2/3 facilitates NHEJ and the maintenance of genome stability.
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Affiliation(s)
- Ye Zhang
- School of Medicine, Tsinghua University, Beijing 100084, PR China
| | - Jian-Feng Chang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Jin Sun
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Lu Chen
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Xiao-Mei Yang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Huan-Yin Tang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Yuan-Ya Jing
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Xuan Kang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Zhi-Min He
- School of Medicine, Tsinghua University, Beijing 100084, PR China
| | - Jun-Yu Wu
- School of Medicine, Tsinghua University, Beijing 100084, PR China
| | - Hui-Min Wei
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Da-Liang Wang
- School of Medicine, Tsinghua University, Beijing 100084, PR China
| | - Rong-Gang Xu
- School of Medicine, Tsinghua University, Beijing 100084, PR China
| | - Rui-Bao Zhu
- School of Medicine, Tsinghua University, Beijing 100084, PR China
| | - Ying Shen
- School of Software Engineering, Tongji University, Shanghai 200092, PR China
| | - Shi-Yang Zeng
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Chen Wang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Kui-Nan Liu
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Yong Zhang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Zhi-Ying Mao
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Ci-Zhong Jiang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Fang-Lin Sun
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
- School of Medicine, Tsinghua University, Beijing 100084, PR China
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18
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Alavattam KG, Kato Y, Sin HS, Maezawa S, Kowalski IJ, Zhang F, Pang Q, Andreassen PR, Namekawa SH. Elucidation of the Fanconi Anemia Protein Network in Meiosis and Its Function in the Regulation of Histone Modifications. Cell Rep 2017; 17:1141-1157. [PMID: 27760317 PMCID: PMC5095620 DOI: 10.1016/j.celrep.2016.09.073] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 08/17/2016] [Accepted: 09/21/2016] [Indexed: 01/14/2023] Open
Abstract
Precise epigenetic regulation of the sex chromosomes is vital for the male germline. Here, we analyze meiosis in eight mouse models deficient for various DNA damage response (DDR) factors, including Fanconi anemia (FA) proteins. We reveal a network of FA and DDR proteins in which FA core factors FANCA, FANCB, and FANCC are essential for FANCD2 foci formation, whereas BRCA1 (FANCS), MDC1, and RNF8 are required for BRCA2 (FANCD1) and SLX4 (FANCP) accumulation on the sex chromosomes during meiosis. In addition, FA proteins modulate distinct histone marks on the sex chromosomes: FA core proteins and FANCD2 regulate H3K9 methylation, while FANCD2 and RNF8 function together to regulate H3K4 methylation independently of FA core proteins. Our data suggest that RNF8 integrates the FA-BRCA pathway. Taken together, our study reveals distinct functions for FA proteins and illuminates the male sex chromosomes as a model to dissect the function of the FA-BRCA pathway.
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Affiliation(s)
- Kris G Alavattam
- Division of Reproductive Sciences and Division of Developmental Biology, Perinatal Institute, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49229, USA
| | - Yasuko Kato
- Division of Reproductive Sciences and Division of Developmental Biology, Perinatal Institute, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49229, USA
| | - Ho-Su Sin
- Division of Reproductive Sciences and Division of Developmental Biology, Perinatal Institute, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49229, USA
| | - So Maezawa
- Division of Reproductive Sciences and Division of Developmental Biology, Perinatal Institute, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49229, USA
| | - Ian J Kowalski
- Division of Reproductive Sciences and Division of Developmental Biology, Perinatal Institute, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49229, USA
| | - Fan Zhang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49229, USA
| | - Qishen Pang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49229, USA
| | - Paul R Andreassen
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49229, USA
| | - Satoshi H Namekawa
- Division of Reproductive Sciences and Division of Developmental Biology, Perinatal Institute, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49229, USA.
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19
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Moriel-Carretero M, Ovejero S, Gérus-Durand M, Vryzas D, Constantinou A. Fanconi anemia FANCD2 and FANCI proteins regulate the nuclear dynamics of splicing factors. J Cell Biol 2017; 216:4007-4026. [PMID: 29030393 PMCID: PMC5716273 DOI: 10.1083/jcb.201702136] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 08/02/2017] [Accepted: 08/25/2017] [Indexed: 01/20/2023] Open
Abstract
Moriel-Carretero et al. show that the Fanconi anemia proteins FANCI and FANCD2 associate with the splicing factor SF3B1 and that DNA replication stress induces the FANCI-dependent release of SF3B1 from nuclear speckles. FANCI and FANCD2 prevent accumulation of postcatalytic intron lariats, suggesting that they help coordinate DNA replication and transcription. Proteins disabled in the cancer-prone disorder Fanconi anemia (FA) ensure the maintenance of chromosomal stability during DNA replication. FA proteins regulate replication dynamics, coordinate replication-coupled repair of interstrand DNA cross-links, and mitigate conflicts between replication and transcription. Here we show that FANCI and FANCD2 associate with splicing factor 3B1 (SF3B1), a key spliceosomal protein of the U2 small nuclear ribonucleoprotein (U2 snRNP). FANCI is in close proximity to SF3B1 in the nucleoplasm of interphase and mitotic cells. Furthermore, we find that DNA replication stress induces the release of SF3B1 from nuclear speckles in a manner that depends on FANCI and on the activity of the checkpoint kinase ATR. In chromatin, both FANCD2 and FANCI associate with SF3B1, prevent accumulation of postcatalytic intron lariats, and contribute to the timely eviction of splicing factors. We propose that FANCD2 and FANCI contribute to the organization of functional domains in chromatin, ensuring the coordination of DNA replication and cotranscriptional processes.
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Affiliation(s)
- María Moriel-Carretero
- Institute of Human Genetics, Centre National de la Recherche Scientifique UMR 9002, Université de Montpellier, Montpellier, France
| | - Sara Ovejero
- Institute of Human Genetics, Centre National de la Recherche Scientifique UMR 9002, Université de Montpellier, Montpellier, France
| | - Marie Gérus-Durand
- Institute of Human Genetics, Centre National de la Recherche Scientifique UMR 9002, Université de Montpellier, Montpellier, France
| | - Dimos Vryzas
- Institute of Human Genetics, Centre National de la Recherche Scientifique UMR 9002, Université de Montpellier, Montpellier, France
| | - Angelos Constantinou
- Institute of Human Genetics, Centre National de la Recherche Scientifique UMR 9002, Université de Montpellier, Montpellier, France
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20
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Inano S, Sato K, Katsuki Y, Kobayashi W, Tanaka H, Nakajima K, Nakada S, Miyoshi H, Knies K, Takaori-Kondo A, Schindler D, Ishiai M, Kurumizaka H, Takata M. RFWD3-Mediated Ubiquitination Promotes Timely Removal of Both RPA and RAD51 from DNA Damage Sites to Facilitate Homologous Recombination. Mol Cell 2017; 66:622-634.e8. [PMID: 28575658 DOI: 10.1016/j.molcel.2017.04.022] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 01/28/2017] [Accepted: 04/26/2017] [Indexed: 12/12/2022]
Abstract
RFWD3 is a recently identified Fanconi anemia protein FANCW whose E3 ligase activity toward RPA is essential in homologous recombination (HR) repair. However, how RPA ubiquitination promotes HR remained unknown. Here, we identified RAD51, the central HR protein, as another target of RFWD3. We show that RFWD3 polyubiquitinates both RPA and RAD51 in vitro and in vivo. Phosphorylation by ATR and ATM kinases is required for this activity in vivo. RFWD3 inhibits persistent mitomycin C (MMC)-induced RAD51 and RPA foci by promoting VCP/p97-mediated protein dynamics and subsequent degradation. Furthermore, MMC-induced chromatin loading of MCM8 and RAD54 is defective in cells with inactivated RFWD3 or expressing a ubiquitination-deficient mutant RAD51. Collectively, our data reveal a mechanism that facilitates timely removal of RPA and RAD51 from DNA damage sites, which is crucial for progression to the late-phase HR and suppression of the FA phenotype.
