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Chen YZ, Zhu XM, Lv P, Hou XK, Pan Y, Li A, Du Z, Xuan JF, Guo X, Xing JX, Liu K, Yao J. Association of histone modification with the development of schizophrenia. Biomed Pharmacother 2024; 175:116747. [PMID: 38744217 DOI: 10.1016/j.biopha.2024.116747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024] Open
Abstract
Schizophrenia, influenced by genetic and environmental factors, may involve epigenetic alterations, notably histone modifications, in its pathogenesis. This review summarizes various histone modifications including acetylation, methylation, phosphorylation, ubiquitination, serotonylation, lactylation, palmitoylation, and dopaminylation, and their implications in schizophrenia. Current research predominantly focuses on histone acetylation and methylation, though other modifications also play significant roles. These modifications are crucial in regulating transcription through chromatin remodeling, which is vital for understanding schizophrenia's development. For instance, histone acetylation enhances transcriptional efficiency by loosening chromatin, while increased histone methyltransferase activity on H3K9 and altered histone phosphorylation, which reduces DNA affinity and destabilizes chromatin structure, are significant markers of schizophrenia.
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Affiliation(s)
- Yun-Zhou Chen
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Xiu-Mei Zhu
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Peng Lv
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Xi-Kai Hou
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Ying Pan
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Ang Li
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Zhe Du
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Jin-Feng Xuan
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Xiaochong Guo
- Laboratory Animal Center, China Medical University, PR China
| | - Jia-Xin Xing
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China.
| | - Kun Liu
- Key Laboratory of Health Ministry in Congenital Malformation, Shengjing Hospital of China Medical University, PR China.
| | - Jun Yao
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China.
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2
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Homma MK, Nakato R, Niida A, Bando M, Fujiki K, Yokota N, Yamamoto S, Shibata T, Takagi M, Yamaki J, Kozuka-Hata H, Oyama M, Shirahige K, Homma Y. Cell cycle-dependent gene networks for cell proliferation activated by nuclear CK2α complexes. Life Sci Alliance 2024; 7:e202302077. [PMID: 37907238 PMCID: PMC10618106 DOI: 10.26508/lsa.202302077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 11/02/2023] Open
Abstract
Nuclear expression of protein kinase CK2α is reportedly elevated in human carcinomas, but mechanisms underlying its variable localization in cells are poorly understood. This study demonstrates a functional connection between nuclear CK2 and gene expression in relation to cell proliferation. Growth stimulation of quiescent human normal fibroblasts and phospho-proteomic analysis identified a pool of CK2α that is highly phosphorylated at serine 7. Phosphorylated CK2α translocates into the nucleus, and this phosphorylation appears essential for nuclear localization and catalytic activity. Protein signatures associated with nuclear CK2 complexes reveal enrichment of apparently unique transcription factors and chromatin remodelers during progression through the G1 phase of the cell cycle. Chromatin immunoprecipitation-sequencing profiling demonstrated recruitment of CK2α to active gene loci, more abundantly in late G1 phase than in early G1, notably at transcriptional start sites of core histone genes, growth stimulus-associated genes, and ribosomal RNAs. Our findings reveal that nuclear CK2α complexes may be essential to facilitate progression of the cell cycle, by activating histone genes and triggering ribosomal biogenesis, specified in association with nuclear and nucleolar transcriptional regulators.
