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Bayona-Feliu A, Herrera-Moyano E, Badra-Fajardo N, Galván-Femenía I, Soler-Oliva ME, Aguilera A. The chromatin network helps prevent cancer-associated mutagenesis at transcription-replication conflicts. Nat Commun 2023; 14:6890. [PMID: 37898641 PMCID: PMC10613258 DOI: 10.1038/s41467-023-42653-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 10/09/2023] [Indexed: 10/30/2023] Open
Abstract
Genome instability is a feature of cancer cells, transcription being an important source of DNA damage. This is in large part associated with R-loops, which hamper replication, especially at head-on transcription-replication conflicts (TRCs). Here we show that TRCs trigger a DNA Damage Response (DDR) involving the chromatin network to prevent genome instability. Depletion of the key chromatin factors INO80, SMARCA5 and MTA2 results in TRCs, fork stalling and R-loop-mediated DNA damage which mostly accumulates at S/G2, while histone H3 Ser10 phosphorylation, a mark of chromatin compaction, is enriched at TRCs. Strikingly, TRC regions show increased mutagenesis in cancer cells with signatures of homologous recombination deficiency, transcription-coupled nucleotide excision repair (TC-NER) and of the AID/APOBEC cytidine deaminases, being predominant at head-on collisions. Thus, our results support that the chromatin network prevents R-loops and TRCs from genomic instability and mutagenic signatures frequently associated with cancer.
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Affiliation(s)
- Aleix Bayona-Feliu
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain.
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012, Seville, Spain.
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
| | - Emilia Herrera-Moyano
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012, Seville, Spain
| | - Nibal Badra-Fajardo
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain
| | - Iván Galván-Femenía
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - María Eugenia Soler-Oliva
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012, Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain.
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012, Seville, Spain.
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2
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Ortega P, Gómez-González B, Aguilera A. Heterogeneity of DNA damage incidence and repair in different chromatin contexts. DNA Repair (Amst) 2021; 107:103210. [PMID: 34416542 DOI: 10.1016/j.dnarep.2021.103210] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/02/2021] [Accepted: 08/11/2021] [Indexed: 11/18/2022]
Abstract
It has been long known that some regions of the genome are more susceptible to damage and mutagenicity than others. Recent advances have determined a critical role of chromatin both in the incidence of damage and in its repair. Thus, chromatin arises as a guardian of the stability of the genome, which is altered in cancer cells. In this review, we focus into the mechanisms by which chromatin influences the occurrence and repair of the most cytotoxic DNA lesions, double-strand breaks, in particular at actively transcribed chromatin or related to DNA replication.
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Affiliation(s)
- Pedro Ortega
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain.
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
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3
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Role of Histone Methylation in Maintenance of Genome Integrity. Genes (Basel) 2021; 12:genes12071000. [PMID: 34209979 PMCID: PMC8307007 DOI: 10.3390/genes12071000] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/15/2021] [Accepted: 06/22/2021] [Indexed: 12/14/2022] Open
Abstract
Packaging of the eukaryotic genome with histone and other proteins forms a chromatin structure that regulates the outcome of all DNA mediated processes. The cellular pathways that ensure genomic stability detect and repair DNA damage through mechanisms that are critically dependent upon chromatin structures established by histones and, particularly upon transient histone post-translational modifications. Though subjected to a range of modifications, histone methylation is especially crucial for DNA damage repair, as the methylated histones often form platforms for subsequent repair protein binding at damaged sites. In this review, we highlight and discuss how histone methylation impacts the maintenance of genome integrity through effects related to DNA repair and repair pathway choice.
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4
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Aleksandrov R, Hristova R, Stoynov S, Gospodinov A. The Chromatin Response to Double-Strand DNA Breaks and Their Repair. Cells 2020; 9:cells9081853. [PMID: 32784607 PMCID: PMC7464352 DOI: 10.3390/cells9081853] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023] Open
Abstract
Cellular DNA is constantly being damaged by numerous internal and external mutagenic factors. Probably the most severe type of insults DNA could suffer are the double-strand DNA breaks (DSBs). They sever both DNA strands and compromise genomic stability, causing deleterious chromosomal aberrations that are implicated in numerous maladies, including cancer. Not surprisingly, cells have evolved several DSB repair pathways encompassing hundreds of different DNA repair proteins to cope with this challenge. In eukaryotic cells, DSB repair is fulfilled in the immensely complex environment of the chromatin. The chromatin is not just a passive background that accommodates the multitude of DNA repair proteins, but it is a highly dynamic and active participant in the repair process. Chromatin alterations, such as changing patterns of histone modifications shaped by numerous histone-modifying enzymes and chromatin remodeling, are pivotal for proficient DSB repair. Dynamic chromatin changes ensure accessibility to the damaged region, recruit DNA repair proteins, and regulate their association and activity, contributing to DSB repair pathway choice and coordination. Given the paramount importance of DSB repair in tumorigenesis and cancer progression, DSB repair has turned into an attractive target for the development of novel anticancer therapies, some of which have already entered the clinic.
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5
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Rad9/53BP1 promotes DNA repair via crossover recombination by limiting the Sgs1 and Mph1 helicases. Nat Commun 2020; 11:3181. [PMID: 32576832 PMCID: PMC7311424 DOI: 10.1038/s41467-020-16997-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 06/05/2020] [Indexed: 12/16/2022] Open
Abstract
The DNA damage checkpoint (DDC) is often robustly activated during the homologous recombination (HR) repair of DNA double strand breaks (DSBs). DDC activation controls several HR repair factors by phosphorylation, preventing premature segregation of entangled chromosomes formed during HR repair. The DDC mediator 53BP1/Rad9 limits the nucleolytic processing (resection) of a DSB, controlling the formation of the 3′ single-stranded DNA (ssDNA) filament needed for recombination, from yeast to human. Here we show that Rad9 promotes stable annealing between the recombinogenic filament and the donor template in yeast, limiting strand rejection by the Sgs1 and Mph1 helicases. This regulation allows repair by long tract gene conversion, crossover recombination and break-induced replication (BIR), only after DDC activation. These findings shed light on how cells couple DDC with the choice and effectiveness of HR sub-pathways, with implications for genome instability and cancer. In budding yeast, the 53BP1 ortholog Rad9 limits the resection nucleolytic processing of DNA double strand breaks. Here the authors reveal that Rad9 promotes long tract gene conversions, BIR and CO, during the HR repair of a DSB via modulation of Sgs1 and Mph1 helicases.
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6
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Nunes VS, Moretti NS, da Silva MS, Elias MC, Janzen CJ, Schenkman S. Trimethylation of histone H3K76 by Dot1B enhances cell cycle progression after mitosis in Trypanosoma cruzi. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118694. [PMID: 32151656 DOI: 10.1016/j.bbamcr.2020.118694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 12/11/2022]
Abstract
Dot1 enzymes are histone methyltransferases that mono-, di- and trimethylate lysine 79 of histone H3 to affect several nuclear processes. The functions of these different methylation states are still largely unknown. Trypanosomes, which are flagellated protozoa that cause several parasitic diseases, have two Dot1 homologues. Dot1A catalyzes the mono- and dimethylation of lysine 76 during late G2 and mitosis, and Dot1B catalyzes trimethylation, which is a modification found in all stages of the cell cycle. Here, we generated Trypanosoma cruzi lines lacking Dot1B. Deletion of one allele resulted in parasites with increased levels of mono- and dimethylation and a reduction in H3K76me3. In the full knockout (DKO), no trimethylation was observed. Both the DKO and the single knockout (SKO) showed aberrant morphology and decreased growth due to cell cycle arrest after G2. This phenotype could be rescued by caffeine in the DKO, as caffeine is a checkpoint inhibitor of the cell cycle. The knockouts also phosphorylated γH2A without producing extensive DNA breaks, and Dot1B-depleted cells were more susceptible to general checkpoint kinase inhibitors, suggesting that a lack of H3K76 trimethylation prevents the initiation and/or completion of cytokinesis.
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Affiliation(s)
- Vinicius Santana Nunes
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, 04032-039 São Paulo, SP, Brazil; Centro de Ensino, Pesquisa e Inovação, Hospital Evangélico de Vila Velha, 29118-060 Vila Velha, ES, Brazil
| | - Nilmar Silvio Moretti
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, 04032-039 São Paulo, SP, Brazil
| | | | - Maria Carolina Elias
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
| | - Christian J Janzen
- Department of Cell & Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Sergio Schenkman
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, 04032-039 São Paulo, SP, Brazil.
