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Impact of Cultured Neuron Models on α-Herpesvirus Latency Research. Viruses 2022; 14:v14061209. [PMID: 35746680 PMCID: PMC9228292 DOI: 10.3390/v14061209] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 02/01/2023] Open
Abstract
A signature trait of neurotropic α-herpesviruses (α-HV) is their ability to establish stable non-productive infections of peripheral neurons termed latency. This specialized gene expression program is the foundation of an evolutionarily successful strategy to ensure lifelong persistence in the host. Various physiological stresses can induce reactivation in a subset of latently-infected neurons allowing a new cycle of viral productive cycle gene expression and synthesis of infectious virus. Recurring reactivation events ensure transmission of the virus to new hosts and contributes to pathogenesis. Efforts to define the molecular basis of α-HV latency and reactivation have been notoriously difficult because the neurons harboring latent virus in humans and in experimentally infected live-animal models, are rare and largely inaccessible to study. Increasingly, researchers are turning to cultured neuron infection models as simpler experimental platforms from which to explore latency and reactivation at the molecular level. In this review, I reflect on the strengths and weaknesses of existing neuronal models and briefly summarize the important mechanistic insights these models have provided. I also discuss areas where prioritization will help to ensure continued progress and integration.
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2
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Benjaskulluecha S, Boonmee A, Pattarakankul T, Wongprom B, Klomsing J, Palaga T. Screening of compounds to identify novel epigenetic regulatory factors that affect innate immune memory in macrophages. Sci Rep 2022; 12:1912. [PMID: 35115604 PMCID: PMC8814160 DOI: 10.1038/s41598-022-05929-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/20/2022] [Indexed: 02/05/2023] Open
Abstract
Trained immunity and tolerance are part of the innate immune memory that allow innate immune cells to differentially respond to a second encounter with stimuli by enhancing or suppressing responses. In trained immunity, treatment of macrophages with β-glucan (BG) facilitates the production of proinflammatory cytokines upon lipopolysaccharide (LPS) stimulation. For the tolerance response, LPS stimulation leads to suppressed inflammatory responses during subsequent LPS exposure. Epigenetic reprogramming plays crucial roles in both phenomena, which are tightly associated with metabolic flux. In this study, we performed a screening of an epigenetics compound library that affects trained immunity or LPS tolerance in macrophages using TNFα as a readout. Among the 181 compounds tested, one compound showed suppressive effects, while 2 compounds showed promoting effects on BG-trained TNFα production. In contrast, various inhibitors targeting Aurora kinase, histone methyltransferase, histone demethylase, histone deacetylase and DNA methyltransferase showed inhibitory activity against LPS tolerance. Several proteins previously unknown to be involved in innate immune memory, such as MGMT, Aurora kinase, LSD1 and PRMT5, were revealed. Protein network analysis revealed that the trained immunity targets are linked via Trp53, while LPS tolerance targets form three clusters of histone-modifying enzymes, cell division and base-excision repair. In trained immunity, the histone lysine methyltransferase SETD7 was identified, and its expression was increased during BG treatment. Level of the histone lysine demethylase, LSD1, increased during LPS priming and siRNA-mediated reduction resulted in increased expression of Il1b in LPS tolerance. Taken together, this screening approach confirmed the importance of epigenetic modifications in innate immune memory and provided potential novel targets for intervention.
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Affiliation(s)
- Salisa Benjaskulluecha
- Medical Microbiology, Interdisciplinary Program, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand
- Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Atsadang Boonmee
- Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok, 10330, Thailand
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thitiporn Pattarakankul
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Center of Excellence in Materials and Bio-Interfaces, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Benjawan Wongprom
- Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok, 10330, Thailand
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Jeerameth Klomsing
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Tanapat Palaga
- Medical Microbiology, Interdisciplinary Program, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand.
- Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok, 10330, Thailand.
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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3
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Thomsen I, Kunowska N, de Souza R, Moody AM, Crawford G, Wang YF, Khadayate S, Whilding C, Strid J, Karimi MM, Barr AR, Dillon N, Sabbattini P. RUNX1 Regulates a Transcription Program That Affects the Dynamics of Cell Cycle Entry of Naive Resting B Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:2976-2991. [PMID: 34810221 PMCID: PMC8675107 DOI: 10.4049/jimmunol.2001367] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 09/28/2021] [Indexed: 11/19/2022]
Abstract
RUNX1 is a transcription factor that plays key roles in hematopoietic development and in hematopoiesis and lymphopoiesis. In this article, we report that RUNX1 regulates a gene expression program in naive mouse B cells that affects the dynamics of cell cycle entry in response to stimulation of the BCR. Conditional knockout of Runx1 in mouse resting B cells resulted in accelerated entry into S-phase after BCR engagement. Our results indicate that Runx1 regulates the cyclin D2 (Ccnd2) gene, the immediate early genes Fosl2, Atf3, and Egr2, and the Notch pathway gene Rbpj in mouse B cells, reducing the rate at which transcription of these genes increases after BCR stimulation. RUNX1 interacts with the chromatin remodeler SNF-2-related CREB-binding protein activator protein (SRCAP), recruiting it to promoter and enhancer regions of the Ccnd2 gene. BCR-mediated activation triggers switching between binding of RUNX1 and its paralog RUNX3 and between SRCAP and the switch/SNF remodeling complex member BRG1. Binding of BRG1 is increased at the Ccnd2 and Rbpj promoters in the Runx1 knockout cells after BCR stimulation. We also find that RUNX1 exerts positive or negative effects on a number of genes that affect the activation response of mouse resting B cells. These include Cd22 and Bank1, which act as negative regulators of the BCR, and the IFN receptor subunit gene Ifnar1 The hyperresponsiveness of the Runx1 knockout B cells to BCR stimulation and its role in regulating genes that are associated with immune regulation suggest that RUNX1 could be involved in regulating B cell tolerance.