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Affiliation(s)
- Miwako Kato Homma
- Department of Biomolecular Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Ryuichiro Nakato
- Laboratory of Computational Genomics, Institute for Quantitative Biosciences, University of Tokyo, Bunkyo, Japan
| | - Atsushi Niida
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato, Japan
| | - Masashige Bando
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Japan
| | - Katsunori Fujiki
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Japan
| | - Naoko Yokota
- Laboratory of Computational Genomics, Institute for Quantitative Biosciences, University of Tokyo, Bunkyo, Japan
| | - So Yamamoto
- Department of Biomolecular Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| | | | - Motoki Takagi
- Translational Research Center, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Junko Yamaki
- Department of Biomolecular Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Hiroko Kozuka-Hata
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Minato, Japan
| | - Masaaki Oyama
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Minato, Japan
| | - Katsuhiko Shirahige
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Japan
- Department of Biosciences and Nutrition, Karolinska Institutet, Biomedicum, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Biomedicum, Stockholm, Sweden
| | - Yoshimi Homma
- Department of Biomolecular Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
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3
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Harris RJ, Heer M, Levasseur MD, Cartwright TN, Weston B, Mitchell JL, Coxhead JM, Gaughan L, Prendergast L, Rico D, Higgins JMG. Release of Histone H3K4-reading transcription factors from chromosomes in mitosis is independent of adjacent H3 phosphorylation. Nat Commun 2023; 14:7243. [PMID: 37945563 PMCID: PMC10636195 DOI: 10.1038/s41467-023-43115-3] [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: 04/05/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Histone modifications influence the recruitment of reader proteins to chromosomes to regulate events including transcription and cell division. The idea of a histone code, where combinations of modifications specify unique downstream functions, is widely accepted and can be demonstrated in vitro. For example, on synthetic peptides, phosphorylation of Histone H3 at threonine-3 (H3T3ph) prevents the binding of reader proteins that recognize trimethylation of the adjacent lysine-4 (H3K4me3), including the TAF3 component of TFIID. To study these combinatorial effects in cells, we analyzed the genome-wide distribution of H3T3ph and H3K4me2/3 during mitosis. We find that H3T3ph anti-correlates with adjacent H3K4me2/3 in cells, and that the PHD domain of TAF3 can bind H3K4me2/3 in isolated mitotic chromatin despite the presence of H3T3ph. Unlike in vitro, H3K4 readers are still displaced from chromosomes in mitosis in Haspin-depleted cells lacking H3T3ph. H3T3ph is therefore unlikely to be responsible for transcriptional downregulation during cell division.
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Affiliation(s)
- Rebecca J Harris
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Maninder Heer
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Mark D Levasseur
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Tyrell N Cartwright
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Bethany Weston
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Jennifer L Mitchell
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Jonathan M Coxhead
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Luke Gaughan
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
- Newcastle University Centre for Cancer, Faculty of Medical Sciences, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Lisa Prendergast
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Daniel Rico
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
- Newcastle University Centre for Cancer, Faculty of Medical Sciences, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad Sevilla-Universidad Pablo de Olavide-Junta de Andalucía, 41092, Seville, Spain.
| | - Jonathan M G Higgins
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
- Newcastle University Centre for Cancer, Faculty of Medical Sciences, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
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Spicer MFD, Gerlich DW. The material properties of mitotic chromosomes. Curr Opin Struct Biol 2023; 81:102617. [PMID: 37279615 PMCID: PMC10448380 DOI: 10.1016/j.sbi.2023.102617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/28/2023] [Accepted: 05/04/2023] [Indexed: 06/08/2023]
Abstract
Chromosomes transform during the cell cycle, allowing transcription and replication during interphase and chromosome segregation during mitosis. Morphological changes are thought to be driven by the combined effects of DNA loop extrusion and a chromatin solubility phase transition. By extruding the chromatin fibre into loops, condensins enrich at an axial core and provide resistance to spindle pulling forces. Mitotic chromosomes are further compacted by deacetylation of histone tails, rendering chromatin insoluble and resistant to penetration by microtubules. Regulation of surface properties by Ki-67 allows independent chromosome movement in early mitosis and clustering during mitotic exit. Recent progress has provided insight into how the extraordinary material properties of chromatin emerge from these activities, and how these properties facilitate faithful chromosome segregation.
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Affiliation(s)
- Maximilian F D Spicer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030, Vienna, Austria. https://twitter.com/Spicer__Max
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030, Vienna, Austria.
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5
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Characterizing crosstalk in epigenetic signaling to understand disease physiology. Biochem J 2023; 480:57-85. [PMID: 36630129 PMCID: PMC10152800 DOI: 10.1042/bcj20220550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
Epigenetics, the inheritance of genomic information independent of DNA sequence, controls the interpretation of extracellular and intracellular signals in cell homeostasis, proliferation and differentiation. On the chromatin level, signal transduction leads to changes in epigenetic marks, such as histone post-translational modifications (PTMs), DNA methylation and chromatin accessibility to regulate gene expression. Crosstalk between different epigenetic mechanisms, such as that between histone PTMs and DNA methylation, leads to an intricate network of chromatin-binding proteins where pre-existing epigenetic marks promote or inhibit the writing of new marks. The recent technical advances in mass spectrometry (MS) -based proteomic methods and in genome-wide DNA sequencing approaches have broadened our understanding of epigenetic networks greatly. However, further development and wider application of these methods is vital in developing treatments for disorders and pathologies that are driven by epigenetic dysregulation.