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7
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House NC, Polleys EJ, Quasem I, De la Rosa Mejia M, Joyce CE, Takacsi-Nagy O, Krebs JE, Fuchs SM, Freudenreich CH. Distinct roles for S. cerevisiae H2A copies in recombination and repeat stability, with a role for H2A.1 threonine 126. eLife 2019; 8:53362. [PMID: 31804179 PMCID: PMC6927750 DOI: 10.7554/elife.53362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/26/2019] [Indexed: 01/14/2023] Open
Abstract
CAG/CTG trinuncleotide repeats are fragile sequences that when expanded form DNA secondary structures and cause human disease. We evaluated CAG/CTG repeat stability and repair outcomes in histone H2 mutants in S. cerevisiae. Although the two copies of H2A are nearly identical in amino acid sequence, CAG repeat stability depends on H2A copy 1 (H2A.1) but not copy 2 (H2A.2). H2A.1 promotes high-fidelity homologous recombination, sister chromatid recombination (SCR), and break-induced replication whereas H2A.2 does not share these functions. Both decreased SCR and the increase in CAG expansions were due to the unique Thr126 residue in H2A.1 and hta1Δ or hta1-T126A mutants were epistatic to deletion of the Polδ subunit Pol32, suggesting a role for H2A.1 in D-loop extension. We conclude that H2A.1 plays a greater repair-specific role compared to H2A.2 and may be a first step towards evolution of a repair-specific function for H2AX compared to H2A in mammalian cells.
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Affiliation(s)
- Nealia Cm House
- Department of Biology, Tufts University, Medford, United States
| | - Erica J Polleys
- Department of Biology, Tufts University, Medford, United States
| | | | | | - Cailin E Joyce
- Department of Biology, Tufts University, Medford, United States
| | | | - Jocelyn E Krebs
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, United States
| | - Stephen M Fuchs
- Department of Biology, Tufts University, Medford, United States
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, United States.,Program in Genetics, Graduate School of Biomedical Sciences, Tufts University, Boston, United States
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8
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Ortega P, Gómez-González B, Aguilera A. Rpd3L and Hda1 histone deacetylases facilitate repair of broken forks by promoting sister chromatid cohesion. Nat Commun 2019; 10:5178. [PMID: 31729385 PMCID: PMC6858524 DOI: 10.1038/s41467-019-13210-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/22/2019] [Indexed: 12/13/2022] Open
Abstract
Genome stability involves accurate replication and DNA repair. Broken replication forks, such as those encountering a nick, lead to double strand breaks (DSBs), which are preferentially repaired by sister-chromatid recombination (SCR). To decipher the role of chromatin in eukaryotic DSB repair, here we analyze a collection of yeast chromatin-modifying mutants using a previously developed system for the molecular analysis of repair of replication-born DSBs by SCR based on a mini-HO site. We confirm the candidates through FLP-based systems based on a mutated version of the FLP flipase that causes nicks on either the leading or lagging DNA strands. We demonstrate that Rpd3L and Hda1 histone deacetylase (HDAC) complexes contribute to the repair of replication-born DSBs by facilitating cohesin loading, with no effect on other types of homology-dependent repair, thus preventing genome instability. We conclude that histone deacetylation favors general sister chromatid cohesion as a necessary step in SCR.
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Affiliation(s)
- Pedro Ortega
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain.
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain.
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9
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Abstract
The Elg1protein forms an RFC-like complex in charge of unloading PCNA from chromatin during DNA replication and repair. Mutations in the ELG1 gene caused genomic instability in all organisms tested and cancer in mammals. Here we show that Elg1 plays a role in the induction of the DNA damage checkpoint, a cellular response to DNA damage. We show that this defect is due to a defect in the signal amplification process during induction. Thus, cells coordinate the cell's response and the PCNA unloading through the activity of Elg1. The PCNA (proliferating cell nuclear antigen) ring plays central roles during DNA replication and repair. The yeast Elg1 RFC-like complex (RLC) is the principal unloader of chromatin-bound PCNA and thus plays a central role in maintaining genome stability. Here we identify a role for Elg1 in the unloading of PCNA during DNA damage. Using DNA damage checkpoint (DC)-inducible and replication checkpoint (RC)-inducible strains, we show that Elg1 is essential for eliciting the signal in the DC branch. In the absence of Elg1 activity, the Rad9 (53BP1) and Dpb11 (TopBP1) adaptor proteins are recruited but fail to be phosphorylated by Mec1 (ATR), resulting in a lack of checkpoint activation. The chromatin immunoprecipitation of PCNA at the Lac operator sites reveals that accumulated local PCNA influences the checkpoint activation process in elg1 mutants. Our data suggest that Elg1 participates in a mechanism that may coordinate PCNA unloading during DNA repair with DNA damage checkpoint induction.
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10
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Litwin I, Pilarczyk E, Wysocki R. The Emerging Role of Cohesin in the DNA Damage Response. Genes (Basel) 2018; 9:genes9120581. [PMID: 30487431 PMCID: PMC6316000 DOI: 10.3390/genes9120581] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 12/23/2022] Open
Abstract
Faithful transmission of genetic material is crucial for all organisms since changes in genetic information may result in genomic instability that causes developmental disorders and cancers. Thus, understanding the mechanisms that preserve genome integrity is of fundamental importance. Cohesin is a multiprotein complex whose canonical function is to hold sister chromatids together from S-phase until the onset of anaphase to ensure the equal division of chromosomes. However, recent research points to a crucial function of cohesin in the DNA damage response (DDR). In this review, we summarize recent advances in the understanding of cohesin function in DNA damage signaling and repair. First, we focus on cohesin architecture and molecular mechanisms that govern sister chromatid cohesion. Next, we briefly characterize the main DDR pathways. Finally, we describe mechanisms that determine cohesin accumulation at DNA damage sites and discuss possible roles of cohesin in DDR.
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Affiliation(s)
- Ireneusz Litwin
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland.
| | - Ewa Pilarczyk
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland.
| | - Robert Wysocki
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland.
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11
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Wood K, Tellier M, Murphy S. DOT1L and H3K79 Methylation in Transcription and Genomic Stability. Biomolecules 2018; 8:E11. [PMID: 29495487 PMCID: PMC5871980 DOI: 10.3390/biom8010011] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 01/08/2023] Open
Abstract
The organization of eukaryotic genomes into chromatin provides challenges for the cell to accomplish basic cellular functions, such as transcription, DNA replication and repair of DNA damage. Accordingly, a range of proteins modify and/or read chromatin states to regulate access to chromosomal DNA. Yeast Dot1 and the mammalian homologue DOT1L are methyltransferases that can add up to three methyl groups to histone H3 lysine 79 (H3K79). H3K79 methylation is implicated in several processes, including transcription elongation by RNA polymerase II, the DNA damage response and cell cycle checkpoint activation. DOT1L is also an important drug target for treatment of mixed lineage leukemia (MLL)-rearranged leukemia where aberrant transcriptional activation is promoted by DOT1L mislocalisation. This review summarizes what is currently known about the role of Dot1/DOT1L and H3K79 methylation in transcription and genomic stability.
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Affiliation(s)
- Katherine Wood
- Department of Biochemistry, University of Oxford, Oxford OX1 3RE, UK.
- School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK.
| | - Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
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12
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Ljungman M, Parks L, Hulbatte R, Bedi K. The role of H3K79 methylation in transcription and the DNA damage response. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 780:48-54. [PMID: 31395348 DOI: 10.1016/j.mrrev.2017.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 10/19/2017] [Accepted: 11/15/2017] [Indexed: 12/16/2022]
Abstract
Chromatin plays a critical role in organizing and protecting DNA. However, chromatin acts as an impediment for transcription and DNA repair. Histone modifications, such as H3K79 methylation, promote transcription and genomic stability by enhancing transcription elongation and by serving as landing sites for proteins involved in the DNA damage response. This review summarizes the current understanding of the role of H3K79 methylation in transcription, how it affects genome stability and opportunities to develop impactful therapeutic interventions for cancer.
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Affiliation(s)
- Mats Ljungman
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, United States; Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States.
| | - Luke Parks
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, United States; Department of Cell and Molecular Biology, Uppsala University, Box 256, 75105 Uppsala, Sweden
| | - Radhika Hulbatte
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, United States
| | - Karan Bedi
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, United States
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13
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Drigeard Desgarnier MC, Fournier F, Droit A, Rochette PJ. Influence of a pre-stimulation with chronic low-dose UVB on stress response mechanisms in human skin fibroblasts. PLoS One 2017; 12:e0173740. [PMID: 28301513 PMCID: PMC5354420 DOI: 10.1371/journal.pone.0173740] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/24/2017] [Indexed: 12/16/2022] Open
Abstract
Exposure to solar ultraviolet type B (UVB), through the induction of cyclobutane pyrimidine dimer (CPD), is the major risk factor for cutaneous cancer. Cells respond to UV-induced CPD by triggering the DNA damage response (DDR) responsible for signaling DNA repair, programmed cell death and cell cycle arrest. Underlying mechanisms implicated in the DDR have been extensively studied using single acute UVB irradiation. However, little is known concerning the consequences of chronic low-dose of UVB (CLUV) on the DDR. Thus, we have investigated the effect of a CLUV pre-stimulation on the different stress response pathways. We found that CLUV pre-stimulation enhances CPD repair capacity and leads to a cell cycle delay but leave residual unrepaired CPD. We further analyzed the consequence of the CLUV regimen on general gene and protein expression. We found that CLUV treatment influences biological processes related to the response to stress at the transcriptomic and proteomic levels. This overview study represents the first demonstration that human cells respond to chronic UV irradiation by modulating their genotoxic stress response mechanisms.