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Affiliation(s)
- Shojiro Inano
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto 606-8501, Japan; Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Koichi Sato
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 169-8050, Japan
| | - Yoko Katsuki
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto 606-8501, Japan
| | - Wataru Kobayashi
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 169-8050, Japan
| | - Hiroki Tanaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 169-8050, Japan
| | - Kazuhiro Nakajima
- Department of Bioregulation and Cellular Response, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Shinichiro Nakada
- Department of Bioregulation and Cellular Response, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan; Institute for Advanced Co-Creation Studies, Osaka University, Osaka 565-0871, Japan
| | - Hiroyuki Miyoshi
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kerstin Knies
- Department of Human Genetics, Biozentrum, University of Wurzburg, 97074 Wurzburg, Germany
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Detlev Schindler
- Department of Human Genetics, Biozentrum, University of Wurzburg, 97074 Wurzburg, Germany
| | - Masamichi Ishiai
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto 606-8501, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 169-8050, Japan
| | - Minoru Takata
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto 606-8501, Japan.
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21
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Madireddy A, Kosiyatrakul ST, Boisvert RA, Herrera-Moyano E, García-Rubio ML, Gerhardt J, Vuono EA, Owen N, Yan Z, Olson S, Aguilera A, Howlett NG, Schildkraut CL. FANCD2 Facilitates Replication through Common Fragile Sites. Mol Cell 2017; 64:388-404. [PMID: 27768874 DOI: 10.1016/j.molcel.2016.09.017] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 08/08/2016] [Accepted: 09/14/2016] [Indexed: 12/27/2022]
Abstract
Common fragile sites (CFSs) are genomic regions that are unstable under conditions of replicative stress. Although the characteristics of CFSs that render them vulnerable to stress are associated mainly with replication, the cellular pathways that protect CFSs during replication remain unclear. Here, we identify and describe a role for FANCD2 as a trans-acting facilitator of CFS replication, in the absence of exogenous replicative stress. In the absence of FANCD2, replication forks stall within the AT-rich fragility core of CFS, leading to dormant origin activation. Furthermore, FANCD2 deficiency is associated with DNA:RNA hybrid formation at CFS-FRA16D, and inhibition of DNA:RNA hybrid formation suppresses replication perturbation. In addition, we also found that FANCD2 reduces the number of potential sites of replication initiation. Our data demonstrate that FANCD2 protein is required to ensure efficient CFS replication and provide mechanistic insight into how FANCD2 regulates CFS stability.
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Affiliation(s)
- Advaitha Madireddy
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | | | - Rebecca A Boisvert
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
| | - Emilia Herrera-Moyano
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, Universidad de Sevilla, 41092 Seville, Spain
| | - María L García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, Universidad de Sevilla, 41092 Seville, Spain
| | - Jeannine Gerhardt
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Elizabeth A Vuono
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
| | - Nichole Owen
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Zi Yan
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Susan Olson
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, Universidad de Sevilla, 41092 Seville, Spain
| | - Niall G Howlett
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
| | - Carl L Schildkraut
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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22
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Ishiai M, Sato K, Tomida J, Kitao H, Kurumizaka H, Takata M. Activation of the FA pathway mediated by phosphorylation and ubiquitination. Mutat Res 2017; 803-805:89-95. [PMID: 28552166 DOI: 10.1016/j.mrfmmm.2017.05.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 05/04/2017] [Accepted: 05/04/2017] [Indexed: 12/15/2022]
Abstract
Fanconi anemia (FA) is a devastating hereditary condition that impacts genome integrity, leading to clinical features such as skeletal and visceral organ malformations, attrition of bone marrow stem cells, and carcinogenesis. At least 21 proteins, when absent or defective, have been implicated in this disorder, and they together constitute the FA pathway, which functions in detection and repair of, and tolerance to, endogenous DNA damage. The damage primarily handled by the FA pathway has been assumed to be related to DNA interstrand crosslinks (ICLs). The FA pathway is activated upon ICL damage, and a hallmark of this activation is the mono-ubiquitination events of the key FANCD2-FANCI protein complex. Recent data have revealed unexpectedly complex details in the regulation of FA pathway activation by ICLs. In this short review, we summarize the knowledge accumulated over the years regarding how the FA pathway is activated via protein modifications.
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Affiliation(s)
- Masamichi Ishiai
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan
| | - Koichi Sato
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Junya Tomida
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan
| | - Hiroyuki Kitao
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
| | - Minoru Takata
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan.
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23
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Yang Z, Nejad MI, Varela JG, Price NE, Wang Y, Gates KS. A role for the base excision repair enzyme NEIL3 in replication-dependent repair of interstrand DNA cross-links derived from psoralen and abasic sites. DNA Repair (Amst) 2017; 52:1-11. [PMID: 28262582 PMCID: PMC5424475 DOI: 10.1016/j.dnarep.2017.02.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 02/13/2017] [Indexed: 12/23/2022]
Abstract
Interstrand DNA-DNA cross-links are highly toxic lesions that are important in medicinal chemistry, toxicology, and endogenous biology. In current models of replication-dependent repair, stalling of a replication fork activates the Fanconi anemia pathway and cross-links are "unhooked" by the action of structure-specific endonucleases such as XPF-ERCC1 that make incisions flanking the cross-link. This process generates a double-strand break, which must be subsequently repaired by homologous recombination. Recent work provided evidence for a new, incision-independent unhooking mechanism involving intrusion of a base excision repair (BER) enzyme, NEIL3, into the world of cross-link repair. The evidence suggests that the glycosylase action of NEIL3 unhooks interstrand cross-links derived from an abasic site or the psoralen derivative trioxsalen. If the incision-independent NEIL3 pathway is blocked, repair reverts to the incision-dependent route. In light of the new model invoking participation of NEIL3 in cross-link repair, we consider the possibility that various BER glycosylases or other DNA-processing enzymes might participate in the unhooking of chemically diverse interstrand DNA cross-links.
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Affiliation(s)
- Zhiyu Yang
- University of Missouri Department of Chemistry, 125 Chemistry Building Columbia, MO 65211, United States
| | - Maryam Imani Nejad
- University of Missouri Department of Chemistry, 125 Chemistry Building Columbia, MO 65211, United States
| | - Jacqueline Gamboa Varela
- University of Missouri Department of Chemistry, 125 Chemistry Building Columbia, MO 65211, United States
| | - Nathan E Price
- University of California-Riverside, Department of Chemistry, 501 Big Springs Road Riverside, CA 92521-0403, United States
| | - Yinsheng Wang
- University of California-Riverside, Department of Chemistry, 501 Big Springs Road Riverside, CA 92521-0403, United States
| | - Kent S Gates
- University of Missouri Department of Chemistry, 125 Chemistry Building Columbia, MO 65211, United States; University of Missouri Department of Biochemistry, 125 Chemistry Building Columbia, MO 65211, United States.
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24
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A defined role for multiple Fanconi anemia gene products in DNA-damage-associated ubiquitination. Exp Hematol 2017; 50:27-32. [PMID: 28315701 DOI: 10.1016/j.exphem.2017.03.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 12/13/2022]
Abstract
Fanconi anemia (FA) is an inherited blood disorder that causes bone marrow failure and high predisposition to cancers. The FA pathway guards the cell's genome stability by orchestrating the repair of interstrand cross-linking during the S phase of the cell cycle, preventing the chromosomal instability that is a key event in bone marrow failure syndrome. Central to the FA pathway is loss of monoubiquitinated forms of the Fanconi proteins FANCI and FANCD2, a process that is normally mediated by a "core complex" of seven other Fanconi proteins. Each protein, when mutated, can cause FA. The FA core-complex-catalyzed reaction is critical for signaling DNA cross-link damage such as that induced by chemotherapies. Here, we present a perspective on the current understanding of FANCI and FANCD2 monoubiquitination-mediated DNA repair. Our recent biochemical reconstitution of the monoubiquitination (and deubiquitination) reactions creates a paradigm for understanding FA. Further biochemical analysis will create new opportunities to address the leukemic phenotype of FA patients.