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6
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James Sanford E, Bustamante Smolka M. A field guide to the proteomics of post-translational modifications in DNA repair. Proteomics 2022; 22:e2200064. [PMID: 35695711 PMCID: PMC9950963 DOI: 10.1002/pmic.202200064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 12/15/2022]
Abstract
All cells incur DNA damage from exogenous and endogenous sources and possess pathways to detect and repair DNA damage. Post-translational modifications (PTMs), in the past 20 years, have risen to ineluctable importance in the study of the regulation of DNA repair mechanisms. For example, DNA damage response kinases are critical in both the initial sensing of DNA damage as well as in orchestrating downstream activities of DNA repair factors. Mass spectrometry-based proteomics revolutionized the study of the role of PTMs in the DNA damage response and has canonized PTMs as central modulators of nearly all aspects of DNA damage signaling and repair. This review provides a biologist-friendly guide for the mass spectrometry analysis of PTMs in the context of DNA repair and DNA damage responses. We reflect on the current state of proteomics for exploring new mechanisms of PTM-based regulation and outline a roadmap for designing PTM mapping experiments that focus on the DNA repair and DNA damage responses.
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Key Words
- LC-MS/MS, technology, bottom-up proteomics, technology, signal transduction, cell biology
- phosphoproteomics, technology, post-translational modification analysis, technology, post-translational modifications, cell biology, mass spectrometry
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Affiliation(s)
- Ethan James Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Marcus Bustamante Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853,Corresponding author:
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7
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Iida S, Shinkai S, Itoh Y, Tamura S, Kanemaki MT, Onami S, Maeshima K. Single-nucleosome imaging reveals steady-state motion of interphase chromatin in living human cells. SCIENCE ADVANCES 2022; 8:eabn5626. [PMID: 35658044 PMCID: PMC9166292 DOI: 10.1126/sciadv.abn5626] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Dynamic chromatin behavior plays a critical role in various genome functions. However, it remains unclear how chromatin behavior changes during interphase, where the nucleus enlarges and genomic DNA doubles. While the previously reported chromatin movements varied during interphase when measured using a minute or longer time scale, we unveil that local chromatin motion captured by single-nucleosome imaging/tracking on a second time scale remained steady throughout G1, S, and G2 phases in live human cells. This motion mode appeared to change beyond this time scale. A defined genomic region also behaved similarly. Combined with Brownian dynamics modeling, our results suggest that this steady-state chromatin motion was mainly driven by thermal fluctuations. Steady-state motion temporarily increased following a DNA damage response. Our findings support the viscoelastic properties of chromatin. We propose that the observed steady-state chromatin motion allows cells to conduct housekeeping functions, such as transcription and DNA replication, under similar environments during interphase.
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Affiliation(s)
- Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Japan
- Department of Genetics, School of Life Science, SOKENDAI, Mishima, Japan
| | - Soya Shinkai
- Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Yuji Itoh
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Japan
| | - Masato T. Kanemaki
- Department of Genetics, School of Life Science, SOKENDAI, Mishima, Japan
- Molecular Cell Engineering Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Japan
| | - Shuichi Onami
- Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Japan
- Department of Genetics, School of Life Science, SOKENDAI, Mishima, Japan
- Corresponding author.