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Affiliation(s)
- Marie-Catherine Drigeard Desgarnier
- Axe Médecine Régénératrice, Centre de Recherche du CHU de Québec – Université Laval, Hôpital du Saint-Sacrement, Québec, Quebec, Canada
- Centre de Recherche en Organogénèse Expérimentale de l'Université Laval/LOEX, Université Laval, Québec, Quebec, Canada
| | - Frédéric Fournier
- Centre de Protéomique, Centre de Recherche du CHU de Québec – Université Laval, Québec, Quebec, Canada
- Département de Médicine Moléculaire, Université Laval, Québec, Canada
| | - Arnaud Droit
- Centre de Protéomique, Centre de Recherche du CHU de Québec – Université Laval, Québec, Quebec, Canada
- Département de Médicine Moléculaire, Université Laval, Québec, Canada
| | - Patrick J. Rochette
- Axe Médecine Régénératrice, Centre de Recherche du CHU de Québec – Université Laval, Hôpital du Saint-Sacrement, Québec, Quebec, Canada
- Centre de Recherche en Organogénèse Expérimentale de l'Université Laval/LOEX, Université Laval, Québec, Quebec, Canada
- Département d’Ophtalmologie et ORL - Chirurgie Cervico-Faciale, Université Laval, Québec, Canada
- * E-mail:
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14
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Uzcanga G, Lara E, Gutiérrez F, Beaty D, Beske T, Teran R, Navarro JC, Pasero P, Benítez W, Poveda A. Nuclear DNA replication and repair in parasites of the genus Leishmania: Exploiting differences to develop innovative therapeutic approaches. Crit Rev Microbiol 2016; 43:156-177. [PMID: 27960617 DOI: 10.1080/1040841x.2016.1188758] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Leishmaniasis is a common tropical disease that affects mainly poor people in underdeveloped and developing countries. This largely neglected infection is caused by Leishmania spp, a parasite from the Trypanosomatidae family. This parasitic disease has different clinical manifestations, ranging from localized cutaneous to more harmful visceral forms. The main limitations of the current treatments are their high cost, toxicity, lack of specificity, and long duration. Efforts to improve treatments are necessary to deal with this infectious disease. Many approved drugs to combat diseases as diverse as cancer, bacterial, or viral infections take advantage of specific features of the causing agent or of the disease. Recent evidence indicates that the specific characteristics of the Trypanosomatidae replication and repair machineries could be used as possible targets for the development of new treatments. Here, we review in detail the molecular mechanisms of DNA replication and repair regulation in trypanosomatids of the genus Leishmania and the drugs that could be useful against this disease.
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Affiliation(s)
- Graciela Uzcanga
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador.,b Programa Prometeo , SENESCYT, Whymper E7-37 y Alpallana, Quito , Ecuador.,c Facultad de Ciencias Naturales y Ambientales, Universidad Internacional SEK Calle Alberto Einstein sn y 5ta transversal , Quito , Ecuador.,d Fundación Instituto de Estudios Avanzados-IDEA , Caracas , Venezuela
| | - Eliana Lara
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador.,e Institute of Human Genetics , CNRS UPR 1142, 141 rue de la Cardonille, Equipe Labellisée Ligue Contre le Cancer , Montpellier cedex 5 , France
| | - Fernanda Gutiérrez
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador
| | - Doyle Beaty
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador
| | - Timo Beske
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador
| | - Rommy Teran
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador
| | - Juan-Carlos Navarro
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador.,f Universidad Central de Venezuela, Instituto de Zoología y Ecología Tropical , Caracas , Venezuela.,g Facultad de Ciencias Naturales y Ambientales, Universidad Internacional SEK, Calle Alberto Einstein sn y 5ta transversal , Quito , Ecuador
| | - Philippe Pasero
- e Institute of Human Genetics , CNRS UPR 1142, 141 rue de la Cardonille, Equipe Labellisée Ligue Contre le Cancer , Montpellier cedex 5 , France
| | - Washington Benítez
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador
| | - Ana Poveda
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador
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15
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Hassanpour M, Cheraghi O, Siavashi V, Rahbarghazi R, Nouri M. A reversal of age-dependent proliferative capacity of endothelial progenitor cells from different species origin in in vitro condition. J Cardiovasc Thorac Res 2016; 8:102-106. [PMID: 27777694 PMCID: PMC5075357 DOI: 10.15171/jcvtr.2016.22] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 07/11/2016] [Indexed: 01/09/2023] Open
Abstract
Introduction: A large number of cardiovascular disorders and abnormalities, notably accelerated vascular deficiencies could be related to aging changes and increased length of life. During the past decades, the discovery of different stem cells facilitates ongoing attempts for attenuating many disorders, especially in vascular beds. Endothelial progenitor cells (EPCs) are a subtype of stem cells that have potent capacity to differentiate into mature endothelial cells (ECs). However, some documented studies reported an age-related decline in proliferation and function of many stem cells. There is no data on aging effect upon proliferation and morphological feature of EPCs. Methods: To show aging effect on EPCs proliferation and multipotentiality, bone marrow samples were provided from old and young cases in three different species; human, mouse and dog. After 7 days of culture, the cell morphology and clonogenic capacity were evaluated. We also calculated the mean number of colonies both in bone marrow samples from old and young subjects. To confirm the cell phenotype, isolated cells were immune-phenotyped by a panel of antibodies against Tie-2, CD133 and CD309 markers. Results: Our results showed that EPCs exhibited prominent spindle form in all bone marrow samples from young cases while the cell shape became more round by aging. Notably, the number of colonies was reduced in aged samples as compared to parallel young subject samples (P < 0.05). We also detected that the expression of endothelial related markers diminished by aging. Conclusion: The results of this study suggest that the age-related vascular abnormalities could be presumably related to the decline in stemness capacity of EPCs.
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Affiliation(s)
- Mehdi Hassanpour
- Department of Clinical Biochemistry and Laboratory Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Omid Cheraghi
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran ; Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahid Siavashi
- Department of Clinical Pathology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Reza Rahbarghazi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Nouri
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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16
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Chen Y, Zhu WG. Biological function and regulation of histone and non-histone lysine methylation in response to DNA damage. Acta Biochim Biophys Sin (Shanghai) 2016; 48:603-16. [PMID: 27217472 DOI: 10.1093/abbs/gmw050] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/21/2016] [Indexed: 02/07/2023] Open
Abstract
DNA damage response (DDR) signaling network is initiated to protect cells from various exogenous and endogenous damage resources. Timely and accurate regulation of DDR proteins is required for distinct DNA damage repair pathways. Post-translational modifications of histone and non-histone proteins play a vital role in the DDR factor foci formation and signaling pathway. Phosphorylation, ubiquitylation, SUMOylation, neddylation, poly(ADP-ribosyl)ation, acetylation, and methylation are all involved in the spatial-temporal regulation of DDR, among which phosphorylation and ubiquitylation are well studied. Studies in the past decade also revealed extensive roles of lysine methylation in response to DNA damage. Lysine methylation is finely regulated by plenty of lysine methyltransferases, lysine demethylases, and can be recognized by proteins with chromodomain, plant homeodomain, Tudor domain, malignant brain tumor domain, or proline-tryptophan-tryptophan-proline domain. In this review, we outline the dynamics and regulation of histone lysine methylation at canonical (H3K4, H3K9, H3K27, H3K36, H3K79, and H4K20) and non-canonical sites after DNA damage, and discuss their context-specific functions in DDR protein recruitment or extraction, chromatin environment establishment, and transcriptional regulation. We also present the emerging advances of lysine methylation in non-histone proteins during DDR.