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Affiliation(s)
- Inesa Thomsen
- Gene Regulation and Chromatin Group, MRC London Institute of Medical Sciences, London, United Kingdom
| | - Natalia Kunowska
- Gene Regulation and Chromatin Group, MRC London Institute of Medical Sciences, London, United Kingdom
| | - Roshni de Souza
- Gene Regulation and Chromatin Group, MRC London Institute of Medical Sciences, London, United Kingdom
| | - Anne-Marie Moody
- Gene Regulation and Chromatin Group, MRC London Institute of Medical Sciences, London, United Kingdom
| | - Greg Crawford
- Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Yi-Fang Wang
- Bioinformatics and Computing, MRC London Institute of Medical Sciences, London, United Kingdom
| | - Sanjay Khadayate
- Bioinformatics and Computing, MRC London Institute of Medical Sciences, London, United Kingdom
| | - Chad Whilding
- Microscopy Facility, MRC London Institute of Medical Sciences, London, United Kingdom
| | - Jessica Strid
- Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Mohammad M Karimi
- Bioinformatics and Computing, MRC London Institute of Medical Sciences, London, United Kingdom
- Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Alexis R Barr
- Cell Cycle Control Group, MRC London Institute of Medical Sciences, London, United Kingdom; and
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Niall Dillon
- Gene Regulation and Chromatin Group, MRC London Institute of Medical Sciences, London, United Kingdom;
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Pierangela Sabbattini
- Gene Regulation and Chromatin Group, MRC London Institute of Medical Sciences, London, United Kingdom;
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Kennedy PGE, Mogensen TH, Cohrs RJ. Recent Issues in Varicella-Zoster Virus Latency. Viruses 2021; 13:v13102018. [PMID: 34696448 PMCID: PMC8540691 DOI: 10.3390/v13102018] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/30/2021] [Accepted: 10/02/2021] [Indexed: 12/16/2022] Open
Abstract
Varicella-zoster virus (VZV) is a human herpes virus which causes varicella (chicken pox) as a primary infection, and, following a variable period of latency in neurons in the peripheral ganglia, may reactivate to cause herpes zoster (shingles) as well as a variety of neurological syndromes. In this overview we consider some recent issues in alphaherpesvirus latency with special focus on VZV ganglionic latency. A key question is the nature and extent of viral gene transcription during viral latency. While it is known that this is highly restricted, it is only recently that the very high degree of that restriction has been clarified, with both VZV gene 63-encoded transcripts and discovery of a novel VZV transcript (VLT) that maps antisense to the viral transactivator gene 61. It has also emerged in recent years that there is significant epigenetic regulation of VZV gene transcription, and the mechanisms underlying this are complex and being unraveled. The last few years has also seen an increased interest in the immunological aspects of VZV latency and reactivation, in particular from the perspective of inborn errors of host immunity that predispose to different VZV reactivation syndromes.
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Affiliation(s)
- Peter G. E. Kennedy
- Institute of Neuroscience and Psychology, University of Glasgow, Glasgow G61 1QH, UK
- Correspondence:
| | - Trine H. Mogensen
- Department of Infectious Diseases, Aarhus University Hospital, 8000 Aarhus, Denmark;
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Randall J. Cohrs
- Department of Neurology, University of Colorado School of Medicine, 80045 Aurora, CO, USA
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Pokrovsky D, Forné I, Straub T, Imhof A, Rupp RAW. A systemic cell cycle block impacts stage-specific histone modification profiles during Xenopus embryogenesis. PLoS Biol 2021; 19:e3001377. [PMID: 34491983 PMCID: PMC8535184 DOI: 10.1371/journal.pbio.3001377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/22/2021] [Accepted: 07/30/2021] [Indexed: 11/26/2022] Open
Abstract
Forming an embryo from a zygote poses an apparent conflict for epigenetic regulation. On the one hand, the de novo induction of cell fate identities requires the establishment and subsequent maintenance of epigenetic information to harness developmental gene expression. On the other hand, the embryo depends on cell proliferation, and every round of DNA replication dilutes preexisting histone modifications by incorporation of new unmodified histones into chromatin. Here, we investigated the possible relationship between the propagation of epigenetic information and the developmental cell proliferation during Xenopus embryogenesis. We systemically inhibited cell proliferation during the G1/S transition in gastrula embryos and followed their development until the tadpole stage. Comparing wild-type and cell cycle-arrested embryos, we show that the inhibition of cell proliferation is principally compatible with embryo survival and cellular differentiation. In parallel, we quantified by mass spectrometry the abundance of a large set of histone modification states, which reflects the developmental maturation of the embryonic epigenome. The arrested embryos developed abnormal stage-specific histone modification profiles (HMPs), in which transcriptionally repressive histone marks were overrepresented. Embryos released from the cell cycle block during neurulation reverted toward normality on morphological, molecular, and epigenetic levels. These results suggest that the cell cycle block by HUA alters stage-specific HMPs. We propose that this influence is strong enough to control developmental decisions, specifically in cell populations that switch between resting and proliferating states such as stem cells.
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Affiliation(s)
- Daniil Pokrovsky
- Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ignasi Forné
- Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Tobias Straub
- Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Axel Imhof
- Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ralph A. W. Rupp
- Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
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Kapell S, Jakobsson ME. Large-scale identification of protein histidine methylation in human cells. NAR Genom Bioinform 2021; 3:lqab045. [PMID: 34046594 PMCID: PMC8140740 DOI: 10.1093/nargab/lqab045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/21/2021] [Accepted: 04/30/2021] [Indexed: 12/14/2022] Open
Abstract
Methylation can occur on histidine, lysine and arginine residues in proteins and often serves a regulatory function. Histidine methylation has recently attracted attention through the discovery of the human histidine methyltransferase enzymes SETD3 and METTL9. There are currently no methods to enrich histidine methylated peptides for mass spectrometry analysis and large-scale studies of the modification are hitherto absent. Here, we query ultra-comprehensive human proteome datasets to generate a resource of histidine methylation sites. In HeLa cells alone, we report 299 histidine methylation sites as well as 895 lysine methylation events. We use this resource to explore the frequency, localization, targeted domains, protein types and sequence requirements of histidine methylation and benchmark all analyses to methylation events on lysine and arginine. Our results demonstrate that histidine methylation is widespread in human cells and tissues and that the modification is over-represented in regions of mono-spaced histidine repeats. We also report colocalization of the modification with functionally important phosphorylation sites and disease associated mutations to identify regions of likely regulatory and functional importance. Taken together, we here report a system level analysis of human histidine methylation and our results represent a comprehensive resource enabling targeted studies of individual histidine methylation events.
