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Aguirre S, Pappa S, Serna-Pujol N, Padilla N, Iacobucci S, Nacht AS, Vicent GP, Jordan A, de la Cruz X, Martínez-Balbás MA. PHF2-mediated H3K9me balance orchestrates heterochromatin stability and neural progenitor proliferation. EMBO Rep 2024; 25:3486-3505. [PMID: 38890452 PMCID: PMC11315909 DOI: 10.1038/s44319-024-00178-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/18/2024] [Accepted: 06/04/2024] [Indexed: 06/20/2024] Open
Abstract
Heterochromatin stability is crucial for progenitor proliferation during early neurogenesis. It relays on the maintenance of local hubs of H3K9me. However, understanding the formation of efficient localized levels of H3K9me remains limited. To address this question, we used neural stem cells to analyze the function of the H3K9me2 demethylase PHF2, which is crucial for progenitor proliferation. Through mass-spectroscopy and genome-wide assays, we show that PHF2 interacts with heterochromatin components and is enriched at pericentromeric heterochromatin (PcH) boundaries where it maintains transcriptional activity. This binding is essential for silencing the satellite repeats, preventing DNA damage and genome instability. PHF2's depletion increases the transcription of heterochromatic repeats, accompanied by a decrease in H3K9me3 levels and alterations in PcH organization. We further show that PHF2's PHD and catalytic domains are crucial for maintaining PcH stability, thereby safeguarding genome integrity. These results highlight the multifaceted nature of PHF2's functions in maintaining heterochromatin stability and regulating gene expression during neural development. Our study unravels the intricate relationship between heterochromatin stability and progenitor proliferation during mammalian neurogenesis.
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Affiliation(s)
- Samuel Aguirre
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08028, Spain
| | - Stella Pappa
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08028, Spain
| | - Núria Serna-Pujol
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08028, Spain
| | - Natalia Padilla
- Vall d'Hebron Institute of Research (VHIR), Passeig de la Vall d'Hebron, 119, E-08035, Barcelona, Spain
| | - Simona Iacobucci
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08028, Spain
| | - A Silvina Nacht
- Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Guillermo P Vicent
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08028, Spain
| | - Albert Jordan
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08028, Spain
| | - Xavier de la Cruz
- Vall d'Hebron Institute of Research (VHIR), Passeig de la Vall d'Hebron, 119, E-08035, Barcelona, Spain
- Institut Català per la Recerca i Estudis Avançats (ICREA), Barcelona, 08018, Spain
| | - Marian A Martínez-Balbás
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08028, Spain.
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2
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Iacobucci S, Padilla N, Gabrielli M, Navarro C, Lombardi M, Vicioso-Mantis M, Verderio C, de la Cruz X, Martínez-Balbás MA. The histone demethylase PHF8 regulates astrocyte differentiation and function. Development 2021; 148:268981. [PMID: 34081130 DOI: 10.1242/dev.194951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 04/15/2021] [Indexed: 12/24/2022]
Abstract
Epigenetic factors have been shown to play a crucial role in X-linked intellectual disability (XLID). Here, we investigate the contribution of the XLID-associated histone demethylase PHF8 to astrocyte differentiation and function. Using genome-wide analyses and biochemical assays in mouse astrocytic cultures, we reveal a regulatory crosstalk between PHF8 and the Notch signaling pathway that balances the expression of the master astrocytic gene Nfia. Moreover, PHF8 regulates key synaptic genes in astrocytes by maintaining low levels of H4K20me3. Accordingly, astrocytic-PHF8 depletion has a striking effect on neuronal synapse formation and maturation in vitro. These data reveal that PHF8 is crucial in astrocyte development to maintain chromatin homeostasis and limit heterochromatin formation at synaptogenic genes. Our studies provide insights into the involvement of epigenetics in intellectual disability.