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Affiliation(s)
- Yongcan Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China Peking University-Tsinghua University Center for Life Sciences, Beijing 100191, China
| | - Wei-Guo Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China Peking University-Tsinghua University Center for Life Sciences, Beijing 100191, China School of Medicine, Shenzhen University, Shenzhen 518060, China
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17
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Morera L, Lübbert M, Jung M. Targeting histone methyltransferases and demethylases in clinical trials for cancer therapy. Clin Epigenetics 2016; 8:57. [PMID: 27222667 PMCID: PMC4877953 DOI: 10.1186/s13148-016-0223-4] [Citation(s) in RCA: 279] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/04/2016] [Indexed: 12/13/2022] Open
Abstract
The term epigenetics is defined as heritable changes in gene expression that are not due to alterations of the DNA sequence. In the last years, it has become more and more evident that dysregulated epigenetic regulatory processes have a central role in cancer onset and progression. In contrast to DNA mutations, epigenetic modifications are reversible and, hence, suitable for pharmacological interventions. Reversible histone methylation is an important process within epigenetic regulation, and the investigation of its role in cancer has led to the identification of lysine methyltransferases and demethylases as promising targets for new anticancer drugs. In this review, we describe those enzymes and their inhibitors that have already reached the first stages of clinical trials in cancer therapy, namely the histone methyltransferases DOT1L and EZH2 as well as the demethylase LSD1.
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Affiliation(s)
- Ludovica Morera
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Michael Lübbert
- Department of Hematology and Oncology, University of Freiburg Medical Center, Hugstetter Straße 55, 79106 Freiburg, Germany ; German Cancer Consortium (DKTK), Freiburg, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstraße 25, 79104 Freiburg, Germany ; German Cancer Consortium (DKTK), Freiburg, Germany
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18
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Histone modifications in DNA damage response. SCIENCE CHINA-LIFE SCIENCES 2016; 59:257-70. [PMID: 26825946 DOI: 10.1007/s11427-016-5011-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/04/2015] [Indexed: 12/20/2022]
Abstract
DNA damage is a relatively common event in eukaryotic cell and may lead to genetic mutation and even cancer. DNA damage induces cellular responses that enable the cell either to repair the damaged DNA or cope with the damage in an appropriate way. Histone proteins are also the fundamental building blocks of eukaryotic chromatin besides DNA, and many types of post-translational modifications often occur on tails of histones. Although the function of these modifications has remained elusive, there is ever-growing studies suggest that histone modifications play vital roles in several chromatin-based processes, such as DNA damage response. In this review, we will discuss the main histone modifications, and their functions in DNA damage response.
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19
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Abstract
Homologous recombination provides high-fidelity DNA repair throughout all domains of life. Live cell fluorescence microscopy offers the opportunity to image individual recombination events in real time providing insight into the in vivo biochemistry of the involved proteins and DNA molecules as well as the cellular organization of the process of homologous recombination. Herein we review the cell biological aspects of mitotic homologous recombination with a focus on Saccharomyces cerevisiae and mammalian cells, but will also draw on findings from other experimental systems. Key topics of this review include the stoichiometry and dynamics of recombination complexes in vivo, the choreography of assembly and disassembly of recombination proteins at sites of DNA damage, the mobilization of damaged DNA during homology search, and the functional compartmentalization of the nucleus with respect to capacity of homologous recombination.
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Affiliation(s)
- Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Rodney Rothstein
- Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032
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20
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McGrath J, Trojer P. Targeting histone lysine methylation in cancer. Pharmacol Ther 2015; 150:1-22. [PMID: 25578037 DOI: 10.1016/j.pharmthera.2015.01.002] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 12/03/2014] [Indexed: 02/06/2023]
Abstract
Within the vast landscape of histone modifications lysine methylation has gained increasing attention because of its profound regulatory potential. The methylation of lysine residues on histone proteins modulates chromatin structure and thereby contributes to the regulation of DNA-based nuclear processes such as transcription, replication and repair. Protein families with opposing catalytic activities, lysine methyltransferases (KMTs) and demethylases (KDMs), dynamically control levels of histone lysine methylation and individual enzymes within these families have become candidate oncology targets in recent years. A number of high quality small molecule inhibitors of these enzymes have been identified. Several of these compounds elicit selective cancer cell killing in vitro and robust efficacy in vivo, suggesting that targeting 'histone lysine methylation pathways' may be a relevant, emerging cancer therapeutic strategy. Here, we discuss individual histone lysine methylation pathway targets, the properties of currently available small molecule inhibitors and their application in the context of cancer.
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Affiliation(s)
- John McGrath
- Constellation Pharmaceuticals, 215 1st Street Suite 200, Cambridge, MA, 02142, USA
| | - Patrick Trojer
- Constellation Pharmaceuticals, 215 1st Street Suite 200, Cambridge, MA, 02142, USA.
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21
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House NCM, Koch MR, Freudenreich CH. Chromatin modifications and DNA repair: beyond double-strand breaks. Front Genet 2014; 5:296. [PMID: 25250043 PMCID: PMC4155812 DOI: 10.3389/fgene.2014.00296] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 08/08/2014] [Indexed: 12/28/2022] Open
Abstract
DNA repair must take place in the context of chromatin, and chromatin modifications and DNA repair are intimately linked. The study of double-strand break repair has revealed numerous histone modifications that occur after induction of a DSB, and modification of the repair factors themselves can also occur. In some cases the function of the modification is at least partially understood, but in many cases it is not yet clear. Although DSB repair is a crucial activity for cell survival, DSBs account for only a small percentage of the DNA lesions that occur over the lifetime of a cell. Repair of single-strand gaps, nicks, stalled forks, alternative DNA structures, and base lesions must also occur in a chromatin context. There is increasing evidence that these repair pathways are also regulated by histone modifications and chromatin remodeling. In this review, we will summarize the current state of knowledge of chromatin modifications that occur during non-DSB repair, highlighting similarities and differences to DSB repair as well as remaining questions.
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Affiliation(s)
| | - Melissa R Koch
- Department of Biology, Tufts University Medford, MA, USA
| | - Catherine H Freudenreich
- Department of Biology, Tufts University Medford, MA, USA ; Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University Boston, MA, USA
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22
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Alpatov R, Lesch BJ, Nakamoto-Kinoshita M, Blanco A, Chen S, Stützer A, Armache KJ, Simon MD, Xu C, Ali M, Murn J, Prisic S, Kutateladze TG, Vakoc CR, Min J, Kingston RE, Fischle W, Warren ST, Page DC, Shi Y. A chromatin-dependent role of the fragile X mental retardation protein FMRP in the DNA damage response. Cell 2014; 157:869-81. [PMID: 24813610 DOI: 10.1016/j.cell.2014.03.040] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 02/04/2014] [Accepted: 03/20/2014] [Indexed: 01/18/2023]
Abstract
Fragile X syndrome, a common form of inherited intellectual disability, is caused by loss of the fragile X mental retardation protein FMRP. FMRP is present predominantly in the cytoplasm, where it regulates translation of proteins that are important for synaptic function. We identify FMRP as a chromatin-binding protein that functions in the DNA damage response (DDR). Specifically, we show that FMRP binds chromatin through its tandem Tudor (Agenet) domain in vitro and associates with chromatin in vivo. We also demonstrate that FMRP participates in the DDR in a chromatin-binding-dependent manner. The DDR machinery is known to play important roles in developmental processes such as gametogenesis. We show that FMRP occupies meiotic chromosomes and regulates the dynamics of the DDR machinery during mouse spermatogenesis. These findings suggest that nuclear FMRP regulates genomic stability at the chromatin interface and may impact gametogenesis and some developmental aspects of fragile X syndrome.
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Affiliation(s)
- Roman Alpatov
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Bluma J Lesch
- Howard Hughes Medical Institute, Whitehead Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Mika Nakamoto-Kinoshita
- Departments of Human Genetics, Biochemistry, and Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andres Blanco
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Shuzhen Chen
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Alexandra Stützer
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Karim J Armache
- Massachusetts General Hospital, Department of Molecular Biology and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Matthew D Simon
- Massachusetts General Hospital, Department of Molecular Biology and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Chao Xu
- Structural Genomics Consortium and Department of Physiology, University of Toronto, Toronto ON M5G 1L7, Canada
| | - Muzaffar Ali
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jernej Murn
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sladjana Prisic
- Division of Infectious Diseases, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | | | - Jinrong Min
- Structural Genomics Consortium and Department of Physiology, University of Toronto, Toronto ON M5G 1L7, Canada
| | - Robert E Kingston
- Massachusetts General Hospital, Department of Molecular Biology and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Stephen T Warren
- Departments of Human Genetics, Biochemistry, and Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David C Page
- Howard Hughes Medical Institute, Whitehead Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Yang Shi
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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23
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Dot1-dependent histone H3K79 methylation promotes the formation of meiotic double-strand breaks in the absence of histone H3K4 methylation in budding yeast. PLoS One 2014; 9:e96648. [PMID: 24797370 PMCID: PMC4010517 DOI: 10.1371/journal.pone.0096648] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/09/2014] [Indexed: 11/19/2022] Open
Abstract
Epigenetic marks such as histone modifications play roles in various chromosome dynamics in mitosis and meiosis. Methylation of histones H3 at positions K4 and K79 is involved in the initiation of recombination and the recombination checkpoint, respectively, during meiosis in the budding yeast. Set1 promotes H3K4 methylation while Dot1 promotes H3K79 methylation. In this study, we carried out detailed analyses of meiosis in mutants of the SET1 and DOT1 genes as well as methylation-defective mutants of histone H3. We confirmed the role of Set1-dependent H3K4 methylation in the formation of double-strand breaks (DSBs) in meiosis for the initiation of meiotic recombination, and we showed the involvement of Dot1 (H3K79 methylation) in DSB formation in the absence of Set1-dependent H3K4 methylation. In addition, we showed that the histone H3K4 methylation-defective mutants are defective in SC elongation, although they seem to have moderate reduction of DSBs. This suggests that high levels of DSBs mediated by histone H3K4 methylation promote SC elongation.