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Affiliation(s)
- Sebastian Kapell
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
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7
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Abstract
Methylation at DNA, RNA and protein levels plays critical roles in many cellular processes and is associated with diverse differentiation events, physiological activities and human diseases. To aid in the diagnostic and therapeutic design for cancer treatment utilising methylation, this review provides a boutique yet comprehensive overview on methylation at different levels including the mechanisms, cross-talking and clinical implications with a particular focus on cancers. We conclude that DNA methylation is the sole type of methylation that has been largely translated into clinics and used for, mostly, early diagnosis. Translating the onco-therapeutic and prognostic values of RNA and protein methylations into clinical use deserves intensive efforts. Simultaneous examination of methylations at multiple levels or together with other forms of molecular markers represents an interesting research direction with profound clinical translational potential.
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Holt MV, Wang T, Young NL. One-Pot Quantitative Top- and Middle-Down Analysis of GluC-Digested Histone H4. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2514-2525. [PMID: 31147891 DOI: 10.1007/s13361-019-02219-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/27/2019] [Accepted: 04/27/2019] [Indexed: 05/28/2023]
Abstract
Histone post-translational modifications (PTMs) have been intensively investigated due to their essential function in eukaryotic genome regulation. Histone modifications have been effectively studied using modified bottom-up proteomics approaches; however, the methods often do not capture single-molecule combinations of PTMs (proteoforms) that mediate known and expected biochemical mechanisms. Both middle-down mass spectrometry (MS) and top-down MS quantitation of H4 proteoforms present viable access to this important information. Histone H4 middle-down has previously avoided GluC digestion due to complex digestion products and interferences; however, the common AspN digestion cleaves at amino acid 23, disconnecting K31ac from other PTMs. Here, we demonstrate the effective use of GluC-based middle-down quantitation and compare it to top-down-based quantitation of proteoforms. Despite potential interferences in the m/z space, the proteoforms arising from all three GluC products (E52, E53, and E63) and intact H4 are chromatographically resolved and successfully analyzed in a single LC-MS analysis. Quantitative results and associated analytical metrics are compared between the different analytes of a single sample digested to different extents to reveal general concordance as well as the relative biases and complementarity of each approach. There is moderate proteoform discordance between digestion products (e.g., E52 and E53); however, each digestion product exhibits high concordance, regardless of digestion time. Under the conditions used, the GluC products are better chromatographically resolved yet show greater variance than the top-down quantitation that are more extensively sampled for MS2. GluC-based middle-down of H4 is thus viable. Both top-down and middle-down approaches have comparable quantitation capacity and are complementary.
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Affiliation(s)
- Matthew V Holt
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Tao Wang
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Nicolas L Young
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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9
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HMGA1 Modulates Gene Transcription Sustaining a Tumor Signalling Pathway Acting on the Epigenetic Status of Triple-Negative Breast Cancer Cells. Cancers (Basel) 2019; 11:cancers11081105. [PMID: 31382504 PMCID: PMC6721465 DOI: 10.3390/cancers11081105] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/19/2019] [Accepted: 07/29/2019] [Indexed: 01/17/2023] Open
Abstract
Chromatin accessibility plays a critical factor in regulating gene expression in cancer cells. Several factors, including the High Mobility Group A (HMGA) family members, are known to participate directly in chromatin relaxation and transcriptional activation. The HMGA1 oncogene encodes an architectural chromatin transcription factor that alters DNA structure and interacts with transcription factors favouring their landing onto transcription regulatory sequences. Here, we provide evidence of an additional mechanism exploited by HMGA1 to modulate transcription. We demonstrate that, in a triple-negative breast cancer cellular model, HMGA1 sustains the action of epigenetic modifiers and in particular it positively influences both histone H3S10 phosphorylation by ribosomal protein S6 kinase alpha-3 (RSK2) and histone H2BK5 acetylation by CREB-binding protein (CBP). HMGA1, RSK2, and CBP control the expression of a set of genes involved in tumor progression and epithelial to mesenchymal transition. These results suggest that HMGA1 has an effect on the epigenetic status of cancer cells and that it could be exploited as a responsiveness predictor for epigenetic therapies in triple-negative breast cancers.
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Billmyre KK, Doebley AL, Spichal M, Heestand B, Belicard T, Sato-Carlton A, Flibotte S, Simon M, Gnazzo M, Skop A, Moerman D, Carlton PM, Sarkies P, Ahmed S. The meiotic phosphatase GSP-2/PP1 promotes germline immortality and small RNA-mediated genome silencing. PLoS Genet 2019; 15:e1008004. [PMID: 30921322 PMCID: PMC6456222 DOI: 10.1371/journal.pgen.1008004] [Citation(s) in RCA: 5] [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: 02/28/2018] [Revised: 04/09/2019] [Accepted: 02/05/2019] [Indexed: 12/21/2022] Open
Abstract
Germ cell immortality, or transgenerational maintenance of the germ line, could be promoted by mechanisms that could occur in either mitotic or meiotic germ cells. Here we report for the first time that the GSP-2 PP1/Glc7 phosphatase promotes germ cell immortality. Small RNA-induced genome silencing is known to promote germ cell immortality, and we identified a separation-of-function allele of C. elegans gsp-2 that is compromised for germ cell immortality and is also defective for small RNA-induced genome silencing and meiotic but not mitotic chromosome segregation. Previous work has shown that GSP-2 is recruited to meiotic chromosomes by LAB-1, which also promoted germ cell immortality. At the generation of sterility, gsp-2 and lab-1 mutant adults displayed germline degeneration, univalents, histone methylation and histone phosphorylation defects in oocytes, phenotypes that mirror those observed in sterile small RNA-mediated genome silencing mutants. Our data suggest that a meiosis-specific function of GSP-2 ties small RNA-mediated silencing of the epigenome to germ cell immortality. We also show that transgenerational epigenomic silencing at hemizygous genetic elements requires the GSP-2 phosphatase, suggesting a functional link to small RNAs. Given that LAB-1 localizes to the interface between homologous chromosomes during pachytene, we hypothesize that small localized discontinuities at this interface could promote genomic silencing in a manner that depends on small RNAs and the GSP-2 phosphatase.