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8
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Epigenetic Factors in Eutopic Endometrium in Women with Endometriosis and Infertility. Int J Mol Sci 2022; 23:ijms23073804. [PMID: 35409163 PMCID: PMC8998720 DOI: 10.3390/ijms23073804] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 02/01/2023] Open
Abstract
Eutopic endometrium in patients with endometriosis is characterized by aberrant expression of essential genes during the implantation window. It predisposes to disturbance of endometrial receptivity. The pathomechanism of implantation failures in women with endometriosis remains unclear. This paper aims to summarize the knowledge on epigenetic mechanisms in eutopic endometrium in the group of patients with both endometriosis and infertility. The impaired DNA methylation patterns of gene promoter regions in eutopic tissue was established. The global profile of histone acetylation and methylation and the analysis of selected histone modifications showed significant differences in the endometrium of women with endometriosis. Aberrant expression of the proposed candidate genes may promote an unfavorable embryonic implantation environment of the endometrium due to an immunological dysfunction, inflammatory reaction, and apoptotic response in women with endometriosis. The role of the newly discovered proteins regulating gene expression, i.e., TET proteins, in endometrial pathology is not yet completely known. The cells of the eutopic endometrium in women with endometriosis contain a stable, impaired methylation pattern and a histone code. Medication targeting critical genes responsible for the aberrant gene expression pattern in eutopic endometrium may help treat infertility in women with endometriosis.
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9
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Li LX, Li X. Epigenetically Mediated Ciliogenesis and Cell Cycle Regulation, and Their Translational Potential. Cells 2021; 10:cells10071662. [PMID: 34359832 PMCID: PMC8307023 DOI: 10.3390/cells10071662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/24/2021] [Accepted: 06/29/2021] [Indexed: 12/13/2022] Open
Abstract
Primary cilia biogenesis has been closely associated with cell cycle progression. Cilia assemble when cells exit the cell cycle and enter a quiescent stage at the post-mitosis phase, and disassemble before cells re-enter a new cell cycle. Studies have focused on how the cell cycle coordinates with the cilia assembly/disassembly process, and whether and how cilia biogenesis affects the cell cycle. Appropriate regulation of the functions and/or expressions of ciliary and cell-cycle-associated proteins is pivotal to maintaining bodily homeostasis. Epigenetic mechanisms, including DNA methylation and histone/chromatin modifications, are involved in the regulation of cell cycle progression and cilia biogenesis. In this review, first, we discuss how epigenetic mechanisms regulate cell cycle progression and cilia biogenesis through the regulation of DNA methylation and chromatin structures, to either promote or repress the transcription of genes associated with those processes and the modification of cytoskeleton network, including microtubule and actin. Next, we discuss the crosstalk between the cell cycle and ciliogenesis, and the involvement of epigenetic regulators in this process. In addition, we discuss cilia-dependent signaling pathways in cell cycle regulation. Understanding the mechanisms of how epigenetic regulators contribute to abnormal cell cycle regulation and ciliogenesis defects would lead to developing therapeutic strategies for the treatment of a wide variety of diseases, such as cancers, polycystic kidney disease (PKD), and other ciliopathy-associated disorders.
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Affiliation(s)
- Linda Xiaoyan Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Correspondence: ; Tel.: +1-507-266-0110
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10
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Lu C, Coradin M, Porter EG, Garcia BA. Accelerating the Field of Epigenetic Histone Modification Through Mass Spectrometry-Based Approaches. Mol Cell Proteomics 2020; 20:100006. [PMID: 33203747 PMCID: PMC7950153 DOI: 10.1074/mcp.r120.002257] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/15/2020] [Accepted: 11/17/2020] [Indexed: 02/06/2023] Open
Abstract
Histone post-translational modifications (PTMs) are one of the main mechanisms of epigenetic regulation. Dysregulation of histone PTMs leads to many human diseases, such as cancer. Because of its high throughput, accuracy, and flexibility, mass spectrometry (MS) has emerged as a powerful tool in the epigenetic histone modification field, allowing the comprehensive and unbiased analysis of histone PTMs and chromatin-associated factors. Coupled with various techniques from molecular biology, biochemistry, chemical biology, and biophysics, MS has been used to characterize distinct aspects of histone PTMs in the epigenetic regulation of chromatin functions. In this review, we will describe advancements in the field of MS that have facilitated the analysis of histone PTMs and chromatin biology. Middle–down is the most suitable to study histone combinatorial post-translational modifications. Crosslinking MS has a variety of potential applications in exploring histone post-translational modifications. Hydrogen–deuterium exchange MS holds great promise to study the compaction of nucleosome. Multi-omics approaches are useful to study complex regulatory networks.