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25
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Bloom syndrome complex promotes FANCM recruitment to stalled replication forks and facilitates both repair and traverse of DNA interstrand crosslinks. Cell Discov 2016; 2:16047. [PMID: 28058110 PMCID: PMC5167996 DOI: 10.1038/celldisc.2016.47] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/10/2016] [Indexed: 12/26/2022] Open
Abstract
The recruitment of FANCM, a conserved DNA translocase and key component of several DNA repair protein complexes, to replication forks stalled by DNA interstrand crosslinks (ICLs) is a step upstream of the Fanconi anemia (FA) repair and replication traverse pathways of ICLs. However, detection of the FANCM recruitment has been technically challenging so that its mechanism remains exclusive. Here, we successfully observed recruitment of FANCM at stalled forks using a newly developed protocol. We report that the FANCM recruitment depends upon its intrinsic DNA translocase activity, and its DNA-binding partner FAAP24. Moreover, it is dependent on the replication checkpoint kinase, ATR; but is independent of the FA core and FANCD2-FANCI complexes, two essential components of the FA pathway, indicating that the FANCM recruitment occurs downstream of ATR but upstream of the FA pathway. Interestingly, the recruitment of FANCM requires its direct interaction with Bloom syndrome complex composed of BLM helicase, Topoisomerase 3α, RMI1 and RMI2; as well as the helicase activity of BLM. We further show that the FANCM-BLM complex interaction is critical for replication stress-induced FANCM hyperphosphorylation, for normal activation of the FA pathway in response to ICLs, and for efficient traverse of ICLs by the replication machinery. Epistasis studies demonstrate that FANCM and BLM work in the same pathway to promote replication traverse of ICLs. We conclude that FANCM and BLM complex work together at stalled forks to promote both FA repair and replication traverse pathways of ICLs.
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26
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Swuec P, Renault L, Borg A, Shah F, Murphy VJ, van Twest S, Snijders AP, Deans AJ, Costa A. The FA Core Complex Contains a Homo-dimeric Catalytic Module for the Symmetric Mono-ubiquitination of FANCI-FANCD2. Cell Rep 2016; 18:611-623. [PMID: 27986592 PMCID: PMC5266791 DOI: 10.1016/j.celrep.2016.11.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/22/2016] [Accepted: 10/31/2016] [Indexed: 12/20/2022] Open
Abstract
Activation of the main DNA interstrand crosslink repair pathway in higher eukaryotes requires mono-ubiquitination of FANCI and FANCD2 by FANCL, the E3 ligase subunit of the Fanconi anemia core complex. FANCI and FANCD2 form a stable complex; however, the molecular basis of their ubiquitination is ill defined. FANCD2 mono-ubiquitination by FANCL is stimulated by the presence of the FANCB and FAAP100 core complex components, through an unknown mechanism. How FANCI mono-ubiquitination is achieved remains unclear. Here, we use structural electron microscopy, combined with crosslink-coupled mass spectrometry, to find that FANCB, FANCL, and FAAP100 form a dimer of trimers, containing two FANCL molecules that are ideally poised to target both FANCI and FANCD2 for mono-ubiquitination. The FANCC-FANCE-FANCF subunits bridge between FANCB-FANCL-FAAP100 and the FANCI-FANCD2 substrate. A transient interaction with FANCC-FANCE-FANCF alters the FANCI-FANCD2 configuration, stabilizing the dimerization interface. Our data provide a model to explain how equivalent mono-ubiquitination of FANCI and FANCD2 occurs. FANCB, FANCL, and FAAP100 form a symmetric dimer of trimers FANCL is ideally poised for the symmetric mono-ubiquitination of FANCI-FANCD2 Two separate FANCC-FANCE-FANCF complexes bind to the opposing poles of FANCB-FANCL-FAAP100 FANCC-FANCE-FANCF stabilizes FANCI-FANCD2 for efficient mono-ubiquitination
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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
| | - Ludovic Renault
- Macromolecular Machines Laboratory, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Aaron Borg
- Mass Spectrometry Proteomics and Metabolomics, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Fenil Shah
- Genome Stability Unit, St. Vincent's Institute of Medical Research, 9 Princes St Fitzroy, Victoria, VIC 3065, Australia
| | - Vincent J Murphy
- Genome Stability Unit, St. Vincent's Institute of Medical Research, 9 Princes St Fitzroy, Victoria, VIC 3065, Australia
| | - Sylvie van Twest
- Genome Stability Unit, St. Vincent's Institute of Medical Research, 9 Princes St Fitzroy, Victoria, VIC 3065, Australia
| | - Ambrosius P Snijders
- Mass Spectrometry Proteomics and Metabolomics, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Andrew J Deans
- Genome Stability Unit, St. Vincent's Institute of Medical Research, 9 Princes St Fitzroy, Victoria, VIC 3065, Australia
| | - Alessandro Costa
- Macromolecular Machines Laboratory, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK.
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27
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Katsuki Y, Takata M. Defects in homologous recombination repair behind the human diseases: FA and HBOC. Endocr Relat Cancer 2016; 23:T19-37. [PMID: 27550963 DOI: 10.1530/erc-16-0221] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 08/22/2016] [Indexed: 12/25/2022]
Abstract
Hereditary breast and ovarian cancer (HBOC) syndrome and a rare childhood disorder Fanconi anemia (FA) are caused by homologous recombination (HR) defects, and some of the causative genes overlap. Recent studies in this field have led to the exciting development of PARP inhibitors as novel cancer therapeutics and have clarified important mechanisms underlying genome instability and tumor suppression in HR-defective disorders. In this review, we provide an overview of the basic molecular mechanisms governing HR and DNA crosslink repair, highlighting BRCA2, and the intriguing relationship between HBOC and FA.
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Affiliation(s)
- Yoko Katsuki
- Laboratory of DNA Damage SignalingDepartment of Late Effects Studies, Radiation Biology Center, Kyoto University, Yoshidakonoecho, Sakyo-ku, Kyoto, Japan
| | - Minoru Takata
- Laboratory of DNA Damage SignalingDepartment of Late Effects Studies, Radiation Biology Center, Kyoto University, Yoshidakonoecho, Sakyo-ku, Kyoto, Japan
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28
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Sato K, Shimomuki M, Katsuki Y, Takahashi D, Kobayashi W, Ishiai M, Miyoshi H, Takata M, Kurumizaka H. FANCI-FANCD2 stabilizes the RAD51-DNA complex by binding RAD51 and protects the 5'-DNA end. Nucleic Acids Res 2016; 44:10758-10771. [PMID: 27694619 PMCID: PMC5159555 DOI: 10.1093/nar/gkw876] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 08/22/2016] [Accepted: 09/21/2016] [Indexed: 01/12/2023] Open
Abstract
The FANCI-FANCD2 (I-D) complex is considered to work with RAD51 to protect the damaged DNA in the stalled replication fork. However, the means by which this DNA protection is accomplished have remained elusive. In the present study, we found that the I-D complex directly binds to RAD51, and stabilizes the RAD51-DNA filament. Unexpectedly, the DNA binding activity of FANCI, but not FANCD2, is explicitly required for the I-D complex-mediated RAD51-DNA filament stabilization. The RAD51 filament stabilized by the I-D complex actually protects the DNA end from nucleolytic degradation by an FA-associated nuclease, FAN1. This DNA end protection is not observed with the RAD51 mutant from FANCR patient cells. These results clearly answer the currently enigmatic question of how RAD51 functions with the I-D complex to prevent genomic instability at the stalled replication fork.