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Affiliation(s)
- Katherine Kretovich Billmyre
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Anna-Lisa Doebley
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Maya Spichal
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Bree Heestand
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Tony Belicard
- Medical Research Council London Institute of Medical Sciences, London, United Kingdom
- Institute for Clinical Sciences, Imperial College London, London, United Kingdom
| | | | - Stephane Flibotte
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matt Simon
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Megan Gnazzo
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ahna Skop
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Donald Moerman
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Peter Sarkies
- Medical Research Council London Institute of Medical Sciences, London, United Kingdom
- Institute for Clinical Sciences, Imperial College London, London, United Kingdom
| | - Shawn Ahmed
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
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11
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Lu C, Sidoli S, Kulej K, Ross K, Wu CH, Garcia BA. Coordination between TGF-β cellular signaling and epigenetic regulation during epithelial to mesenchymal transition. Epigenetics Chromatin 2019; 12:11. [PMID: 30736855 PMCID: PMC6368739 DOI: 10.1186/s13072-019-0256-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/23/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Epithelial to mesenchymal transition (EMT) plays a crucial role in cancer propagation. It can be orchestrated by the activation of multiple signaling pathways, which have been found to be highly coordinated with many epigenetic regulators. Although the mechanism of EMT has been studied over decades, cross talk between signaling and epigenetic regulation is not fully understood. RESULTS Here, we present a time-resolved multi-omics strategy, which featured the identification of the correlation between protein changes (proteome), signaling pathways (phosphoproteome) and chromatin modulation (histone modifications) dynamics during TGF-β-induced EMT. Our data revealed that Erk signaling was activated in 5-min stimulation and structural proteins involved in cytoskeleton rearrangement were regulated after 1-day treatment, constituting a detailed map of systematic changes. The comprehensive profiling of histone post-translational modifications identified H3K27me3 as the most significantly up-regulated mark. We thus speculated and confirmed that a combined inhibition of Erk signaling and Ezh2 (H3K27me3 methyltransferase) was more effective in blocking EMT progress than individual inhibitions. CONCLUSIONS In summary, our data provided a more detailed map of cross talk between signaling pathway and chromatin regulation comparing to previous EMT studies. Our findings point to a promising therapeutic strategy for EMT-related diseases by combining Erk inhibitor (singling pathway) and Ezh2 inhibitor (epigenetic regulation).
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Affiliation(s)
- Congcong Lu
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Simone Sidoli
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Katarzyna Kulej
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Karen Ross
- Center for Bioinformatics and Computational Biology, Department of Computer and Information Sciences, University of Delaware, Newark, DE, 19711, USA
| | - Cathy H Wu
- Center for Bioinformatics and Computational Biology, Department of Computer and Information Sciences, University of Delaware, Newark, DE, 19711, USA
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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12
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Feiner B, Chase KA, Melbourne JK, Rosen C, Sharma RP. Risperidone effects on heterochromatin: the role of kinase signaling. Clin Exp Immunol 2019; 196:67-75. [PMID: 30714144 DOI: 10.1111/cei.13250] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2018] [Indexed: 01/03/2023] Open
Abstract
Epigenetic effects of anti-psychotic medications are poorly understood. We have appropriated a model whereby heterochromatin is established through 24- or 48-h lipopolysaccharide (LPS) treatment, and tested the epigenetic effects of risperidone along the adenylyl cyclase/protein kinase A (AC/PKA) pathway in human liposarcoma cells that express the LPS-sensitive Toll-like receptor (TLR)-4. Human SW872 cells were cultured with LPS and mRNA expression levels and epigenetic modifications of dimethylated lysine 9 of histone 2 (H3K9me2), geterochromatin protein 1γ (HP1γ) and phospho-H3S10 at promoters of interleukin (IL)-6, tumor necrosis factor (TNF)-α and IL1β were measured. Pharmacological manipulation of the AC/PKA pathway was achieved through treatment with a PKA inhibitor (H89), mitogen- and stress-activated kinase 1 (MSK1) inhibitor (SB-747651A) or forskolin. Twenty-four and 48-h LPS treatment establishes heterochromatin at selected promoters, corresponding to decreased mRNA expression. Concurrent risperidone treatment with LPS treatment can both 'block' and 'reverse' heterochromatin formation. Forskolin treatment resulted in a similar disassembling effect on heterochromatin. Conversely, inhibition of PKA by H89 or MSK1 both blocked 'normalizing' effects of risperidone on LPS-induced heterochromatin. Our results demonstrate that risperidone can disassemble heterochromatin, exerting this effect along the G-protein/AC/PKA pathway. This approach can also be utilized to investigate functional outcomes of single or combined pharmacological treatments on chromatin assemblies in human cells.