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24
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Rossodivita AA, Boudoures AL, Mecoli JP, Steenkiste EM, Karl AL, Vines EM, Cole AM, Ansbro MR, Thompson JS. Histone H3 K79 methylation states play distinct roles in UV-induced sister chromatid exchange and cell cycle checkpoint arrest in Saccharomyces cerevisiae. Nucleic Acids Res 2014; 42:6286-99. [PMID: 24748660 PMCID: PMC4041417 DOI: 10.1093/nar/gku242] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Histone post-translational modifications have been shown to contribute to DNA damage repair. Prior studies have suggested that specific H3K79 methylation states play distinct roles in the response to UV-induced DNA damage. To evaluate these observations, we examined the effect of altered H3K79 methylation patterns on UV-induced G1/S checkpoint response and sister chromatid exchange (SCE). We found that the di- and trimethylated states both contribute to activation of the G1/S checkpoint to varying degrees, depending on the synchronization method, although methylation is not required for checkpoint in response to high levels of UV damage. In contrast, UV-induced SCE is largely a product of the trimethylated state, which influences the usage of gene conversion versus popout mechanisms. Regulation of H3K79 methylation by H2BK123 ubiquitylation is important for both checkpoint function and SCE. H3K79 methylation is not required for the repair of double-stranded breaks caused by transient HO endonuclease expression, but does play a modest role in survival from continuous exposure. The overall results provide evidence for the participation of H3K79 methylation in UV-induced recombination repair and checkpoint activation, and further indicate that the di- and trimethylation states play distinct roles in these DNA damage response pathways.
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Affiliation(s)
| | - Anna L Boudoures
- Department of Biology, Denison University, Granville, OH 43023, USA
| | | | | | - Andrea L Karl
- Department of Biology, Denison University, Granville, OH 43023, USA
| | - Eudora M Vines
- Department of Biology, Denison University, Granville, OH 43023, USA
| | - Arron M Cole
- Department of Biology, Denison University, Granville, OH 43023, USA
| | - Megan R Ansbro
- Department of Biology, Denison University, Granville, OH 43023, USA
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25
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Kim W, Choi M, Kim JE. The histone methyltransferase Dot1/DOT1L as a critical regulator of the cell cycle. Cell Cycle 2014; 13:726-38. [PMID: 24526115 PMCID: PMC3979909 DOI: 10.4161/cc.28104] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Dot1/DOT1L catalyzes the methylation of histone H3 lysine 79 (H3K79), which regulates diverse cellular processes, such as development, reprogramming, differentiation, and proliferation. In regards to these processes, studies of Dot1/DOT1L-dependent H3K79 methylation have mainly focused on the transcriptional regulation of specific genes. Although the gene transcription mediated by Dot1/DOT1L during the cell cycle is not fully understood, H3K79 methylation plays a critical role in the progression of G 1 phase, S phase, mitosis, and meiosis. This modification may contribute to the chromatin structure that controls gene expression, replication initiation, DNA damage response, microtubule reorganization, chromosome segregation, and heterochromatin formation. Overall, Dot1/DOT1L is required to maintain genomic and chromosomal stability. This review summarizes the several functions of Dot1/DOT1L and highlights its role in cell cycle regulation.
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Affiliation(s)
- Wootae Kim
- Department of Pharmacology; School of Medicine; Kyung Hee University; Seoul, Republic of Korea; Department of Biomedical Science; Graduate School; Kyung Hee University; Seoul, Republic of Korea
| | - Minji Choi
- Department of Pharmacology; School of Medicine; Kyung Hee University; Seoul, Republic of Korea; Department of Biomedical Science; Graduate School; Kyung Hee University; Seoul, Republic of Korea
| | - Ja-Eun Kim
- Department of Pharmacology; School of Medicine; Kyung Hee University; Seoul, Republic of Korea; Department of Biomedical Science; Graduate School; Kyung Hee University; Seoul, Republic of Korea
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26
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Fedorov DV, Kovaltsova SV, Evstuhina TA, Peshekhonov VT, Chernenkov AY, Korolev VG. HSM6 gene is identical to PSY4 gene in Saccharomyces cerevisiae yeasts. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413020063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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27
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Distinct requirements within the Msh3 nucleotide binding pocket for mismatch and double-strand break repair. J Mol Biol 2013; 425:1881-1898. [PMID: 23458407 DOI: 10.1016/j.jmb.2013.02.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 02/21/2013] [Accepted: 02/22/2013] [Indexed: 11/20/2022]
Abstract
In Saccharomyces cerevisiae, repair of insertion/deletion loops is carried out by Msh2-Msh3-mediated mismatch repair (MMR). Msh2-Msh3 is also required for 3' non-homologous tail removal (3' NHTR) in double-strand break repair. In both pathways, Msh2-Msh3 binds double-strand/single-strand junctions and initiates repair in an ATP-dependent manner. However, the kinetics of the two processes appear different; MMR is likely rapid in order to coordinate with the replication fork, whereas 3' NHTR has been shown to be a slower process. To understand the molecular requirements in both repair pathways, we performed an in vivo analysis of well-conserved residues in Msh3 that are hypothesized to be required for MMR and/or 3' NHTR. These residues are predicted to be involved in either communication between the DNA-binding and ATPase domains within the complex or nucleotide binding and/or exchange within Msh2-Msh3. We identified a set of aromatic residues within the FLY motif of the predicted Msh3 nucleotide binding pocket that are essential for Msh2-Msh3-mediated MMR but are largely dispensable for 3' NHTR. In contrast, mutations in other regions gave similar phenotypes in both assays. Based on these results, we suggest that the two pathways have distinct requirements with respect to the position of the bound ATP within Msh3. We propose that the differences are related, at least in part, to the kinetics of each pathway. Proper binding and positioning of ATP is required to induce rapid conformational changes at the replication fork, but is less important when more time is available for repair, as in 3' NHTR.
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28
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Ontoso D, Acosta I, van Leeuwen F, Freire R, San-Segundo PA. Dot1-dependent histone H3K79 methylation promotes activation of the Mek1 meiotic checkpoint effector kinase by regulating the Hop1 adaptor. PLoS Genet 2013; 9:e1003262. [PMID: 23382701 PMCID: PMC3561090 DOI: 10.1371/journal.pgen.1003262] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 12/06/2012] [Indexed: 12/20/2022] Open
Abstract
During meiosis, accurate chromosome segregation relies on the proper interaction between homologous chromosomes, including synapsis and recombination. The meiotic recombination checkpoint is a quality control mechanism that monitors those crucial events. In response to defects in synapsis and/or recombination, this checkpoint blocks or delays progression of meiosis, preventing the formation of aberrant gametes. Meiotic recombination occurs in the context of chromatin and histone modifications, which play crucial roles in the maintenance of genomic integrity. Here, we unveil the role of Dot1-dependent histone H3 methylation at lysine 79 (H3K79me) in this meiotic surveillance mechanism. We demonstrate that the meiotic checkpoint function of Dot1 relies on H3K79me because, like the dot1 deletion, H3-K79A or H3-K79R mutations suppress the checkpoint-imposed meiotic delay of a synapsis-defective zip1 mutant. Moreover, by genetically manipulating Dot1 catalytic activity, we find that the status of H3K79me modulates the meiotic checkpoint response. We also define the phosphorylation events involving activation of the meiotic checkpoint effector Mek1 kinase. Dot1 is required for Mek1 autophosphorylation, but not for its Mec1/Tel1-dependent phosphorylation. Dot1-dependent H3K79me also promotes Hop1 activation and its proper distribution along zip1 meiotic chromosomes, at least in part, by regulating Pch2 localization. Furthermore, HOP1 overexpression bypasses the Dot1 requirement for checkpoint activation. We propose that chromatin remodeling resulting from unrepaired meiotic DSBs and/or faulty interhomolog interactions allows Dot1-mediated H3K79-me to exclude Pch2 from the chromosomes, thus driving localization of Hop1 along chromosome axes and enabling Mek1 full activation to trigger downstream responses, such as meiotic arrest. In sexually reproducing organisms, meiosis divides the number of chromosomes by half to generate gametes. Meiosis involves a series of interactions between maternal and paternal chromosomes leading to the exchange of genetic material by recombination. Completion of these processes is required for accurate distribution of chromosomes to the gametes. Meiotic cells possess quality-control mechanisms (checkpoints) to monitor those critical events. When failures occur, the checkpoint blocks meiotic progression to prevent the formation of aneuploid gametes. Genetic information is packaged into chromatin; histone modifications regulate multiple aspects of DNA metabolism to maintain genomic integrity. Dot1 is a conserved methyltransferase, responsible for histone H3 methylation at lysine 79, that is required for the meiotic recombination checkpoint. Here we decipher the molecular mechanism underlying Dot1 meiotic checkpoint function. We show that Dot1 catalytic activity correlates with the strength of the checkpoint response. By regulating Pch2 chromatin distribution, Dot1 controls localization of the chromosome axial component Hop1, which, in turn, contributes to activation of Mek1, the major effector kinase of the checkpoint. Our findings suggest that, in response to meiotic defects, the chromatin environment created by a constitutive histone mark orchestrates distribution of structural components of the chromosomes supporting activation of the meiotic checkpoint.