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Affiliation(s)
- Koichi Sato
- Laboratory of Structural Biology, Graduate School of Advanced Science & Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Mayo Shimomuki
- Laboratory of Structural Biology, Graduate School of Advanced Science & Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yoko Katsuki
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto 606-8501, Japan
| | - Daisuke Takahashi
- Laboratory of Structural Biology, Graduate School of Advanced Science & Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Wataru Kobayashi
- Laboratory of Structural Biology, Graduate School of Advanced Science & Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Masamichi Ishiai
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto 606-8501, Japan
| | - Hiroyuki Miyoshi
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Minoru Takata
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto 606-8501, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science & Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan .,Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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29
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Sato Y, Kujirai T, Arai R, Asakawa H, Ohtsuki C, Horikoshi N, Yamagata K, Ueda J, Nagase T, Haraguchi T, Hiraoka Y, Kimura A, Kurumizaka H, Kimura H. A Genetically Encoded Probe for Live-Cell Imaging of H4K20 Monomethylation. J Mol Biol 2016; 428:3885-3902. [PMID: 27534817 DOI: 10.1016/j.jmb.2016.08.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 08/04/2016] [Accepted: 08/05/2016] [Indexed: 01/28/2023]
Abstract
Eukaryotic gene expression is regulated in the context of chromatin. Dynamic changes in post-translational histone modification are thought to play key roles in fundamental cellular functions such as regulation of the cell cycle, development, and differentiation. To elucidate the relationship between histone modifications and cellular functions, it is important to monitor the dynamics of modifications in single living cells. A genetically encoded probe called mintbody (modification-specific intracellular antibody), which is a single-chain variable fragment tagged with a fluorescent protein, has been proposed as a useful visualization tool. However, the efficacy of intracellular expression of antibody fragments has been limited, in part due to different environmental conditions in the cytoplasm compared to the endoplasmic reticulum where secreted proteins such as antibodies are folded. In this study, we have developed a new mintbody specific for histone H4 Lys20 monomethylation (H4K20me1). The specificity of the H4K20me1-mintbody in living cells was verified using yeast mutants and mammalian cells in which this target modification was diminished. Expression of the H4K20me1-mintbody allowed us to monitor the oscillation of H4K20me1 levels during the cell cycle. Moreover, dosage-compensated X chromosomes were visualized using the H4K20me1-mintbody in mouse and nematode cells. Using X-ray crystallography and mutational analyses, we identified critical amino acids that contributed to stabilization and/or proper folding of the mintbody. Taken together, these data provide important implications for future studies aimed at developing functional intracellular antibodies. Specifically, the H4K20me1-mintbody provides a powerful tool to track this particular histone modification in living cells and organisms.
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Affiliation(s)
- Yuko Sato
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Tomoya Kujirai
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Ritsuko Arai
- Cell Architecture Laboratory, Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Haruhiko Asakawa
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Chizuru Ohtsuki
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Naoki Horikoshi
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Kazuo Yamagata
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa City, Wakayama 649-6493, Japan
| | - Jun Ueda
- Center for Education in Laboratory Animal Research, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Takahiro Nagase
- Public Relations Team, Kazusa DNA Research Institute, Chiba 292-0818, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan; Advanced ICT Research Institute, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan; Advanced ICT Research Institute, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan
| | - Akatsuki Kimura
- Cell Architecture Laboratory, Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiroshi Kimura
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
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30
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Tripathi AK, Pareek A, Singla-Pareek SL. A NAP-Family Histone Chaperone Functions in Abiotic Stress Response and Adaptation. PLANT PHYSIOLOGY 2016; 171:2854-68. [PMID: 27342307 PMCID: PMC4972273 DOI: 10.1104/pp.16.00408] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/20/2016] [Indexed: 05/20/2023]
Abstract
Modulation of gene expression is one of the most significant molecular mechanisms of abiotic stress response in plants. Via altering DNA accessibility, histone chaperones affect the transcriptional competence of genomic loci. However, in contrast to other factors affecting chromatin dynamics, the role of plant histone chaperones in abiotic stress response and adaptation remains elusive. Here, we studied the physiological function of a stress-responsive putative rice (Oryza sativa) histone chaperone of the NAP superfamily: OsNAPL6. We show that OsNAPL6 is a nuclear-localized H3/H4 histone chaperone capable of assembling a nucleosome-like structure. Utilizing overexpression and knockdown approaches, we found a positive correlation between OsNAPL6 expression levels and adaptation to multiple abiotic stresses. Results of comparative transcriptome profiling and promoter-recruitment studies indicate that OsNAPL6 functions during stress response via modulation of expression of various genes involved in diverse functions. For instance, we show that OsNAPL6 is recruited to OsRad51 promoter, activating its expression and leading to more efficient DNA repair and abrogation of programmed cell death under salinity and genotoxic stress conditions. These results suggest that the histone chaperone OsNAPL6 may serve a regulatory role in abiotic stress physiology possibly via modulating nucleosome dynamics at various stress-associated genomic loci. Taken together, our findings establish a hitherto unknown link between histone chaperones and abiotic stress response in plants.
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Affiliation(s)
- Amit K Tripathi
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India (A.K.T., S.L.S.-P.); andStress Physiology and Molecular Biology, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, India (A.P.)
| | - Ashwani Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India (A.K.T., S.L.S.-P.); andStress Physiology and Molecular Biology, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, India (A.P.)
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India (A.K.T., S.L.S.-P.); andStress Physiology and Molecular Biology, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, India (A.P.)
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Dubois ÉL, Béliveau M, Masson JY. [Fanconi anemia animal models - How differences can teach us as much as similarities…]. Med Sci (Paris) 2016; 32:598-605. [PMID: 27406770 DOI: 10.1051/medsci/20163206023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Fanconi Anemia is a rare autosomal recessive genetic disease with heterogenous phenotypes including myelosuppression, congenital malformations and heightened cancer predisposition. FA cells are highly sensitive to cross-linking agents. Since the 90's, at least 19 FANC proteins (FANCA to FANCT) have been identified as working together in a unique pathway detecting and triggering the repair of DNA crosslinks. Since then, the creation of animal models in various species (nematode, fruit fly, zebrafish and mouse) contributed to a better understanding of the physiopathology of the disease. This review aims to summarize the main discoveries made in these in vivo models, as well as to discuss some controversies that arose from these studies.
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Affiliation(s)
- Émilie L Dubois
- Département de biologie moléculaire, biochimie médicale, et pathologie et Centre de Recherche sur le Cancer, Université Laval, Canada - CRCHU de Québec, axe oncologie, 9 McMahon, Québec, QC, G1R 3S3, Canada
| | - Mariline Béliveau
- Département de biologie moléculaire, biochimie médicale, et pathologie et Centre de Recherche sur le Cancer, Université Laval, Canada - CRCHU de Québec, axe oncologie, 9 McMahon, Québec, QC, G1R 3S3, Canada
| | - Jean-Yves Masson
- Département de biologie moléculaire, biochimie médicale, et pathologie et Centre de Recherche sur le Cancer, Université Laval, Canada - CRCHU de Québec, axe oncologie, 9 McMahon, Québec, QC, G1R 3S3, Canada
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Schwab RA, Nieminuszczy J, Shah F, Langton J, Lopez Martinez D, Liang CC, Cohn MA, Gibbons RJ, Deans AJ, Niedzwiedz W. The Fanconi Anemia Pathway Maintains Genome Stability by Coordinating Replication and Transcription. Mol Cell 2015; 60:351-61. [PMID: 26593718 PMCID: PMC4644232 DOI: 10.1016/j.molcel.2015.09.012] [Citation(s) in RCA: 249] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/20/2015] [Accepted: 09/16/2015] [Indexed: 01/27/2023]
Abstract
DNA replication stress can cause chromosomal instability and tumor progression. One key pathway that counteracts replication stress and promotes faithful DNA replication consists of the Fanconi anemia (FA) proteins. However, how these proteins limit replication stress remains largely elusive. Here we show that conflicts between replication and transcription activate the FA pathway. Inhibition of transcription or enzymatic degradation of transcription-associated R-loops (DNA:RNA hybrids) suppresses replication fork arrest and DNA damage occurring in the absence of a functional FA pathway. Furthermore, we show that simple aldehydes, known to cause leukemia in FA-deficient mice, induce DNA:RNA hybrids in FA-depleted cells. Finally, we demonstrate that the molecular mechanism by which the FA pathway limits R-loop accumulation requires FANCM translocase activity. Failure to activate a response to physiologically occurring DNA:RNA hybrids may critically contribute to the heightened cancer predisposition and bone marrow failure of individuals with mutated FA proteins. Replication and transcription collisions cause genome instability in FA A functional FA pathway protects cells from unscheduled accumulation of R-loops Transcription inhibition or R-loop removal restores normal replication in FA cells FANCM resolves R-loops via its translocase activity
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Affiliation(s)
- Rebekka A Schwab
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Jadwiga Nieminuszczy
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Fenil Shah
- Genome Stability Unit, St. Vincent's Institute, Fitzroy, VIC 3065, Australia
| | - Jamie Langton
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | | | - Chih-Chao Liang
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Martin A Cohn
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Richard J Gibbons
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Andrew J Deans
- Genome Stability Unit, St. Vincent's Institute, Fitzroy, VIC 3065, Australia
| | - Wojciech Niedzwiedz
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.