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Affiliation(s)
- B Feiner
- The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, USA
| | - K A Chase
- The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, USA.,Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA
| | - J K Melbourne
- The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, USA
| | - C Rosen
- The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, USA
| | - R P Sharma
- The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, USA.,Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA
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N-terminal acetylation and methylation differentially affect the function of MYL9. Biochem J 2018; 475:3201-3219. [PMID: 30242065 DOI: 10.1042/bcj20180638] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 12/30/2022]
Abstract
Deciphering the histone code has illustrated that acetylation or methylation on the same residue can have analogous or opposing roles. However, little is known about the interplay between these post-translational modifications (PTMs) on the same nonhistone residues. We have recently discovered that N-terminal acetyltransferases (NATs) and N-terminal methyltransferases (NRMTs) can have overlapping substrates and identified myosin regulatory light chain 9 (MYL9) as the first confirmed protein to occur in either α-amino-methylated (Nα-methyl) or α-amino-acetylated (Nα-acetyl) states in vivo Here we aim to determine if these PTMs function similarly or create different MYL9 proteoforms with distinct roles. We use enzymatic assays to directly verify MYL9 is a substrate of both NRMT1 and NatA and generate mutants of MYL9 that are exclusive for Nα-acetylation or Nα-methylation. We then employ eukaryotic cell models to probe the regulatory functions of these Nα-PTMs on MYL9. Our results show that, contrary to prevailing dogma, neither of these modifications regulate the stability of MYL9. Rather, exclusive Nα-acetylation promotes cytoplasmic roles of MYL9, while exclusive Nα-methylation promotes the nuclear role of MYL9 as a transcription factor. The increased cytoplasmic activity of Nα-acetylated MYL9 corresponds with increased phosphorylation at serine 19, a key MYL9 activating PTM. Increased nuclear activity of Nα-methylated MYL9 corresponds with increased DNA binding. Nα-methylation also results in a decrease of interactions between the N-terminus of MYL9 and a host of cytoskeletal proteins. These results confirm that Nα-acetylation and Nα-methylation differentially affect MYL9 function by creating distinct proteoforms with different internal PTM patterns and binding properties.
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14
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Wang C, Wang Q, Xu X, Xie B, Zhao Y, Li N, Cao X. The methyltransferase NSD3 promotes antiviral innate immunity via direct lysine methylation of IRF3. J Exp Med 2017; 214:3597-3610. [PMID: 29101251 PMCID: PMC5716042 DOI: 10.1084/jem.20170856] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/18/2017] [Accepted: 09/15/2017] [Indexed: 12/30/2022] Open
Abstract
Wang et al. demonstrate that methyltransferase NSD3 directly methylates IRF3 and maintains IRF3 phosphorylation to enhance its transcriptional activity by disassociating the methylated IRF3 and PP1cc to prevent IRF3 dephosphorylation, consequently promoting antiviral innate immune response. Lysine methylation is an important posttranslational modification, implicated in various biological pathological conditions. The transcription factor interferon regulatory factor 3 (IRF3) is essential for antiviral innate immunity, yet the mechanism for methylation control of IRF3 activation remains unclear. In this paper, we discovered monomethylation of IRF3 at K366 is critical for IRF3 transcription activity in antiviral innate immunity. By mass spectrometry analysis of IRF3-associated proteins, we identified nuclear receptor–binding SET domain 3 (NSD3) as the lysine methyltransferase that directly binds to the IRF3 C-terminal region through its PWWP1 domain and methylates IRF3 at K366 via its SET domain. Deficiency of NSD3 impairs the antiviral innate immune response in vivo. Mechanistically, NSD3 enhances the transcription activity of IRF3 dependent on K366 monomethylation, which maintains IRF3 phosphorylation by promoting IRF3 dissociation of protein phosphatase PP1cc and consequently promotes type I interferon production. Our study reveals a critical role of NSD3-mediated IRF3 methylation in enhancing antiviral innate immunity.
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Affiliation(s)
- Chunmei Wang
- Department of Immunology and Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Qinlan Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoqing Xu
- Department of Immunology and Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Bin Xie
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong Zhao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nan Li
- National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Xuetao Cao
- Department of Immunology and Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China .,National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China.,Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
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15
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Kumar R, Deivendran S, Santhoshkumar TR, Pillai MR. Signaling coupled epigenomic regulation of gene expression. Oncogene 2017. [DOI: 10.1038/onc.2017.201] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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16
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Wu Z, Connolly J, Biggar KK. Beyond histones - the expanding roles of protein lysine methylation. FEBS J 2017; 284:2732-2744. [DOI: 10.1111/febs.14056] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 02/05/2017] [Accepted: 03/07/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Zhouran Wu
- Department of Chemistry and Biochemistry; University of Regina; Canada
| | - Justin Connolly
- Institute of Biochemistry and Department of Biology; Carleton University; Ottawa Canada
| | - Kyle K. Biggar
- Institute of Biochemistry and Department of Biology; Carleton University; Ottawa Canada
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17
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Farzaneh K, Thaler R, Paradise CR, Deyle DR, Julio MKD, Galindo M, Gordon JA, Stein GS, Dudakovic A, van Wijnen AJ. Histone H4 Methyltransferase Suv420h2 Maintains Fidelity of Osteoblast Differentiation. J Cell Biochem 2017; 118:1262-1272. [PMID: 27862226 PMCID: PMC5357582 DOI: 10.1002/jcb.25787] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 11/07/2016] [Indexed: 12/13/2022]
Abstract
Osteogenic lineage commitment and progression is controlled by multiple signaling pathways (e.g., WNT, BMP, FGF) that converge on bone-related transcription factors. Access of osteogenic transcription factors to chromatin is controlled by epigenetic regulators that generate post-translational modifications of histones ("histone code"), as well as read, edit and/or erase these modifications. Our understanding of the biological role of epigenetic regulators in osteoblast differentiation remains limited. Therefore, we performed next-generation RNA sequencing (RNA-seq) and established which chromatin-related proteins are robustly expressed in mouse bone tissues (e.g., fracture callus, calvarial bone). These studies also revealed that cells with increased osteogenic potential have higher levels of the H4K20 methyl transferase Suv420h2 compared to other methyl transferases (e.g., Suv39h1, Suv39h2, Suv420h1, Ezh1, Ezh2). We find that all six epigenetic regulators are transiently expressed at different stages of osteoblast differentiation in culture, with maximal mRNAs levels of Suv39h1 and Suv39h2 (at day 3) preceding maximal expression of Suv420h1 and Suv420h2 (at day 7) and developmental stages that reflect, respectively, early and later collagen matrix deposition. Loss of function analysis of Suv420h2 by siRNA depletion shows loss of H4K20 methylation and decreased expression of bone biomarkers (e.g., alkaline phosphatase/Alpl) and osteogenic transcription factors (e.g., Sp7/Osterix). Furthermore, Suv420h2 is required for matrix mineralization during osteoblast differentiation. We conclude that Suv420h2 controls the H4K20 methylome of osteoblasts and is critical for normal progression of osteoblastogenesis. J. Cell. Biochem. 118: 1262-1272, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Khani Farzaneh