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Affiliation(s)
- Simona Iacobucci
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - Natalia Padilla
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR), Passeig de la Vall d'Hebron, 119; E-08035 Barcelona, Spain. Institut Català per la Recerca i Estudis Avançats (ICREA), Barcelona 08018, Spain
| | - Martina Gabrielli
- CNR Institute of Neuroscience, via Vanvitelli 32, 20129 Milan, Italy
| | - Claudia Navarro
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - Marta Lombardi
- CNR Institute of Neuroscience, via Vanvitelli 32, 20129 Milan, Italy
| | - Marta Vicioso-Mantis
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - Claudia Verderio
- CNR Institute of Neuroscience, via Vanvitelli 32, 20129 Milan, Italy
| | - Xavier de la Cruz
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR), Passeig de la Vall d'Hebron, 119; E-08035 Barcelona, Spain. Institut Català per la Recerca i Estudis Avançats (ICREA), Barcelona 08018, Spain
| | - Marian A Martínez-Balbás
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
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PHF2 histone demethylase prevents DNA damage and genome instability by controlling cell cycle progression of neural progenitors. Proc Natl Acad Sci U S A 2019; 116:19464-19473. [PMID: 31488723 DOI: 10.1073/pnas.1903188116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Histone H3 lysine 9 methylation (H3K9me) is essential for cellular homeostasis; however, its contribution to development is not well established. Here, we demonstrate that the H3K9me2 demethylase PHF2 is essential for neural progenitor proliferation in vitro and for early neurogenesis in the chicken spinal cord. Using genome-wide analyses and biochemical assays we show that PHF2 controls the expression of critical cell cycle progression genes, particularly those related to DNA replication, by keeping low levels of H3K9me3 at promoters. Accordingly, PHF2 depletion induces R-loop accumulation that leads to extensive DNA damage and cell cycle arrest. These data reveal a role of PHF2 as a guarantor of genome stability that allows proper expansion of neural progenitors during development.
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Campillo-Marcos I, Lazo PA. Olaparib and ionizing radiation trigger a cooperative DNA-damage repair response that is impaired by depletion of the VRK1 chromatin kinase. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:203. [PMID: 31101118 PMCID: PMC6525392 DOI: 10.1186/s13046-019-1204-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/01/2019] [Indexed: 12/18/2022]
Abstract
Background The VRK1 chromatin kinase regulates the organization of locally altered chromatin induced by DNA damage. The combination of ionizing radiation with inhibitors of DNA damage responses increases the accumulation of DNA damage in cancer cells, which facilitates their antitumor effect, a process regulated by VRK1. Methods Tumor cell lines with different genetic backgrounds were treated with olaparib to determine their effect on the activation of DNA repair pathways induced by ionizing radiation. The effect of combining olaparib with depletion of the chromatin kinase VRK1 was studied in the context of double-strand breaks repair pathway after treatment with ionizing radiation. The initiation and progression of DDR were studied by specific histone acetylation, as a marker of local chromatin relaxation, and formation of γH2AX and 53BP1 foci. Results In this work, we have studied the effect that VRK1 by itself or in collaboration with olaparib, an inhibitor of PARP, has on the DNA oxidative damage induced by irradiation in order to identify its potential as a new drug target. The combination of olaparib and ionizing radiation increases DNA damage permitting a significant reduction of their respective doses to achieve a similar amount of DNA damage detected by γH2AX and 53BP1 foci. Different treatment combinations of olaparib and ionizing radiation permitted to reach the maximum level of DNA damage at lower doses of both treatments. Furthermore, we have studied the effect that depletion of the VRK1 chromatin kinase, a regulator of DDR, has on this response. VRK1 knockdown impaired all steps in the DDR induced by these treatments, which were detected by a reduction of sequential markers such as H4K16 ac, γH2AX, NBS1 and 53BP1. Moreover, this effect of VRK1 is independent of TP53 or ATM, two genes frequently mutated in cancer. Conclusion The protective DNA damage response induced by ionizing radiation is impaired by the combination of olaparib with depletion of VRK1, and can be used to reduce doses of radiation and their associated toxicity. Proteins implicated in DNA damage responses are suitable targets for development of new therapeutic strategies and their combination can be an alternative form of synthetic lethality. Electronic supplementary material The online version of this article (10.1186/s13046-019-1204-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ignacio Campillo-Marcos
- Experimental Therapeutics and Traslational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Salamanca, 37007, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Pedro A Lazo
- Experimental Therapeutics and Traslational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Salamanca, 37007, Salamanca, Spain. .,Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain.