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Affiliation(s)
- David Ontoso
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas and University of Salamanca, Salamanca, Spain
| | - Isabel Acosta
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas and University of Salamanca, Salamanca, Spain
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de Canarias, Tenerife, Spain
| | - Pedro A. San-Segundo
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas and University of Salamanca, Salamanca, Spain
- * E-mail:
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Cruz LA, Guecheva TN, Bonato D, Henriques JAP. Relationships between chromatin remodeling and DNA damage repair induced by 8-methoxypsoralen and UVA in yeast Saccharomyces cerevisiae. Genet Mol Biol 2012; 35:1052-9. [PMID: 23412648 PMCID: PMC3571434 DOI: 10.1590/s1415-47572012000600021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Eukaryotic cells have developed mechanisms to prevent genomic instability, such as DNA damage detection and repair, control of cell cycle progression and cell death induction. The bifunctional compound furocumarin 8-methoxypsoralen (8-MOP) is widely used in the treatment of various inflammatory skin diseases. In this review, we summarize recent data about the role of chromatin remodeling in the repair of DNA damage induced by treatment with 8-methoxypsoralen plus UVA (8-MOP+UVA), focusing on repair proteins in budding yeast Saccharomyces cerevisiae, an established model system for studying DNA repair pathways. The interstrand crosslinks (ICL) formed by the 8-MOP+UVA treatment are detrimental lesions that can block transcription and replication, leading to cell death if not repaired. Current data show the involvement of different pathways in ICL processing, such as nucleotide excision repair (NER), base excision repair (BER), translesion repair (TLS) and double-strand break repair. 8-MOP+UVA treatment in yeast enhances the expression of genes involved in the DNA damage response, double strand break repair by homologous replication, as well as genes related to cell cycle regulation. Moreover, alterations in the expression of subtelomeric genes and genes related to chromatin remodeling are consistent with structural modifications of chromatin relevant to DNA repair. Taken together, these findings indicate a specific profile in 8-MOP+UVA responses related to chromatin remodeling and DNA repair.
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Affiliation(s)
- Lavínia Almeida Cruz
- Programa de Pós-Gradução em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Abstract
DNA damage in cells is often the result of constant genotoxic insult. Nevertheless, efficient DNA repair pathways are able to maintain genomic integrity. Over the past decade it has been revealed that it is not only kinase signalling pathways which play a central role in this process, but also the different post-translational modifications at lysine residues of histone (chromatin) and non-histone proteins. These lysine modifications include acetylation, methylation, ubiquitination and SUMOylation. Genomic instability is often the major cause of different diseases, especially cancer, where lysine modifications are altered and thereby have an impact on the various DNA repair mechanisms. This chapter will discuss the recent advances in our understanding of the role of different lysine modifications in DNA repair and its physiological consequences.
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31
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Dion V, Kalck V, Horigome C, Towbin BD, Gasser SM. Increased mobility of double-strand breaks requires Mec1, Rad9 and the homologous recombination machinery. Nat Cell Biol 2012; 14:502-9. [PMID: 22484486 DOI: 10.1038/ncb2465] [Citation(s) in RCA: 236] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 02/14/2012] [Indexed: 01/13/2023]
Abstract
Chromatin mobility is thought to facilitate homology search during homologous recombination and to shift damage either towards or away from specialized repair compartments. However, unconstrained mobility of double-strand breaks could also promote deleterious chromosomal translocations. Here we use live time-lapse fluorescence microscopy to track the mobility of damaged DNA in budding yeast. We found that a Rad52-YFP focus formed at an irreparable double-strand break moves in a larger subnuclear volume than the undamaged locus. In contrast, Rad52-YFP bound at damage arising from a protein-DNA adduct shows no increase in movement. Mutant analysis shows that enhanced double-strand-break mobility requires Rad51, the ATPase activity of Rad54, the ATR homologue Mec1 and the DNA-damage-response mediator Rad9. Consistent with a role for movement in the homology-search step of homologous recombination, we show that recombination intermediates take longer to form in cells lacking Rad9.
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Affiliation(s)
- Vincent Dion
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
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32
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The yeast forkhead transcription factors fkh1 and fkh2 regulate lifespan and stress response together with the anaphase-promoting complex. PLoS Genet 2012; 8:e1002583. [PMID: 22438832 PMCID: PMC3305399 DOI: 10.1371/journal.pgen.1002583] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 01/20/2012] [Indexed: 11/19/2022] Open
Abstract
Forkhead box O (FOXO) transcription factors have a conserved function in regulating metazoan lifespan. A key function in this process involves the regulation of the cell cycle and stress responses including free radical scavenging. We employed yeast chronological and replicative lifespan assays, as well as oxidative stress assays, to explore the potential evolutionary conservation of function between the FOXOs and the yeast forkhead box transcription factors FKH1 and FKH2. We report that the deletion of both FKH genes impedes normal lifespan and stress resistance, particularly in stationary phase cells, which are non-responsive to caloric restriction. Conversely, increased expression of the FKHs leads to extended lifespan and improved stress response. Here we show the Anaphase-Promoting Complex (APC) genetically interacts with the Fkh pathway, likely working in a linear pathway under normal conditions, as fkh1Δ fkh2Δ post-mitotic survival is epistatic to that observed in apc5(CA) mutants. However, under stress conditions, post-mitotic survival is dramatically impaired in apc5(CA) fkh1Δ fkh2Δ, while increased expression of either FKH rescues APC mutant growth defects. This study establishes the FKHs role as evolutionarily conserved regulators of lifespan in yeast and identifies the APC as a novel component of this mechanism under certain conditions, likely through combined regulation of stress response, genomic stability, and cell cycle regulation.
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Hansen L, Kim NK, Mariño-Ramírez L, Landsman D. Analysis of biological features associated with meiotic recombination hot and cold spots in Saccharomyces cerevisiae. PLoS One 2011; 6:e29711. [PMID: 22242140 PMCID: PMC3248464 DOI: 10.1371/journal.pone.0029711] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 12/01/2011] [Indexed: 01/19/2023] Open
Abstract
Meiotic recombination is not distributed uniformly throughout the genome. There are regions of high and low recombination rates called hot and cold spots, respectively. The recombination rate parallels the frequency of DNA double-strand breaks (DSBs) that initiate meiotic recombination. The aim is to identify biological features associated with DSB frequency. We constructed vectors representing various chromatin and sequence-based features for 1179 DSB hot spots and 1028 DSB cold spots. Using a feature selection approach, we have identified five features that distinguish hot from cold spots in Saccharomyces cerevisiae with high accuracy, namely the histone marks H3K4me3, H3K14ac, H3K36me3, and H3K79me3; and GC content. Previous studies have associated H3K4me3, H3K36me3, and GC content with areas of mitotic recombination. H3K14ac and H3K79me3 are novel predictions and thus represent good candidates for further experimental study. We also show nucleosome occupancy maps produced using next generation sequencing exhibit a bias at DSB hot spots and this bias is strong enough to obscure biologically relevant information. A computational approach using feature selection can productively be used to identify promising biological associations. H3K14ac and H3K79me3 are novel predictions of chromatin marks associated with meiotic DSBs. Next generation sequencing can exhibit a bias that is strong enough to lead to incorrect conclusions. Care must be taken when interpreting high throughput sequencing data where systematic biases have been documented.