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Roman Thaler
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Mario Galindo
- Millennium Institute on Immunology and Immunotherapy, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Jonathan A. Gordon
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, Vermont 05405
| | - Gary S. Stein
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, Vermont 05405
| | - Amel Dudakovic
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Andre J. van Wijnen
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
- Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
- Corresponding author: Andre J. van Wijnen, Ph.D., Mayo Clinic, 200 First Street SW, Rochester, MN 55905, Phone: 507- 293-2105, Fax: 507-284-5075,
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18
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Wang M, Han J, Marcar L, Black J, Liu Q, Li X, Nagulapalli K, Sequist LV, Mak RH, Benes CH, Hong TS, Gurtner K, Krause M, Baumann M, Kang JX, Whetstine JR, Willers H. Radiation Resistance in KRAS-Mutated Lung Cancer Is Enabled by Stem-like Properties Mediated by an Osteopontin-EGFR Pathway. Cancer Res 2017; 77:2018-2028. [PMID: 28202526 DOI: 10.1158/0008-5472.can-16-0808] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 12/23/2016] [Accepted: 01/13/2017] [Indexed: 12/31/2022]
Abstract
Lung cancers with activating KRAS mutations are characterized by treatment resistance and poor prognosis. In particular, the basis for their resistance to radiation therapy is poorly understood. Here, we describe a radiation resistance phenotype conferred by a stem-like subpopulation characterized by mitosis-like condensed chromatin (MLCC), high CD133 expression, invasive potential, and tumor-initiating properties. Mechanistic investigations defined a pathway involving osteopontin and the EGFR in promoting this phenotype. Osteopontin/EGFR-dependent MLCC protected cells against radiation-induced DNA double-strand breaks and repressed putative negative regulators of stem-like properties, such as CRMP1 and BIM. The MLCC-positive phenotype defined a subset of KRAS-mutated lung cancers that were enriched for co-occurring genomic alterations in TP53 and CDKN2A. Our results illuminate the basis for the radiation resistance of KRAS-mutated lung cancers, with possible implications for prognostic and therapeutic strategies. Cancer Res; 77(8); 2018-28. ©2017 AACR.
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Affiliation(s)
- Meng Wang
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jing Han
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.,Jinan Municipal Center for Disease Control and Prevention, Shandong, China
| | - Lynnette Marcar
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Josh Black
- University of Colorado School of Medicine, Aurora, Colorado.,Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Qi Liu
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Xiangyong Li
- Laboratory for Lipid Medicine and Technology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Kshithija Nagulapalli
- Center for Computational Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lecia V Sequist
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Raymond H Mak
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Cyril H Benes
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Theodore S Hong
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Kristin Gurtner
- Department of Radiation Oncology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,OncoRay National Center for Radiation Research in Oncology, Dresden, Germany.,Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany.,Institute of Radiation Oncology, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany.,Cancer Consortium (DKTK) Partner Site Dresden and German Cancer Research Center (DKFZ) Heidelberg, Dresden, Germany
| | - Mechthild Krause
- Department of Radiation Oncology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,OncoRay National Center for Radiation Research in Oncology, Dresden, Germany.,Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany.,Institute of Radiation Oncology, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany.,Cancer Consortium (DKTK) Partner Site Dresden and German Cancer Research Center (DKFZ) Heidelberg, Dresden, Germany
| | - Michael Baumann
- Department of Radiation Oncology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,OncoRay National Center for Radiation Research in Oncology, Dresden, Germany.,Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany.,Institute of Radiation Oncology, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany.,Cancer Consortium (DKTK) Partner Site Dresden and German Cancer Research Center (DKFZ) Heidelberg, Dresden, Germany
| | - Jing X Kang
- Laboratory for Lipid Medicine and Technology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Johnathan R Whetstine
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Henning Willers
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.
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19
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Wiersma M, Bussiere M, Halsall JA, Turan N, Slany R, Turner BM, Nightingale KP. Protein kinase Msk1 physically and functionally interacts with the KMT2A/MLL1 methyltransferase complex and contributes to the regulation of multiple target genes. Epigenetics Chromatin 2016; 9:52. [PMID: 27895715 PMCID: PMC5106815 DOI: 10.1186/s13072-016-0103-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 11/03/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The KMT2A/MLL1 lysine methyltransferase complex is an epigenetic regulator of selected developmental genes, in part through the SET domain-catalysed methylation of H3K4. It is essential for normal embryonic development and haematopoiesis and frequently mutated in cancer. The catalytic properties and targeting of KMT2A/MLL1 depend on the proteins with which it complexes and the post-translational protein modifications which some of these proteins put in place, though detailed mechanisms remain unclear. RESULTS KMT2A/MLL1 (both native and FLAG-tagged) and Msk1 (RPS6KA5) co-immunoprecipitated in various cell types. KMT2A/MLL1 and Msk1 knockdown demonstrated that the great majority of genes whose activity changed on KTM2A/MLL1 knockdown, responded comparably to Msk1 knockdown, as did levels of H3K4 methylation and H3S10 phosphorylation at KTM2A target genes HoxA4, HoxA5. Knockdown experiments also showed that KMT2A/MLL1 is required for the genomic targeting of Msk1, but not vice versa. CONCLUSION The KMT2A/MLL1 complex is associated with, and functionally dependent upon, the kinase Msk1, part of the MAP kinase signalling pathway. We propose that Msk1-catalysed phosphorylation at H3 serines 10 and 28, supports H3K4 methylation by the KMT2A/MLL1 complex both by making H3 a more attractive substrate for its SET domain, and improving target gene accessibility by prevention of HP1- and Polycomb-mediated chromatin condensation.