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Affiliation(s)
- Congcong Lu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mariel Coradin
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elizabeth G Porter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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12
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Cappelli C, Sepulveda H, Rivas S, Pola V, Urzúa U, Donoso G, Sagredo E, Carrero D, Casanova-Ortiz E, Sagredo A, González M, Manterola M, Nardocci G, Armisén R, Montecino M, Marcelain K. Ski Is Required for Tri-Methylation of H3K9 in Major Satellite and for Repression of Pericentromeric Genes: Mmp3, Mmp10 and Mmp13, in Mouse Fibroblasts. J Mol Biol 2020; 432:3222-3238. [PMID: 32198114 DOI: 10.1016/j.jmb.2020.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/23/2020] [Accepted: 03/11/2020] [Indexed: 11/27/2022]
Abstract
Several mechanisms directing a rapid transcriptional reactivation of genes immediately after mitosis have been described. However, little is known about the maintenance of repressive signals during mitosis. In this work, we address the role of Ski in the repression of gene expression during M/G1 transition in mouse embryonic fibroblasts (MEFs). We found that Ski localises as a distinct pair of dots at the pericentromeric region of mitotic chromosomes, and the absence of the protein is related to high acetylation and low tri-methylation of H3K9 in pericentromeric major satellite. Moreover, differential expression assays in early G1 cells showed that the presence of Ski is significantly associated with repression of genes localised nearby to pericentromeric DNA. In mitotic cells, chromatin immunoprecipitation assays confirmed the association of Ski to major satellite and the promoters of the most repressed genes: Mmp3, Mmp10 and Mmp13. These genes are at pericentromeric region of chromosome 9. In these promoters, the presence of Ski resulted in increased H3K9 tri-methylation levels. This Ski-dependent regulation is also observed during interphase. Consequently, Mmp activity is augmented in Ski-/- MEFs. Altogether, these data indicate that association of Ski with the pericentromeric region of chromosomes during mitosis is required to maintain the silencing bookmarks of underlying chromatin.
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Affiliation(s)
- Claudio Cappelli
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile; Instituto de Bioquimica y Microbiologia, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Hugo Sepulveda
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Solange Rivas
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Víctor Pola
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Ulises Urzúa
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Gerardo Donoso
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Eduardo Sagredo
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile; Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - David Carrero
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Emmanuel Casanova-Ortiz
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Alfredo Sagredo
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Marisel González
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Marcia Manterola
- Instituto de Ciencias Biomédicas. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Gino Nardocci
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile; FONDAP Center for Genome Regulation, Santiago, Chile
| | - Ricardo Armisén
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile; Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Martin Montecino
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile; FONDAP Center for Genome Regulation, Santiago, Chile
| | - Katherine Marcelain
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile.
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13
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Li X. Epigenetics and cell cycle regulation in cystogenesis. Cell Signal 2019; 68:109509. [PMID: 31874209 DOI: 10.1016/j.cellsig.2019.109509] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 12/16/2022]
Abstract
The role of genetic mutations in the development of polycystic kidney disease (PKD), such as alterations in PKD1 and PKD2 genes in autosomal dominant PKD (ADPKD), is well understood. However, the significance of epigenetic mechanisms in the progression of PKD remains unclear and is increasingly being investigated. The term of epigenetics describes a range of mechanisms in genome function that do not solely result from the DNA sequence itself. Epigenetic information can be inherited during mammalian cell division to sustain phenotype specifically and physiologically responsive gene expression in the progeny cells. A multitude of functional studies of epigenetic modifiers and systematic genome-wide mapping of epigenetic marks reveal the importance of epigenomic mechanisms, including DNA methylation, histone/chromatin modifications and non-coding RNAs, in PKD pathologies. Deregulated proliferation is a characteristic feature of cystic renal epithelial cells. Moreover, defects in many of the molecules that regulate the cell cycle have been implicated in cyst formation and progression. Recent evidence suggests that alterations of DNA methylation and histone modifications on specific genes and the whole genome involved in cell cycle regulation and contribute to the pathogenesis of PKD. This review summarizes the recent advances of epigenetic mechanisms in PKD, which helps us to define the term of "PKD epigenetics" and group PKD epigenetic changes in three categories. In particularly, this review focuses on the interplay of epigenetic mechanisms with cell cycle regulation during normal cell cycle progression and cystic cell proliferation, and discusses the potential to detect and quantify DNA methylation from body fluids as diagnostic/prognostic biomarkers. Collectively, this review provides concepts and examples of epigenetics in cell cycle regulation to reveal a broad view of different aspects of epigenetics in biology and PKD, which may facilitate to identify possible novel therapeutic intervention points and to explore epigenetic biomarkers in PKD.