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5
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McCarthy A, Deiulio A, Martin ET, Upadhyay M, Rangan P. Tip60 complex promotes expression of a differentiation factor to regulate germline differentiation in female Drosophila. Mol Biol Cell 2018; 29:2933-2945. [PMID: 30230973 PMCID: PMC6329907 DOI: 10.1091/mbc.e18-06-0385] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/06/2018] [Accepted: 09/13/2018] [Indexed: 01/23/2023] Open
Abstract
Germline stem cells (GSCs) self-renew and differentiate to sustain a continuous production of gametes. In the female Drosophila germ line, two differentiation factors, bag of marbles ( bam) and benign gonial cell neoplasm ( bgcn), work in concert in the stem cell daughter to promote the generation of eggs. In GSCs, bam transcription is repressed by signaling from the niche and is activated in stem cell daughters. In contrast, bgcn is transcribed in both the GSCs and stem cell daughters, but little is known about how bgcn is transcriptionally modulated. Here we find that the conserved protein Nipped-A acts through the Tat interactive protein 60-kDa (Tip60) histone acetyl transferase complex in the germ line to promote GSC daughter differentiation. We find that Nipped-A is required for efficient exit from the gap phase 2 (G2) of cell cycle of the GSC daughter and for expression of a differentiation factor, bgcn. Loss of Nipped-A results in accumulation of GSC daughters . Forced expression of bgcn in Nipped-A germline-depleted ovaries rescues this differentiation defect. Together, our results indicate that Tip60 complex coordinates cell cycle progression and expression of bgcn to help drive GSC daughters toward a differentiation program.
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Affiliation(s)
- Alicia McCarthy
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222
| | - Aron Deiulio
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222
| | - Elliot Todd Martin
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222
| | - Maitreyi Upadhyay
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222
| | - Prashanth Rangan
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222
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6
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Campos-Fernández E, Matsuo FS, Andrade MF, Servato JPS, Loyola AM, Cardoso SV, Siva SJ, Moraes ADS, de Faria PR. Prognostic value of histone H3 serine 10 phosphorylation and histone H4 lysine 12 acetylation in oral squamous cell carcinoma. Histopathology 2018; 74:227-238. [DOI: 10.1111/his.13713] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/13/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Esther Campos-Fernández
- Laboratório de Nanobiotecnologia; Instituto de Biotecnologia; Universidade Federal de Uberlândia; Uberlândia Brazil
| | - Flavia S Matsuo
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos; Faculdade de Medicina; Universidade de São Paulo; Ribeirão Preto Brazil
| | - Marília F Andrade
- Departamento de Imunologia; Instituto de Ciências Biomédicas; Universidade Federal de Uberlândia; Uberlândia Brazil
| | - João P S Servato
- Área de Biopatologia; Faculdade de Odontologia; Universidade de Uberaba (UNIUBE); Uberaba Brazil
| | - Adriano M Loyola
- Departamento de Patologia Oral; Faculdade de Odontologia; Universidade Federal de Uberlândia; Uberlândia Brazil
| | - Sérgio V Cardoso
- Departamento de Patologia Oral; Faculdade de Odontologia; Universidade Federal de Uberlândia; Uberlândia Brazil
| | - Sindeval J Siva
- Departamento de Cirurgia de Cabeça e Pescoço; Faculdade de Medicina; Universidade Federal de Uberlândia; Uberlândia Brazil
| | - Alberto da S Moraes
- Departamento de Biologia Celular, Histologia e Embriologia; Instituto de Ciências Biomédicas; Universidade Federal de Uberlândia; Uberlândia Brazil
| | - Paulo R de Faria
- Departamento de Biologia Celular, Histologia e Embriologia; Instituto de Ciências Biomédicas; Universidade Federal de Uberlândia; Uberlândia Brazil
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7
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Brauns-Schubert P, Schubert F, Wissler M, Weiss M, Schlicher L, Bessler S, Safavi M, Miething C, Borner C, Brummer T, Maurer U. CDK9-mediated phosphorylation controls the interaction of TIP60 with the transcriptional machinery. EMBO Rep 2018; 19:244-256. [PMID: 29335245 PMCID: PMC5797957 DOI: 10.15252/embr.201744311] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 11/03/2017] [Accepted: 12/06/2017] [Indexed: 01/12/2023] Open
Abstract
The acetyltransferase TIP60 is regulated by phosphorylation, and we have previously shown that phosphorylation of TIP60 on S86 by GSK-3 promotes p53-mediated induction of the BCL-2 protein PUMA. TIP60 phosphorylation by GSK-3 requires a priming phosphorylation on S90, and here, we identify CDK9 as a TIP60S90 kinase. We demonstrate that a phosphorylation-deficient mutant, TIP60S90A, exhibits reduced interaction with chromatin, histone 3 and RNA Pol II, while its association with the TIP60 complex subunit EPC1 is not affected. Consistently, we find a diminished association of TIP60S90A with the MYC gene. We show that cells expressing TIP60S90A, but also TIP60S86A, which retains S90 phosphorylation, exhibit reduced histone 4 acetylation and proliferation. Thus, our data indicate that, during transcription, phosphorylation of TIP60 at two sites has different regulatory effects on TIP60, whereby S90 phosphorylation controls association with the transcription machinery, and S86 phosphorylation is regulating TIP60 HAT activity.