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Affiliation(s)
- Maaike Wiersma
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Marianne Bussiere
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
- Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 22f, Box 2404, 3001 Louvain, Belgium
| | - John A. Halsall
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Nil Turan
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Robert Slany
- Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Bryan M. Turner
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Karl P. Nightingale
- Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
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20
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Cliffe AR, Arbuckle JH, Vogel JL, Geden MJ, Rothbart SB, Cusack CL, Strahl BD, Kristie TM, Deshmukh M. Neuronal Stress Pathway Mediating a Histone Methyl/Phospho Switch Is Required for Herpes Simplex Virus Reactivation. Cell Host Microbe 2016; 18:649-58. [PMID: 26651941 DOI: 10.1016/j.chom.2015.11.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/13/2015] [Accepted: 11/19/2015] [Indexed: 01/27/2023]
Abstract
Herpes simplex virus (HSV) reactivation from latent neuronal infection requires stimulation of lytic gene expression from promoters associated with repressive heterochromatin. Various neuronal stresses trigger reactivation, but how these stimuli activate silenced promoters remains unknown. We show that a neuronal pathway involving activation of c-Jun N-terminal kinase (JNK), common to many stress responses, is essential for initial HSV gene expression during reactivation. This JNK activation in neurons is mediated by dual leucine zipper kinase (DLK) and JNK-interacting protein 3 (JIP3), which direct JNK toward stress responses instead of other cellular functions. Surprisingly, JNK-mediated viral gene induction occurs independently of histone demethylases that remove repressive lysine modifications. Rather, JNK signaling results in a histone methyl/phospho switch on HSV lytic promoters, a mechanism permitting gene expression in the presence of repressive lysine methylation. JNK is present on viral promoters during reactivation, thereby linking a neuronal-specific stress pathway and HSV reactivation from latency.
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Affiliation(s)
- Anna R Cliffe
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Jesse H Arbuckle
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jodi L Vogel
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew J Geden
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Scott B Rothbart
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Corey L Cusack
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Neurobiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Thomas M Kristie
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mohanish Deshmukh
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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21
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Minarovits J, Banati F, Szenthe K, Niller HH. Epigenetic Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 879:1-25. [DOI: 10.1007/978-3-319-24738-0_1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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22
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Abstract
ATRX was identified over 20 years ago as the gene responsible for a rare developmental disorder characterized by α-thalassemia and intellectual disability. Similarities to the sucrose nonfermentable SNF2 type chromatin remodelers initially suggested a role in transcriptional regulation. However, over the last years, our knowledge of the epigenetic activities of ATRX has expanded steadily. Recent exciting discoveries have propelled ATRX into the limelight of chromatin and telomere biology, development and cancer research. This review summarizes recent breakthroughs in understanding ATRX function in heterochromatin structure, genome stability and its frequent dysregulation in a variety of cancers.
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Affiliation(s)
- L Ashley Watson
- Departments of Paediatrics, Biochemistry & Oncology, University of Western Ontario, Victoria Research Laboratories, 800 Commissioners Road East, London, Canada.,Children's Health Research Institute, London, Canada.,Lawson Health Research Institute, London, Canada
| | - Hannah Goldberg
- Departments of Paediatrics, Biochemistry & Oncology, University of Western Ontario, Victoria Research Laboratories, 800 Commissioners Road East, London, Canada.,Children's Health Research Institute, London, Canada.,Lawson Health Research Institute, London, Canada
| | - Nathalie G Bérubé
- Departments of Paediatrics, Biochemistry & Oncology, University of Western Ontario, Victoria Research Laboratories, 800 Commissioners Road East, London, Canada.,Children's Health Research Institute, London, Canada.,Lawson Health Research Institute, London, Canada
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23
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Abstract
The different cell types of an organism share the same DNA, but during cell differentiation their genomes undergo diverse structural and organizational changes that affect gene expression and other cellular functions. These can range from large-scale folding of whole chromosomes or of smaller genomic regions, to the re-organization of local interactions between enhancers and promoters, mediated by the binding of transcription factors and chromatin looping. The higher-order organization of chromatin is also influenced by the specificity of the contacts that it makes with nuclear structures such as the lamina. Sophisticated methods for mapping chromatin contacts are generating genome-wide data that provide deep insights into the formation of chromatin interactions, and into their roles in the organization and function of the eukaryotic cell nucleus.
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24
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Sijare F, Geißler AL, Fichter CD, Hergeth SP, Bogatyreva L, Hauschke D, Schneider R, Werner M, Lassmann S. Aurora B expression and histone variant H1.4S27 phosphorylation are no longer coordinated during metaphase in aneuploid colorectal carcinomas. Virchows Arch 2015; 466:503-15. [PMID: 25680570 DOI: 10.1007/s00428-015-1727-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 11/24/2014] [Accepted: 01/22/2015] [Indexed: 12/11/2022]
Abstract
Experimental model systems identified phosphorylation of linker histone variant H1.4 at Ser 27 (H1.4S27p) as a novel mitotic mark set by Aurora B kinase. Here, we examined expression of Aurora B and H1.4S27p in colorectal carcinoma (CRC) cell lines (HCT116, DLD1, Caco-2, HT29) and tissue specimens (n = 36), in relation to microsatellite instability (MSI) status and ploidy. In vitro, Aurora B (pro-/meta-/anaphase) and H1.4S27p (pro-/metaphase) were localized in mitotic figures. The proportion of labeled mitoses was significantly different between cell lines for Aurora B (p = 0.019) but not for H1.4S27p (p = 0.879). For Aurora B, these differences were not associated with an altered Aurora B gene copy number (FISH) or messenger RNA (mRNA) expression level (qRT-PCR). Moreover, Aurora B expression and H1.4S27 phosphorylation were no longer coordinated during metaphase in aneuploid HT29 cells (p = 0.039). In CRCs, immunoreactivity for Aurora B or H1.4S27p did not correlate with T- or N-stage, grade, or MSI status. However, metaphase labeling of H1.4S27p was significantly higher in diploid than in aneuploid CRCs (p = 0.011). Aurora B was significantly correlated with H1.4S27p-positive metaphases in MSI (p = 0.010) or diploid (p = 0.003) CRCs. Finally, combined classification of MSI status and ploidy revealed a significant positive correlation of Aurora B with H1.4S27p in metaphases of diploid/MSI (p = 0.010) and diploid/microsatellite-stable (MSS; p = 0.031) but not of aneuploid/MSS (p = 0.458) CRCs. The present study underlines the functional link of Aurora B expression and H1.4S27p during specific phases of mitosis in diploid and/or MSI-positive CRCs in vitro and in situ. Importantly, the study shows that the coordination between Aurora B expression and phosphorylation of H1.4 at Ser 27 is lost in cycling aneuploid CRC cells.