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Abstract
Fanconi anemia (FA) is a rare recessive genetic disease characterized by congenital abnormalities, bone marrow failure and heightened cancer susceptibility in early adulthood. FA is caused by biallelic germ-line mutation of any one of 16 genes. While several functions for the FA proteins have been ascribed, the prevailing hypothesis is that the FA proteins function cooperatively in the FA-BRCA pathway to repair damaged DNA. A pivotal step in the activation of the FA-BRCA pathway is the monoubiquitination of the FANCD2 and FANCI proteins. Despite their importance for DNA repair, the domain structure, regulation, and function of FANCD2 and FANCI remain poorly understood. In this review, we provide an overview of our current understanding of FANCD2 and FANCI, with an emphasis on their posttranslational modification and common and unique functions.
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Key Words
- AML , acute myeloid leukemia
- APC/C, anaphase-promoting complex/cyclosome
- APH, aphidicolin
- ARM, armadillo repeat domain
- AT, ataxia-telangiectasia
- ATM, ataxia-telangiectasia mutated
- ATR, ATM and Rad3-related
- BAC, bacterial-artificial-chromosome
- BS, Bloom syndrome
- CUE, coupling of ubiquitin conjugation to endoplasmic reticulum degradation
- ChIP-seq, CHIP sequencing
- CtBP, C-terminal binding protein
- CtIP, CtBP-interacting protein
- DNA interstrand crosslink repair
- DNA repair
- EPS15, epidermal growth factor receptor pathway substrate 15
- FA, Fanconi anemia
- FAN1, FANCD2-associated nuclease1
- FANCD2
- FANCI
- FISH, fluorescence in situ hybridization
- Fanconi anemia
- HECT, homologous to E6-AP Carboxy Terminus
- HJ, Holliday junction
- HR, homologous recombination
- MCM2-MCM7, minichromosome maintenance 2–7
- MEFs, mouse embryonic fibroblasts
- MMC, mitomycin C
- MRN, MRE11/RAD50/NBS1
- NLS, nuclear localization signal
- PCNA, proliferating cell nuclear antigen
- PIKK, phosphatidylinositol-3-OH-kinase-like family of protein kinases
- PIP-box, PCNA-interacting protein motif
- POL κ, DNA polymerase κ
- RACE, rapid amplification of cDNA ends
- RING, really interesting new gene
- RTK, receptor tyrosine kinase
- SCF, Skp1/Cullin/F-box protein complex
- SCKL1, seckel syndrome
- SILAC, stable isotope labeling with amino acids in cell culture
- SLD1/SLD2, SUMO-like domains
- SLIM, SUMO-like domain interacting motif
- TIP60, 60 kDa Tat-interactive protein
- TLS, Translesion DNA synthesis
- UAF1, USP1-associated factor 1
- UBD, ubiquitin-binding domain
- UBZ, ubiquitin-binding zinc finger
- UFB, ultra-fine DNA bridges
- UIM, ubiquitin-interacting motif
- ULD, ubiquitin-like domain
- USP1, ubiquitin-specific protease 1
- VRR-nuc, virus-type replication repair nuclease
- iPOND, isolation of proteins on nascent DNA
- ubiquitin
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Affiliation(s)
- Rebecca A Boisvert
- a Department of Cell and Molecular Biology ; University of Rhode Island ; Kingston , RI USA
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Role of the Exocyst Complex Component Sec6/8 in Genomic Stability. Mol Cell Biol 2015; 35:3633-45. [PMID: 26283729 DOI: 10.1128/mcb.00768-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 08/07/2015] [Indexed: 11/20/2022] Open
Abstract
The exocyst is a heterooctomeric complex well appreciated for its role in the dynamic assembly of specialized membrane domains. Accumulating evidence indicates that this macromolecular machine also serves as a physical platform that coordinates regulatory cascades supporting biological systems such as host defense signaling, cell fate, and energy homeostasis. The isolation of multiple components of the DNA damage response (DDR) as exocyst-interacting proteins, together with the identification of Sec8 as a suppressor of the p53 response, suggested functional interactions between the exocyst and the DDR. We found that exocyst perturbation resulted in resistance to ionizing radiation (IR) and accelerated resolution of DNA damage. This occurred at the expense of genomic integrity, as enhanced recombination frequencies correlated with the accumulation of aberrant chromatid exchanges. Sec8 perturbation resulted in the accumulation of ATF2 and RNF20 and the promiscuous accumulation of DDR-associated chromatin marks and Rad51 repairosomes. Thus, the exocyst supports DNA repair fidelity by limiting the formation of repair chromatin in the absence of DNA damage.
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Sugimoto N, Maehara K, Yoshida K, Yasukouchi S, Osano S, Watanabe S, Aizawa M, Yugawa T, Kiyono T, Kurumizaka H, Ohkawa Y, Fujita M. Cdt1-binding protein GRWD1 is a novel histone-binding protein that facilitates MCM loading through its influence on chromatin architecture. Nucleic Acids Res 2015; 43:5898-911. [PMID: 25990725 PMCID: PMC4499137 DOI: 10.1093/nar/gkv509] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 05/04/2015] [Accepted: 05/05/2015] [Indexed: 12/16/2022] Open
Abstract
Efficient pre-replication complex (pre-RC) formation on chromatin templates is crucial for the maintenance of genome integrity. However, the regulation of chromatin dynamics during this process has remained elusive. We found that a conserved protein, GRWD1 (glutamate-rich WD40 repeat containing 1), binds to two representative replication origins specifically during G1 phase in a CDC6- and Cdt1-dependent manner, and that depletion of GRWD1 reduces loading of MCM but not CDC6 and Cdt1. Furthermore, chromatin immunoprecipitation coupled with high-throughput sequencing (Seq) revealed significant genome-wide co-localization of GRWD1 with CDC6. We found that GRWD1 has histone-binding activity. To investigate the effect of GRWD1 on chromatin architecture, we used formaldehyde-assisted isolation of regulatory elements (FAIRE)-seq or FAIRE-quantitative PCR analyses, and the results suggest that GRWD1 regulates chromatin openness at specific chromatin locations. Taken together, these findings suggest that GRWD1 may be a novel histone-binding protein that regulates chromatin dynamics and MCM loading at replication origins.
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Affiliation(s)
- Nozomi Sugimoto
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kazumitsu Maehara
- Faculty of Medicine, Division of Epigenetics, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kazumasa Yoshida
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shuhei Yasukouchi
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Satoko Osano
- Division of Virology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Shinya Watanabe
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masahiro Aizawa
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takashi Yugawa
- Division of Virology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Tohru Kiyono
- Division of Virology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yasuyuki Ohkawa
- Faculty of Medicine, Division of Epigenetics, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masatoshi Fujita
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Dobbelstein M, Sørensen CS. Exploiting replicative stress to treat cancer. Nat Rev Drug Discov 2015; 14:405-23. [PMID: 25953507 DOI: 10.1038/nrd4553] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA replication in cancer cells is accompanied by stalling and collapse of the replication fork and signalling in response to DNA damage and/or premature mitosis; these processes are collectively known as 'replicative stress'. Progress is being made to increase our understanding of the mechanisms that govern replicative stress, thus providing ample opportunities to enhance replicative stress for therapeutic purposes. Rather than trying to halt cell cycle progression, cancer therapeutics could aim to increase replicative stress by further loosening the checkpoints that remain available to cancer cells and ultimately inducing the catastrophic failure of proliferative machineries. In this Review, we outline current and future approaches to achieve this, emphasizing the combination of conventional chemotherapy with targeted approaches.