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Affiliation(s)
- Prisca Brauns-Schubert
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- BIOSS, Centre for Biological Signaling Studies, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Florian Schubert
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- BIOSS, Centre for Biological Signaling Studies, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Manuela Wissler
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Martina Weiss
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Lisa Schlicher
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- BIOSS, Centre for Biological Signaling Studies, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Simon Bessler
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Mariam Safavi
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Cornelius Miething
- Department of Hematology/Oncology, University Medical Center Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, Freiburg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Borner
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- BIOSS, Centre for Biological Signaling Studies, Freiburg, Germany
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- BIOSS, Centre for Biological Signaling Studies, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, Freiburg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ulrich Maurer
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- BIOSS, Centre for Biological Signaling Studies, Freiburg, Germany
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Oncogenic N-Ras Stimulates SRF-Mediated Transactivation via H3 Acetylation at Lysine 9. BIOMED RESEARCH INTERNATIONAL 2018; 2018:5473725. [PMID: 29511684 PMCID: PMC5817314 DOI: 10.1155/2018/5473725] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 10/18/2017] [Accepted: 11/21/2017] [Indexed: 01/10/2023]
Abstract
Signal transduction pathways regulate the gene expression by altering chromatin dynamics in response to mitogens. Ras proteins are key regulators linking extracellular stimuli to a diverse range of biological responses associated with gene regulation. In mammals, the three ras genes encode four Ras protein isoforms: H-Ras, K-Ras4A, K-Ras4B, and N-Ras. Although emerging evidence suggests that Ras isoforms differentially regulate gene expressions and are functionally nonredundant, the mechanisms underlying Ras specificity and Ras signaling effects on gene expression remain unclear. Here, we show that oncogenic N-Ras acts as the most potent regulator of SRF-, NF-κB-, and AP-1-dependent transcription. N-Ras-RGL2 axis is a distinct signaling pathway for SRF target gene expression such as Egr1 and JunB, as RGL2 Ras binding domain (RBD) significantly impaired oncogenic N-Ras-induced SRE activation. By monitoring the effect of Ras isoforms upon the change of global histone modifications in oncogenic Ras-overexpressed cells, we discovered that oncogenic N-Ras elevates H3K9ac/H3K23ac levels globally in the chromatin context. Importantly, chromatin immunoprecipitation (ChIP) assays revealed that H3K9ac is significantly enriched at the promoter and coding regions of Egr1 and JunB. Collectively, our findings define an undocumented role of N-Ras in modulating of H3 acetylation and in gene regulation.
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9
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Asensio-Juan E, Fueyo R, Pappa S, Iacobucci S, Badosa C, Lois S, Balada M, Bosch-Presegué L, Vaquero A, Gutiérrez S, Caelles C, Gallego C, de la Cruz X, Martínez-Balbás MA. The histone demethylase PHF8 is a molecular safeguard of the IFNγ response. Nucleic Acids Res 2017; 45:3800-3811. [PMID: 28100697 PMCID: PMC5397186 DOI: 10.1093/nar/gkw1346] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 01/12/2017] [Indexed: 11/14/2022] Open
Abstract
A precise immune response is essential for cellular homeostasis and animal survival. The paramount importance of its control is reflected by the fact that its non-specific activation leads to inflammatory events that ultimately contribute to the appearance of many chronic diseases. However, the molecular mechanisms preventing non-specific activation and allowing a quick response upon signal activation are not yet fully understood. In this paper we uncover a new function of PHF8 blocking signal independent activation of immune gene promoters. Affinity purifications coupled with mass spectrometry analysis identified SIN3A and HDAC1 corepressors as new PHF8 interacting partners. Further molecular analysis demonstrated that prior to interferon gamma (IFNγ) stimulation, PHF8 is bound to a subset of IFNγ-responsive promoters. Through the association with HDAC1 and SIN3A, PHF8 keeps the promoters in a silent state, maintaining low levels of H4K20me1. Upon IFNγ treatment, PHF8 is phosphorylated by ERK2 and evicted from the promoters, correlating with an increase in H4K20me1 and transcriptional activation. Our data strongly indicate that in addition to its well-characterized function as a coactivator, PHF8 safeguards transcription to allow an accurate immune response.