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Affiliation(s)
- Loren Hansen
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
- Boston University, Bioinformatics Program, Boston, Massachusetts, United States of America
| | - Nak-Kyeong Kim
- Department of Mathematics and Statistics, Old Dominion University, Norfolk, Virginia, United States of America
| | - Leonardo Mariño-Ramírez
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
- PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia
- * E-mail:
| | - David Landsman
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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34
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Lightfoot J, Testori S, Barroso C, Martinez-Perez E. Loading of meiotic cohesin by SCC-2 is required for early processing of DSBs and for the DNA damage checkpoint. Curr Biol 2011; 21:1421-30. [PMID: 21856158 DOI: 10.1016/j.cub.2011.07.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/21/2011] [Accepted: 07/07/2011] [Indexed: 12/20/2022]
Abstract
BACKGROUND Chromosome segregation and the repair of DNA double-strand breaks (DSBs) by homologous recombination require cohesin, the protein complex that mediates sister chromatid cohesion (SCC). In addition, cohesin is also required for the integrity of DNA damage checkpoints in somatic cells, where cohesin loading depends on a conserved complex containing the Scc2/Nipbl protein. Although cohesin is required for the completion of meiotic recombination, little is known about how cohesin promotes the repair of meiotic DSBs and about the factors that promote loading of cohesin during meiosis. RESULTS Here we show that during Caenorhabditis elegans meiosis, loading of cohesin requires SCC-2, whereas the cohesin-related complexes condensin and SMC-5/6 can be loaded by mechanisms independent of both SCC-2 and cohesin. Although the lack of cohesin in scc-2 mutants impairs the repair of meiotic DSBs, surprisingly, the persistent DNA damage fails to trigger an apoptotic response of the conserved pachytene DNA damage checkpoint. Mutants carrying an scc-3 allele that abrogates loading of meiotic cohesin are also deficient in the apoptotic response of the pachytene checkpoint, and both scc-2 and scc-3 mutants fail to recruit the DNA damage sensor 9-1-1 complex onto persistent damage sites during meiosis. Furthermore, we show that meiotic cohesin is also required for the timely loading of the RAD-51 recombinase to irradiation-induced DSBs. CONCLUSIONS We propose that meiotic cohesin promotes DSB processing and recruitment of DNA damage checkpoint proteins, thus implicating cohesin in the earliest steps of the DNA damage response during meiosis.
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Affiliation(s)
- James Lightfoot
- MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London W12 0NN, UK
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35
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Abstract
DOT1 (disruptor of telomeric silencing; also called Kmt4) was initially discovered in budding yeast in a genetic screen for genes whose deletion confers defects in telomeric silencing. Since the discovery ∼10 years ago that Dot1 and its mammalian homolog, DOT1L (DOT1-Like), possess histone methyltransferase activity toward histone H3 Lys 79, great progress has been made in characterizing their enzymatic activities and the role of Dot1/DOT1L-mediated H3K79 methylation in transcriptional regulation, cell cycle regulation, and the DNA damage response. In addition, gene disruption in mice has revealed that mouse DOT1L plays an essential role in embryonic development, hematopoiesis, cardiac function, and the development of leukemia. The involvement of DOT1L enzymatic activity in leukemogenesis driven by a subset of MLL (mixed-lineage leukemia) fusion proteins raises the possibility of targeting DOT1L for therapeutic intervention.
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Affiliation(s)
- Anh Tram Nguyen
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
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36
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Abstract
Adult stem cells exist in most mammalian organs and tissues and are indispensable for normal tissue homeostasis and repair. In most tissues, there is an age-related decline in stem cell functionality but not a depletion of stem cells. Such functional changes reflect deleterious effects of age on the genome, epigenome, and proteome, some of which arise cell autonomously and others of which are imposed by an age-related change in the local milieu or systemic environment. Notably, some of the changes, particularly epigenomic and proteomic, are potentially reversible, and both environmental and genetic interventions can result in the rejuvenation of aged stem cells. Such findings have profound implications for the stem cell–based therapy of age-related diseases.
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Affiliation(s)
- Ling Liu
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
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37
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38
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Nguyen AT, Xiao B, Neppl RL, Kallin EM, Li J, Chen T, Wang DZ, Xiao X, Zhang Y. DOT1L regulates dystrophin expression and is critical for cardiac function. Genes Dev 2011; 25:263-74. [PMID: 21289070 DOI: 10.1101/gad.2018511] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Histone methylation plays an important role in regulating gene expression. One such methylation occurs at Lys 79 of histone H3 (H3K79) and is catalyzed by the yeast DOT1 (disruptor of telomeric silencing) and its mammalian homolog, DOT1L. Previous studies have demonstrated that germline disruption of Dot1L in mice resulted in embryonic lethality. Here we report that cardiac-specific knockout of Dot1L results in increased mortality rate with chamber dilation, increased cardiomyocyte cell death, systolic dysfunction, and conduction abnormalities. These phenotypes mimic those exhibited in patients with dilated cardiomyopathy (DCM). Mechanistic studies reveal that DOT1L performs its function in cardiomyocytes through regulating Dystrophin (Dmd) transcription and, consequently, stability of the Dystrophin-glycoprotein complex important for cardiomyocyte viability. Importantly, expression of a miniDmd can largely rescue the DCM phenotypes, indicating that Dmd is a major target mediating DOT1L function in cardiomyocytes. Interestingly, analysis of available gene expression data sets indicates that DOT1L is down-regulated in idiopathic DCM patient samples compared with normal controls. Therefore, our study not only establishes a critical role for DOT1L-mediated H3K79 methylation in cardiomyocyte function, but also reveals the mechanism underlying the role of DOT1L in DCM. In addition, our study may open new avenues for the diagnosis and treatment of human heart disease.
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Affiliation(s)
- Anh T Nguyen
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, NC 27599, USA
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39
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Müller-Taubenberger A, Bönisch C, Fürbringer M, Wittek F, Hake SB. The histone methyltransferase Dot1 is required for DNA damage repair and proper development in Dictyostelium. Biochem Biophys Res Commun 2010; 404:1016-22. [PMID: 21187070 DOI: 10.1016/j.bbrc.2010.12.101] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 12/20/2010] [Indexed: 10/18/2022]
Abstract
Posttranslational histone modifications play an important role in modulating gene expression and chromatin structure. Here we report the identification of histone H3K79 dimethylation in the simple eukaryote Dictyostelium discoideum. We have deleted the D. discoideum Dot1/KMT4 homologue and demonstrate that it is the sole enzyme responsible for histone H3K79me2. Cells lacking Dot1 are reduced in growth and delayed in development, but do not show apparent changes in cell cycle regulation. Furthermore, our results indicate that Dot1 contributes to UV damage resistance and DNA repair in D. discoideum. In summary, the data support the view that the machinery controlling the setting of histone marks is evolutionary highly conserved and provide evidence that D. discoideum is a suitable model system to analyze these modifications and their functions during development and differentiation.
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Affiliation(s)
- Annette Müller-Taubenberger
- Institute for Anatomy and Cell Biology, Schillerstr. 42, Ludwig Maximilians University of Munich, 80336 Munich, Germany.
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40
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Lévesque N, Leung GP, Fok AK, Schmidt TI, Kobor MS. Loss of H3 K79 trimethylation leads to suppression of Rtt107-dependent DNA damage sensitivity through the translesion synthesis pathway. J Biol Chem 2010; 285:35113-22. [PMID: 20810656 DOI: 10.1074/jbc.m110.116855] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Genomic integrity is maintained by the coordinated interaction of many DNA damage response pathways, including checkpoints, DNA repair processes, and cell cycle restart. In Saccharomyces cerevisiae, the BRCA1 C-terminal domain-containing protein Rtt107/Esc4 is required for restart of DNA replication after successful repair of DNA damage and for cellular resistance to DNA-damaging agents. Rtt107 and its interaction partner Slx4 are phosphorylated during the initial phase of DNA damage response by the checkpoint kinases Mec1 and Tel1. Because the natural chromatin template plays an important role during the DNA damage response, we tested whether chromatin modifications affected the requirement for Rtt107 and Slx4 during DNA damage repair. Here, we report that the sensitivity to DNA-damaging agents of rtt107Δ and slx4Δ mutants was rescued by inactivation of the chromatin regulatory pathway leading to H3 K79 trimethylation. Further analysis revealed that lack of Dot1, the H3 K79 methyltransferase, led to activation of the translesion synthesis pathway, thereby allowing the survival in the presence of DNA damage. The DNA damage-induced phosphorylation of Rtt107 and Slx4, which was mutually dependent, was not restored in the absence of Dot1. The antagonistic relationship between Rtt107 and Dot1 was specific for DNA damage-induced phenotypes, whereas the genomic instability caused by loss of Rtt107 was not rescued. These data revealed a multifaceted functional relationship between Rtt107 and Dot1 in the DNA damage response and maintenance of genome integrity.