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Affiliation(s)
- Fahima Sijare
- Department of Pathology, University Medical Center, Breisacherstrasse 115A, 79106, Freiburg, Germany
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25
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Kunowska N, Rotival M, Yu L, Choudhary J, Dillon N. Identification of protein complexes that bind to histone H3 combinatorial modifications using super-SILAC and weighted correlation network analysis. Nucleic Acids Res 2015; 43:1418-32. [PMID: 25605797 PMCID: PMC4330348 DOI: 10.1093/nar/gku1350] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The large number of chemical modifications that are found on the histone proteins of eukaryotic cells form multiple complex combinations, which can act as recognition signals for reader proteins. We have used peptide capture in conjunction with super-SILAC quantification to carry out an unbiased high-throughput analysis of the composition of protein complexes that bind to histone H3K9/S10 and H3K27/S28 methyl-phospho modifications. The accurate quantification allowed us to perform Weighted correlation network analysis (WGCNA) to obtain a systems-level view of the histone H3 histone tail interactome. The analysis reveals the underlying modularity of the histone reader network with members of nuclear complexes exhibiting very similar binding signatures, which suggests that many proteins bind to histones as part of pre-organized complexes. Our results identify a novel complex that binds to the double H3K9me3/S10ph modification, which includes Atrx, Daxx and members of the FACT complex. The super-SILAC approach allows comparison of binding to multiple peptides with different combinations of modifications and the resolution of the WGCNA analysis is enhanced by maximizing the number of combinations that are compared. This makes it a useful approach for assessing the effects of changes in histone modification combinations on the composition and function of bound complexes.
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Affiliation(s)
- Natalia Kunowska
- Gene Regulation and Chromatin Group, MRC Clinical Sciences Centre, Imperial College, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Maxime Rotival
- Integrative Genomics and Medicine Group, MRC Clinical Sciences Centre, Imperial College, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Lu Yu
- Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | - Jyoti Choudhary
- Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | - Niall Dillon
- Gene Regulation and Chromatin Group, MRC Clinical Sciences Centre, Imperial College, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
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26
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Non-histone protein methylation as a regulator of cellular signalling and function. Nat Rev Mol Cell Biol 2014; 16:5-17. [PMID: 25491103 DOI: 10.1038/nrm3915] [Citation(s) in RCA: 322] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Methylation of Lys and Arg residues on non-histone proteins has emerged as a prevalent post-translational modification and as an important regulator of cellular signal transduction mediated by the MAPK, WNT, BMP, Hippo and JAK-STAT signalling pathways. Crosstalk between methylation and other types of post-translational modifications, and between histone and non-histone protein methylation frequently occurs and affects cellular functions such as chromatin remodelling, gene transcription, protein synthesis, signal transduction and DNA repair. With recent advances in proteomic techniques, in particular mass spectrometry, the stage is now set to decode the methylproteome and define its functions in health and disease.
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Malik P, Zuleger N, de las Heras JI, Saiz-Ros N, Makarov AA, Lazou V, Meinke P, Waterfall M, Kelly DA, Schirmer EC. NET23/STING promotes chromatin compaction from the nuclear envelope. PLoS One 2014; 9:e111851. [PMID: 25386906 PMCID: PMC4227661 DOI: 10.1371/journal.pone.0111851] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 10/07/2014] [Indexed: 12/19/2022] Open
Abstract
Changes in the peripheral distribution and amount of condensed chromatin are observed in a number of diseases linked to mutations in the lamin A protein of the nuclear envelope. We postulated that lamin A interactions with nuclear envelope transmembrane proteins (NETs) that affect chromatin structure might be altered in these diseases and so screened thirty-one NETs for those that promote chromatin compaction as determined by an increase in the number of chromatin clusters of high pixel intensity. One of these, NET23 (also called STING, MITA, MPYS, ERIS, Tmem173), strongly promoted chromatin compaction. A correlation between chromatin compaction and endogenous levels of NET23/STING was observed for a number of human cell lines, suggesting that NET23/STING may contribute generally to chromatin condensation. NET23/STING has separately been found to be involved in innate immune response signaling. Upon infection cells make a choice to either apoptose or to alter chromatin architecture to support focused expression of interferon genes and other response factors. We postulate that the chromatin compaction induced by NET23/STING may contribute to this choice because the cells expressing NET23/STING eventually apoptose, but the chromatin compaction effect is separate from this as the condensation was still observed when cells were treated with Z-VAD to block apoptosis. NET23/STING-induced compacted chromatin revealed changes in epigenetic marks including changes in histone methylation and acetylation. This indicates a previously uncharacterized nuclear role for NET23/STING potentially in both innate immune signaling and general chromatin architecture.
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Affiliation(s)
- Poonam Malik
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Nikolaj Zuleger
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Jose I. de las Heras
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Natalia Saiz-Ros
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Alexandr A. Makarov
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Vassiliki Lazou
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter Meinke
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Martin Waterfall
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
| | - David A. Kelly
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Eric C. Schirmer
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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