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Affiliation(s)
- Elena Asensio-Juan
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - Raquel Fueyo
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - Stella Pappa
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - Simona Iacobucci
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - Carmen Badosa
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - Sergi Lois
- Vall d'Hebron Institute of Research (VHIR), Passeig de la Vall d'Hebron, 119, E-08035 Barcelona, Spain
| | - Miriam Balada
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - Laia Bosch-Presegué
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Institut d?Investigació Biomèdica de Bellvitge (IDIBELL), 08907- L'Hospitalet de Llobregat, Barcelona, Spain
| | - Alex Vaquero
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Institut d?Investigació Biomèdica de Bellvitge (IDIBELL), 08907- L'Hospitalet de Llobregat, Barcelona, Spain
| | - Sara Gutiérrez
- Department of Cell Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - Carme Caelles
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Barcelona, Barcelona 08028, Spain
| | - Carme Gallego
- Department of Cell Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - Xavier de la Cruz
- Vall d'Hebron Institute of Research (VHIR), Passeig de la Vall d'Hebron, 119, E-08035 Barcelona, Spain.,Institut Català per la Recerca i Estudis Avançats (ICREA), Barcelona 08018, Spain
| | - Marian A Martínez-Balbás
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
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10
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Fluhr S, Boerries M, Busch H, Symeonidi A, Witte T, Lipka DB, Mücke O, Nöllke P, Krombholz CF, Niemeyer CM, Plass C, Flotho C. CREBBP is a target of epigenetic, but not genetic, modification in juvenile myelomonocytic leukemia. Clin Epigenetics 2016; 8:50. [PMID: 27158276 PMCID: PMC4858931 DOI: 10.1186/s13148-016-0216-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/27/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Juvenile myelomonocytic leukemia (JMML) is a myeloproliferative neoplasm of childhood whose clinical heterogeneity is only poorly represented by gene sequence alterations. It was previously shown that aberrant DNA methylation of distinct target genes defines a more aggressive variant of JMML, but only few significant targets are known so far. To get a broader picture of disturbed CpG methylation patterns in JMML, we carried out a methylation screen of 34 candidate genes in 45 patients using quantitative mass spectrometry. FINDINGS Five of 34 candidate genes analyzed showed recurrent hypermethylation in JMML. cAMP-responsive element-binding protein-binding protein (CREBBP) was the most frequent target of epigenetic modification (77 % of cases). However, no pathogenic mutations of CREBBP were identified in a genetic analysis of 64 patients. CREBBP hypermethylation correlated with clinical parameters known to predict poor outcome. CONCLUSIONS This study supports the relevance of epigenetic aberrations in JMML pathophysiology. Our data confirm that DNA hypermethylation in JMML is highly target-specific and associated with higher-risk features. These findings encourage the development of prognostic markers based on epigenetic alterations, which will be helpful in the difficult clinical management of this heterogeneous disease.
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Affiliation(s)
- Silvia Fluhr
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, University Medical Center, Mathildenstrasse 1, 79106 Freiburg, Germany.,Hermann Staudinger Graduate School, University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Hauke Busch
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Aikaterini Symeonidi
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
| | - Tania Witte
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, Germany
| | - Daniel B Lipka
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, Germany
| | - Oliver Mücke
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, Germany
| | - Peter Nöllke
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, University Medical Center, Mathildenstrasse 1, 79106 Freiburg, Germany
| | - Christopher Felix Krombholz
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, University Medical Center, Mathildenstrasse 1, 79106 Freiburg, Germany
| | - Charlotte M Niemeyer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, University Medical Center, Mathildenstrasse 1, 79106 Freiburg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christoph Plass
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, Germany
| | - Christian Flotho
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, University Medical Center, Mathildenstrasse 1, 79106 Freiburg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
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