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Affiliation(s)
- Matthias Dobbelstein
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences, Ernst Caspari Haus, University of Göttingen, 37077 Göttingen, Germany
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Sato K, Ishiai M, Takata M, Kurumizaka H. Defective FANCI binding by a fanconi anemia-related FANCD2 mutant. PLoS One 2014; 9:e114752. [PMID: 25489943 PMCID: PMC4260917 DOI: 10.1371/journal.pone.0114752] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 11/13/2014] [Indexed: 12/24/2022] Open
Abstract
FANCD2 is a product of one of the genes associated with Fanconi anemia (FA), a rare recessive disease characterized by bone marrow failure, skeletal malformations, developmental defects, and cancer predisposition. FANCD2 forms a complex with FANCI (ID complex) and is monoubiquitinated, which facilitates the downstream interstrand crosslink (ICL) repair steps, such as ICL unhooking and nucleolytic end resection. In the present study, we focused on the chicken FANCD2 (cFANCD2) mutant harboring the Leu234 to Arg (L234R) substitution. cFANCD2 L234R corresponds to the human FANCD2 L231R mutation identified in an FA patient. We found that cFANCD2 L234R did not complement the defective ICL repair in FANCD2−/− DT40 cells. Purified cFANCD2 L234R did not bind to chicken FANCI, and its monoubiquitination was significantly deficient, probably due to the abnormal ID complex formation. In addition, the histone chaperone activity of cFANCD2 L234R was also defective. These findings may explain some aspects of Fanconi anemia pathogenesis by a FANCD2 missense mutation.
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Affiliation(s)
- Koichi Sato
- Laboratory of Structural Biology, Graduate School of Advanced Science & Engineering, Waseda University, Tokyo, Japan
| | - Masamichi Ishiai
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan
| | - Minoru Takata
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science & Engineering, Waseda University, Tokyo, Japan
- * E-mail:
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38
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Takahashi D, Sato K, Shimomuki M, Takata M, Kurumizaka H. Expression and purification of human FANCI and FANCD2 using Escherichia coli cells. Protein Expr Purif 2014; 103:8-15. [PMID: 25168188 DOI: 10.1016/j.pep.2014.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 08/18/2014] [Accepted: 08/18/2014] [Indexed: 12/11/2022]
Abstract
The DNA interstrand crosslink (ICL) is an extremely deleterious DNA lesion that covalently crosslinks complementary strands and prevents the strand-separation reaction. In higher eukaryotes, the Fanconi anemia proteins, FANCI and FANCD2, form a heterodimer and play essential roles in ICL repair. Human FANCI and FANCD2 are large proteins with molecular masses of 149kDa and 164kDa, respectively, and were reportedly purified using a baculovirus expression system with insect cells. We have established a novel expression and purification procedure for human FANCD2 and FANCI, using Escherichia coli cells. The human FANCD2 and FANCI proteins purified by this bacterial expression method formed a stable heterodimer, and exhibited DNA binding and histone chaperone activities, as previously reported for the proteins purified by the baculovirus system. Therefore, these purification methods for human FANCI and FANCD2 provide novel procedures to facilitate structural and biochemical studies of human FANCI and FANCD2.
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Affiliation(s)
- Daisuke Takahashi
- Laboratory of Structural Biology, Graduate School of Advanced Science & Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Koichi Sato
- Laboratory of Structural Biology, Graduate School of Advanced Science & Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Mayo Shimomuki
- Laboratory of Structural Biology, Graduate School of Advanced Science & Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Minoru Takata
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto 606-8501, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science & Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
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39
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Unno J, Itaya A, Taoka M, Sato K, Tomida J, Sakai W, Sugasawa K, Ishiai M, Ikura T, Isobe T, Kurumizaka H, Takata M. FANCD2 binds CtIP and regulates DNA-end resection during DNA interstrand crosslink repair. Cell Rep 2014; 7:1039-47. [PMID: 24794430 DOI: 10.1016/j.celrep.2014.04.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 03/10/2014] [Accepted: 04/04/2014] [Indexed: 11/26/2022] Open
Abstract
The Fanconi anemia (FA) pathway is critically involved in the maintenance of hematopoietic stem cells and the suppression of carcinogenesis. A key FA protein, FANCD2, is monoubiquitinated and accumulates in chromatin in response to DNA interstrand crosslinks (ICLs), where it coordinates DNA repair through mechanisms that are still poorly understood. Here, we report that CtIP protein directly interacts with FANCD2. A region spanning amino acids 166 to 273 of CtIP and monoubiquitination of FANCD2 are both essential for the FANCD2-CtIP interaction and mitomycin C (MMC)-induced CtIP foci. Remarkably, both FANCD2 and CtIP are critical for MMC-induced RPA2 hyperphosphorylation, an event that accompanies end resection of double-strand breaks. Collectively, our results reveal a role of monoubiquitinated FANCD2 in end resection that depends on its binding to CtIP during ICL repair.
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Affiliation(s)
- Junya Unno
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto 606-8501, Japan
| | - Akiko Itaya
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto 606-8501, Japan; Japan Society for the Promotion of Science (JSPS), Tokyo 102-0083, Japan
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Koichi Sato
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 162-8480, Japan
| | - Junya Tomida
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto 606-8501, Japan
| | - Wataru Sakai
- Biosignal Research Center, Organization of Advanced Science and Technology and Department of Biology, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Kaoru Sugasawa
- Biosignal Research Center, Organization of Advanced Science and Technology and Department of Biology, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Masamichi Ishiai
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto 606-8501, Japan
| | - Tsuyoshi Ikura
- Laboratory of Chromatin Regulatory Network, Department of Mutagenesis, Radiation Biology Center, Kyoto University, Kyoto 606-8501, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 162-8480, Japan
| | - Minoru Takata
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto 606-8501, Japan.
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40
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Murina O, von Aesch C, Karakus U, Ferretti LP, Bolck HA, Hänggi K, Sartori AA. FANCD2 and CtIP cooperate to repair DNA interstrand crosslinks. Cell Rep 2014; 7:1030-8. [PMID: 24794434 DOI: 10.1016/j.celrep.2014.03.069] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 03/04/2014] [Accepted: 03/27/2014] [Indexed: 12/19/2022] Open
Abstract
The resolution of DNA interstrand crosslinks (ICLs) requires a complex interplay between several processes of DNA metabolism, including the Fanconi anemia (FA) pathway and homologous recombination (HR). FANCD2 monoubiquitination and CtIP-dependent DNA-end resection represent key events in FA and HR activation, respectively, but very little is known about their functional relationship. Here, we show that CtIP physically interacts with both FANCD2 and ubiquitin and that monoubiquitinated FANCD2 tethers CtIP to damaged chromatin, which helps channel DNA double-strand breaks generated during ICL processing into the HR pathway. Consequently, CtIP mutants defective in FANCD2 binding fail to associate with damaged chromatin, which leads to increased levels of nonhomologous end-joining activity and ICL hypersensitivity. Interestingly, we also observe that CtIP depletion aggravates the genomic instability in FANCD2-deficient cells. Thus, our data indicate that FANCD2 primes CtIP-dependent resection during HR after ICL induction but that CtIP helps prevent illegitimate recombination in FA cells.
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Affiliation(s)
- Olga Murina
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Christine von Aesch
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Ufuk Karakus
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Lorenza P Ferretti
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Hella A Bolck
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Kay Hänggi
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
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41
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Mouw KW, D'Andrea AD. Crosstalk between the nucleotide excision repair and Fanconi anemia/BRCA pathways. DNA Repair (Amst) 2014; 19:130-4. [PMID: 24768451 DOI: 10.1016/j.dnarep.2014.03.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Cells have evolved multiple distinct DNA repair pathways to efficiently correct a variety of genotoxic lesions, and decades of study have led to an improved understanding of the mechanisms and regulation of these individual pathways. However, there is now an increasing appreciation that extensive crosstalk exists among DNA repair pathways and that this crosstalk serves to increase the efficiency and diversity of response to damage. The Fanconi anemia (FA)/BRCA and nucleotide excision repair (NER) pathways have been shown to share common factors, and often work in concert to repair damage. Genomic studies are now revealing that many tumors harbor somatic mutations in FA/BRCA or NER genes, which may provide a growth advantage, but which could also be exploited therapeutically.