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Affiliation(s)
- Nancy Lévesque
- Department of Medical Genetics, University of British Columbia, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
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41
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Abstract
Histone methylation is an important regulator of gene expression; its coordinated activity is critical in complex developmental processes such as hematopoiesis. Disruptor of telomere silencing 1-like (DOT1L) is a unique histone methyltransferase that specifically methylates histone H3 at lysine 79. We analyzed Dot1L-mutant mice to determine influence of this enzyme on embryonic hematopoiesis. Mutant mice developed more slowly than wild-type embryos and died between embryonic days 10.5 and 13.5, displaying a striking anemia, especially apparent in small vessels of the yolk sac. Further, a severe, selective defect in erythroid, but not myeloid, differentiation was observed. Erythroid progenitors failed to develop normally, showing retarded progression through the cell cycle, accumulation during G₀/G₁ stage, and marked increase in apoptosis in response to erythroid growth factors. GATA2, a factor essential for early erythropoiesis, was significantly reduced in Dot1L-deficient cells, whereas expression of PU.1, a transcription factor that inhibits erythropoiesis and promotes myelopoiesis, was increased. These data suggest a model whereby DOT1L-dependent lysine 79 of histone H3 methylation serves as a critical regulator of a differentiation switch during early hematopoiesis, regulating steady-state levels of GATA2 and PU.1 transcription, thus controlling numbers of circulating erythroid and myeloid cells.
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42
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Conde F, Ontoso D, Acosta I, Gallego-Sánchez A, Bueno A, San-Segundo PA. Regulation of tolerance to DNA alkylating damage by Dot1 and Rad53 in Saccharomyces cerevisiae. DNA Repair (Amst) 2010; 9:1038-49. [PMID: 20674515 DOI: 10.1016/j.dnarep.2010.07.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 06/24/2010] [Accepted: 07/05/2010] [Indexed: 10/19/2022]
Abstract
To maintain genomic integrity cells have to respond properly to a variety of exogenous and endogenous factors that produce genome injuries and interfere with DNA replication. DNA integrity checkpoints coordinate this response by slowing cell cycle progression to provide time for the cell to repair the damage, stabilizing replication forks and stimulating DNA repair to restore the original DNA sequence and structure. In addition, there are also mechanisms of damage tolerance, such as translesion synthesis (TLS), which are important for survival after DNA damage. TLS allows replication to continue without removing the damage, but results in a higher frequency of mutagenesis. Here, we investigate the functional contribution of the Dot1 histone methyltransferase and the Rad53 checkpoint kinase to TLS regulation in Saccharomyces cerevisiae. We demonstrate that the Dot1-dependent status of H3K79 methylation modulates the resistance to the alkylating agent MMS, which depends on PCNA ubiquitylation at lysine 164. Strikingkly, either the absence of DOT1, which prevents full activation of Rad53, or the expression of an HA-tagged version of RAD53, which produces low amounts of the kinase, confer increased MMS resistance. However, the dot1Δ rad53-HA double mutant is hypersensitive to MMS and shows barely detectable amounts of activated kinase. Furthermore, moderate overexpression of RAD53 partially suppresses the MMS resistance of dot1Δ. In addition, we show that MMS-treated dot1Δ and rad53-HA cells display increased number of chromosome-associated Rev1 foci. We propose that threshold levels of Rad53 activity exquisitely modulate the tolerance to alkylating damage at least by controlling the abundance of the key TLS factor Rev1 bound to chromatin.
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Affiliation(s)
- Francisco Conde
- Instituto de Microbiología Bioquímica, Consejo Superior de Investigaciones Científicas and University of Salamanca, 37007 Salamanca, Spain
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43
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Lamarche BJ, Orazio NI, Weitzman MD. The MRN complex in double-strand break repair and telomere maintenance. FEBS Lett 2010; 584:3682-95. [PMID: 20655309 DOI: 10.1016/j.febslet.2010.07.029] [Citation(s) in RCA: 301] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Revised: 07/16/2010] [Accepted: 07/19/2010] [Indexed: 10/25/2022]
Abstract
Genomes are subject to constant threat by damaging agents that generate DNA double-strand breaks (DSBs). The ends of linear chromosomes need to be protected from DNA damage recognition and end-joining, and this is achieved through protein-DNA complexes known as telomeres. The Mre11-Rad50-Nbs1 (MRN) complex plays important roles in detection and signaling of DSBs, as well as the repair pathways of homologous recombination (HR) and non-homologous end-joining (NHEJ). In addition, MRN associates with telomeres and contributes to their maintenance. Here, we provide an overview of MRN functions at DSBs, and examine its roles in telomere maintenance and dysfunction.
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Affiliation(s)
- Brandon J Lamarche
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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44
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Murakami-Sekimata A, Huang D, Piening BD, Bangur C, Paulovich AG. The Saccharomyces cerevisiae RAD9, RAD17 and RAD24 genes are required for suppression of mutagenic post-replicative repair during chronic DNA damage. DNA Repair (Amst) 2010; 9:824-34. [PMID: 20472512 DOI: 10.1016/j.dnarep.2010.04.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 03/25/2010] [Accepted: 04/16/2010] [Indexed: 12/31/2022]
Abstract
In Saccharomyces cerevisiae, a DNA damage checkpoint in the S-phase is responsible for delaying DNA replication in response to genotoxic stress. This pathway is partially regulated by the checkpoint proteins Rad9, Rad17 and Rad24. Here, we describe a novel hypermutable phenotype for rad9Delta, rad17Delta and rad24Delta cells in response to a chronic 0.01% dose of the DNA alkylating agent MMS. We report that this hypermutability results from DNA damage introduction during the S-phase and is dependent on a functional translesion synthesis pathway. In addition, we performed a genetic screen for interactions with rad9Delta that confer sensitivity to 0.01% MMS. We report and quantify 25 genetic interactions with rad9Delta, many of which involve the post-replication repair machinery. From these data, we conclude that defects in S-phase checkpoint regulation lead to increased reliance on mutagenic translesion synthesis, and we describe a novel role for members of the S-phase DNA damage checkpoint in suppressing mutagenic post-replicative repair in response to sublethal MMS treatment.
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45
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Park G, Gong Z, Chen J, Kim JE. Characterization of the DOT1L Network: Implications of Diverse Roles for DOT1L. Protein J 2010; 29:213-23. [DOI: 10.1007/s10930-010-9242-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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46
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Mohan M, Herz HM, Takahashi YH, Lin C, Lai KC, Zhang Y, Washburn MP, Florens L, Shilatifard A. Linking H3K79 trimethylation to Wnt signaling through a novel Dot1-containing complex (DotCom). Genes Dev 2010; 24:574-89. [PMID: 20203130 DOI: 10.1101/gad.1898410] [Citation(s) in RCA: 242] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Epigenetic modifications of chromatin play an important role in the regulation of gene expression. KMT4/Dot1 is a conserved histone methyltransferase capable of methylating chromatin on Lys79 of histone H3 (H3K79). Here we report the identification of a multisubunit Dot1 complex (DotCom), which includes several of the mixed lineage leukemia (MLL) partners in leukemia such as ENL, AF9/MLLT3, AF17/MLLT6, and AF10/MLLT10, as well as the known Wnt pathway modifiers TRRAP, Skp1, and beta-catenin. We demonstrated that the human DotCom is indeed capable of trimethylating H3K79 and, given the association of beta-catenin, Skp1, and TRRAP, we investigated, and found, a role for Dot1 in Wnt/Wingless signaling in an in vivo model system. Knockdown of Dot1 in Drosophila results in decreased expression of a subset of Wingless target genes. Furthermore, the loss of expression for the Drosophila homologs of the Dot1-associated proteins involved in the regulation of H3K79 shows a similar reduction in expression of these Wingless targets. From yeast to human, specific trimethylation of H3K79 by Dot1 requires the monoubiquitination of histone H2B by the Rad6/Bre1 complex. Here, we demonstrate that depletion of Bre1, the E3 ligase required for H2B monoubiquitination, leads specifically to reduced bulk H3K79 trimethylation levels and a reduction in expression of many Wingless targets. Overall, our study describes for the first time the components of DotCom and links the specific regulation of H3K79 trimethylation by Dot1 and its associated factors to the Wnt/Wingless signaling pathway.
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Affiliation(s)
- Man Mohan
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
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47
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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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48
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Abstract
In a recent issue of Molecular Cell, Schulze et al. (2009) described distinct distributions and regulation of Dot1-dependent methylation states at lysine 79 on histone H3 and showed cell-cycle regulation of K79 dimethylation on genes expressed during the G1/S phase.
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Affiliation(s)
- Jane Mellor
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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