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Affiliation(s)
- Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States; Harvard Radiation Oncology Program, Boston, MA, United States
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States.
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Longerich S, Kwon Y, Tsai MS, Hlaing AS, Kupfer GM, Sung P. Regulation of FANCD2 and FANCI monoubiquitination by their interaction and by DNA. Nucleic Acids Res 2014; 42:5657-70. [PMID: 24623813 PMCID: PMC4027212 DOI: 10.1093/nar/gku198] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
FANCD2 and FANCI function together in the Fanconi anemia network of deoxyribonucleic acid (DNA) crosslink repair. These proteins form the dimeric ID2 complex that binds DNA and becomes monoubiquitinated upon exposure of cells to DNA crosslinking agents. The monoubiquitinated ID2 complex is thought to facilitate DNA repair via recruitment of specific nucleases, translesion DNA polymerases and the homologous recombination machinery. Using the ubiquitin conjugating enzyme (E2) UBE2T and ubiquitin ligase (E3) FANCL, monoubiquitination of human FANCD2 and FANCI was examined. The ID2 complex is a poor substrate for monoubiquitination, consistent with the published crystal structure showing the solvent inaccessibility of the target lysines. Importantly, FANCD2 monoubiquitination within the ID2 complex is strongly stimulated by duplex or branched DNA, but unstructured single-stranded DNA or chromatinized DNA is ineffective. Interaction of FANCL with the ID2 complex is indispensable for its E3 ligase efficacy. Interestingly, mutations in FANCI that impair its DNA binding activity compromise DNA-stimulated FANCD2 monoubiquitination. Moreover, we demonstrate that in the absence of FANCD2, DNA also stimulates FANCI monoubiquitination, but in a FANCL-independent manner. These results implicate the role of a proper DNA ligand in FANCD2 and FANCI monoubiquitination, and reveal regulatory mechanisms that are dependent on protein-protein and protein-DNA interactions.
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Affiliation(s)
- Simonne Longerich
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Youngho Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Miaw-Sheue Tsai
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Aye Su Hlaing
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Gary M Kupfer
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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Arimura Y, Kimura H, Oda T, Sato K, Osakabe A, Tachiwana H, Sato Y, Kinugasa Y, Ikura T, Sugiyama M, Sato M, Kurumizaka H. Structural basis of a nucleosome containing histone H2A.B/H2A.Bbd that transiently associates with reorganized chromatin. Sci Rep 2013; 3:3510. [PMID: 24336483 PMCID: PMC3863819 DOI: 10.1038/srep03510] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 11/29/2013] [Indexed: 01/26/2023] Open
Abstract
Human histone H2A.B (formerly H2A.Bbd), a non-allelic H2A variant, exchanges rapidly as compared to canonical H2A, and preferentially associates with actively transcribed genes. We found that H2A.B transiently accumulated at DNA replication and repair foci in living cells. To explore the biochemical function of H2A.B, we performed nucleosome reconstitution analyses using various lengths of DNA. Two types of H2A.B nucleosomes, octasome and hexasome, were formed with 116, 124, or 130 base pairs (bp) of DNA, and only the octasome was formed with 136 or 146 bp DNA. In contrast, only hexasome formation was observed by canonical H2A with 116 or 124 bp DNA. A small-angle X-ray scattering analysis revealed that the H2A.B octasome is more extended, due to the flexible detachment of the DNA regions at the entry/exit sites from the histone surface. These results suggested that H2A.B rapidly and transiently forms nucleosomes with short DNA segments during chromatin reorganization.
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Affiliation(s)
- Yasuhiro Arimura
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiroshi Kimura
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
- JST, CREST, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takashi Oda
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Koichi Sato
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Akihisa Osakabe
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiroaki Tachiwana
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yuko Sato
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
- JST, CREST, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yasuha Kinugasa
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tsuyoshi Ikura
- Department of Mutagenesis, Division of Chromatin Regulatory Network, Radiation Biology Center, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masaaki Sugiyama
- Research Reactor Institute, Kyoto University, Kumatori, Osaka, 590-0494, Japan
| | - Mamoru Sato
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN SPring-8 Center, 1-1-1 koto, Sayo, Hyogo 679-5148, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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Clauson C, Schärer OD, Niedernhofer L. Advances in understanding the complex mechanisms of DNA interstrand cross-link repair. Cold Spring Harb Perspect Biol 2013; 5:a012732. [PMID: 24086043 DOI: 10.1101/cshperspect.a012732] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA interstrand cross-links (ICLs) are lesions caused by a variety of endogenous metabolites, environmental exposures, and cancer chemotherapeutic agents that have two reactive groups. The common feature of these diverse lesions is that two nucleotides on opposite strands are covalently joined. ICLs prevent the separation of two DNA strands and therefore essential cellular processes including DNA replication and transcription. ICLs are mainly detected in S phase when a replication fork stalls at an ICL. Damage signaling and repair of ICLs are promoted by the Fanconi anemia pathway and numerous posttranslational modifications of DNA repair and chromatin structural proteins. ICLs are also detected and repaired in nonreplicating cells, although the mechanism is less clear. A unique feature of ICL repair is that both strands of DNA must be incised to completely remove the lesion. This is accomplished in sequential steps to prevent creating multiple double-strand breaks. Unhooking of an ICL from one strand is followed by translesion synthesis to fill the gap and create an intact duplex DNA, harboring a remnant of the ICL. Removal of the lesion from the second strand is likely accomplished by nucleotide excision repair. Inadequate repair of ICLs is particularly detrimental to rapidly dividing cells, explaining the bone marrow failure characteristic of Fanconi anemia and why cross-linking agents are efficacious in cancer therapy. Herein, recent advances in our understanding of ICLs and the biological responses they trigger are discussed.
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Affiliation(s)
- Cheryl Clauson
- Department of Microbiology and Molecular Genetics, The University of Pittsburgh, Pittsburgh, Pennsylvania 15219
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45
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Karakasilioti I, Kamileri I, Chatzinikolaou G, Kosteas T, Vergadi E, Robinson AR, Tsamardinos I, Rozgaja TA, Siakouli S, Tsatsanis C, Niedernhofer LJ, Garinis GA. DNA damage triggers a chronic autoinflammatory response, leading to fat depletion in NER progeria. Cell Metab 2013; 18:403-15. [PMID: 24011075 PMCID: PMC4116679 DOI: 10.1016/j.cmet.2013.08.011] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 05/18/2013] [Accepted: 08/09/2013] [Indexed: 12/21/2022]
Abstract
Lipodystrophies represent a group of heterogeneous disorders characterized by loss of fat tissue. However, the underlying mechanisms remain poorly understood. Using mice carrying an ERCC1-XPF DNA repair defect systematically or in adipocytes, we show that DNA damage signaling triggers a chronic autoinflammatory response leading to fat depletion. Ercc1-/- and aP2-Ercc1F/- fat depots show extensive gene expression similarities to lipodystrophic Pparγ(ldi/+) animals, focal areas of ruptured basement membrane, the reappearance of primary cilia, necrosis, fibrosis, and a marked decrease in adiposity. We find that persistent DNA damage in aP2-Ercc1F/- fat depots and in adipocytes ex vivo triggers the induction of proinflammatory factors by promoting transcriptionally active histone marks and the dissociation of nuclear receptor corepressor complexes from promoters; the response is cell autonomous and requires ataxia telangiectasia mutated (ATM). Thus, persistent DNA damage-driven autoinflammation plays a causative role in adipose tissue degeneration, with important ramifications for progressive lipodystrophies and natural aging.
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Affiliation(s)
- Ismene Karakasilioti
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Crete, Greece; Department of Biology, University of Crete, 71409 Heraklion, Crete, Greece
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46
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Tomida J, Itaya A, Shigechi T, Unno J, Uchida E, Ikura M, Masuda Y, Matsuda S, Adachi J, Kobayashi M, Meetei AR, Maehara Y, Yamamoto KI, Kamiya K, Matsuura A, Matsuda T, Ikura T, Ishiai M, Takata M. A novel interplay between the Fanconi anemia core complex and ATR-ATRIP kinase during DNA cross-link repair. Nucleic Acids Res 2013; 41:6930-41. [PMID: 23723247 PMCID: PMC3737553 DOI: 10.1093/nar/gkt467] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
When DNA replication is stalled at sites of DNA damage, a cascade of responses is activated in the cell to halt cell cycle progression and promote DNA repair. A pathway initiated by the kinase Ataxia teleangiectasia and Rad3 related (ATR) and its partner ATR interacting protein (ATRIP) plays an important role in this response. The Fanconi anemia (FA) pathway is also activated following genomic stress, and defects in this pathway cause a cancer-prone hematologic disorder in humans. Little is known about how these two pathways are coordinated. We report here that following cellular exposure to DNA cross-linking damage, the FA core complex enhances binding and localization of ATRIP within damaged chromatin. In cells lacking the core complex, ATR-mediated phosphorylation of two functional response targets, ATRIP and FANCI, is defective. We also provide evidence that the canonical ATR activation pathway involving RAD17 and TOPBP1 is largely dispensable for the FA pathway activation. Indeed DT40 mutant cells lacking both RAD17 and FANCD2 were synergistically more sensitive to cisplatin compared with either single mutant. Collectively, these data reveal new aspects of the interplay between regulation of ATR-ATRIP kinase and activation of the FA pathway.
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Affiliation(s)
- Junya Tomida
- Department of Late Effects Studies, Laboratory of DNA Damage Signaling, Kyoto University, Kyoto 606-8501, Japan, Japan Society for the Promotion of Science (JSPS), Tokyo 102-0083, Japan
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47
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Murtaza M, Dawson SJ, Tsui DWY, Gale D, Forshew T, Piskorz AM, Parkinson C, Chin SF, Kingsbury Z, Wong ASC, Marass F, Humphray S, Hadfield J, Bentley D, Chin TM, Brenton JD, Caldas C, Rosenfeld N. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature 2013; 497:108-12. [PMID: 23563269 DOI: 10.1038/nature12065] [Citation(s) in RCA: 1263] [Impact Index Per Article: 114.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 03/11/2013] [Indexed: 02/07/2023]
Abstract
Cancers acquire resistance to systemic treatment as a result of clonal evolution and selection. Repeat biopsies to study genomic evolution as a result of therapy are difficult, invasive and may be confounded by intra-tumour heterogeneity. Recent studies have shown that genomic alterations in solid cancers can be characterized by massively parallel sequencing of circulating cell-free tumour DNA released from cancer cells into plasma, representing a non-invasive liquid biopsy. Here we report sequencing of cancer exomes in serial plasma samples to track genomic evolution of metastatic cancers in response to therapy. Six patients with advanced breast, ovarian and lung cancers were followed over 1-2 years. For each case, exome sequencing was performed on 2-5 plasma samples (19 in total) spanning multiple courses of treatment, at selected time points when the allele fraction of tumour mutations in plasma was high, allowing improved sensitivity. For two cases, synchronous biopsies were also analysed, confirming genome-wide representation of the tumour genome in plasma. Quantification of allele fractions in plasma identified increased representation of mutant alleles in association with emergence of therapy resistance. These included an activating mutation in PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha) following treatment with paclitaxel; a truncating mutation in RB1 (retinoblastoma 1) following treatment with cisplatin; a truncating mutation in MED1 (mediator complex subunit 1) following treatment with tamoxifen and trastuzumab, and following subsequent treatment with lapatinib, a splicing mutation in GAS6 (growth arrest-specific 6) in the same patient; and a resistance-conferring mutation in EGFR (epidermal growth factor receptor; T790M) following treatment with gefitinib. These results establish proof of principle that exome-wide analysis of circulating tumour DNA could complement current invasive biopsy approaches to identify mutations associated with acquired drug resistance in advanced cancers. Serial analysis of cancer genomes in plasma constitutes a new paradigm for the study of clonal evolution in human cancers.
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Affiliation(s)
- Muhammed Murtaza
- Cancer Research UK Cambridge Institute and University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
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48
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Singh S, Shemesh K, Liefshitz B, Kupiec M. Genetic and physical interactions between the yeast ELG1 gene and orthologs of the Fanconi anemia pathway. Cell Cycle 2013; 12:1625-36. [PMID: 23624835 PMCID: PMC3680542 DOI: 10.4161/cc.24756] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Fanconi anemia (FA) is a human syndrome characterized by genomic instability and increased incidence of cancer. FA is a genetically heterogeneous disease caused by mutations in at least 15 different genes; several of these genes are conserved in the yeast Saccharomyces cerevisiae. Elg1 is also a conserved protein that forms an RFC-like complex, which interacts with SUMOylated PCNA. The mammalian Elg1 protein has been recently found to interact with the FA complex. Here we analyze the genetic interactions between elg1Δand mutants of the yeast FA-like pathway. We show that Elg1 physically contacts the Mhf1/Mhf2 histone-like complex and genetically interacts with MPH1 (ortholog of the FANCM helicase) and CHL1 (ortholog of the FANCJ helicase) genes. We analyze the sensitivity of double, triple, quadruple and quintuple mutants to methylmethane sulfonate (MMS) and to hydroxyurea (HU). Our results show that genetic interactions depend on the type of DNA damaging agent used and show a hierarchy: Chl1 and Elg1 play major roles in the survival to these genotoxins and exhibit synthetic fitness reduction. Mph1 plays a lesser role, and the effect of the Mhf1/2 complex is seen only in the absence of Elg1 on HU-containing medium. Finally, we dissect the relationship between yeast FA-like mutants and the replication clamp, PCNA. Our results point to an intricate network of interactions rather than a single, linear repair pathway.
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Affiliation(s)
- Shivani Singh
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
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49
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Quinlan RA, Ellis RJ. Chaperones: needed for both the good times and the bad times. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130091. [PMID: 23530265 DOI: 10.1098/rstb.2013.0091] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this issue, we explore the assembly roles of protein chaperones, mainly through the portal of their associated human diseases (e.g. cardiomyopathy, cataract, neurodegeneration, cancer and neuropathy). There is a diversity to chaperone function that goes beyond the current emphasis in the scientific literature on their undoubted roles in protein folding and refolding. The focus on chaperone-mediated protein folding needs to be broadened by the original Laskey discovery that a chaperone assists the assembly of an oligomeric structure, the nucleosome, and the subsequent suggestion by Ellis that other chaperones may function in assembly processes, as well as in folding. There have been a number of recent discoveries that extend this relatively neglected aspect of chaperone biology to include proteostasis, maintenance of the cellular redox potential, genome stability, transcriptional regulation and cytoskeletal dynamics. So central are these processes that we propose that chaperones stand at the crossroads of life and death because they mediate essential functions, not only during the bad times, but also in the good times. We suggest that chaperones facilitate the success of a species, and hence the evolution of individuals within populations, because of their contributions to so many key cellular processes, of which protein folding is only one.
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Affiliation(s)
- Roy A Quinlan
- School of Biological and Biomedical Sciences, University of Durham, South Road, Durham DH1 3LE, UK.
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50
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Kottemann MC, Smogorzewska A. Fanconi anaemia and the repair of Watson and Crick DNA crosslinks. Nature 2013; 493:356-63. [PMID: 23325218 DOI: 10.1038/nature11863] [Citation(s) in RCA: 449] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 11/08/2012] [Indexed: 12/16/2022]
Abstract
The function of Fanconi anaemia proteins is to maintain genomic stability. Their main role is in the repair of DNA interstrand crosslinks, which, by covalently binding the Watson and the Crick strands of DNA, impede replication and transcription. Inappropriate repair of interstrand crosslinks causes genomic instability, leading to cancer; conversely, the toxicity of crosslinking agents makes them a powerful chemotherapeutic. Fanconi anaemia proteins can promote stem-cell function, prevent tumorigenesis, stabilize replication forks and inhibit inaccurate repair. Recent advances have identified endogenous aldehydes as possible culprits of DNA damage that may induce the phenotypes seen in patients with Fanconi anaemia.
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Affiliation(s)
- Molly C Kottemann
- Laboratory of Genome Maintenance, The Rockefeller University, New York 10065, USA
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