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Affiliation(s)
- Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, United States of America; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, United States of America.
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14
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Karakkat JV, Kaimala S, Sreedharan SP, Jayaprakash P, Adeghate EA, Ansari SA, Guccione E, Mensah-Brown EPK, Starling Emerald B. The metabolic sensor PASK is a histone 3 kinase that also regulates H3K4 methylation by associating with H3K4 MLL2 methyltransferase complex. Nucleic Acids Res 2019; 47:10086-10103. [PMID: 31529049 PMCID: PMC6821284 DOI: 10.1093/nar/gkz786] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 09/02/2019] [Accepted: 09/04/2019] [Indexed: 12/19/2022] Open
Abstract
The metabolic sensor Per-Arnt-Sim (Pas) domain-containing serine/threonine kinase (PASK) is expressed predominantly in the cytoplasm of different cell types, although a small percentage is also expressed in the nucleus. Herein, we show that the nuclear PASK associates with the mammalian H3K4 MLL2 methyltransferase complex and enhances H3K4 di- and tri-methylation. We also show that PASK is a histone kinase that phosphorylates H3 at T3, T6, S10 and T11. Taken together, these results suggest that PASK regulates two different H3 tail modifications involving H3K4 methylation and H3 phosphorylation. Using muscle satellite cell differentiation and functional analysis after loss or gain of Pask expression using the CRISPR/Cas9 system, we provide evidence that some of the regulatory functions of PASK during development and differentiation may occur through the regulation of these histone modifications.
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Affiliation(s)
- Jimsheena V Karakkat
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, UAE
| | - Suneesh Kaimala
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, UAE
| | - Sreejisha P Sreedharan
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, UAE
| | - Princy Jayaprakash
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, UAE
| | - Ernest A Adeghate
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, UAE
| | - Suraiya A Ansari
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, UAE
| | - Ernesto Guccione
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 138673, Singapore
| | - Eric P K Mensah-Brown
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, UAE
| | - Bright Starling Emerald
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, UAE
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15
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Chen J, Hu Y, Yu Y, Zhang L, Yang P, Jin H. Quantitative analysis of post-translational modifications of histone H3 variants during the cell cycle. Anal Chim Acta 2019; 1080:116-126. [DOI: 10.1016/j.aca.2019.06.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/09/2019] [Accepted: 06/10/2019] [Indexed: 10/26/2022]
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Abstract
Although central to regulating the access to genetic information, most lysine methyltransferases remain poorly characterised relative to other family of enzymes. Herein, I report new substrates for the lysine methyltransferase SETD6. Based on the SETD6-catalysed site on the histone variant H2AZ, I identified similar sequences in the canonical histones H2A, H3, and H4 that are modified by SETD6 in vitro, and putative non-histone substrates. I herein expend the repertoire of substrates for methylation by SETD6.
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Affiliation(s)
- Olivier Binda
- Newcastle Cancer Centre at the Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, England
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17
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Profiling of Epigenetic Features in Clinical Samples Reveals Novel Widespread Changes in Cancer. Cancers (Basel) 2019; 11:cancers11050723. [PMID: 31137727 PMCID: PMC6562406 DOI: 10.3390/cancers11050723] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/09/2019] [Accepted: 05/20/2019] [Indexed: 12/31/2022] Open
Abstract
Aberrations in histone post-translational modifications (PTMs), as well as in the histone modifying enzymes (HMEs) that catalyze their deposition and removal, have been reported in many tumors and many epigenetic inhibitors are currently under investigation for cancer treatment. Therefore, profiling epigenetic features in cancer could have important implications for the discovery of both biomarkers for patient stratification and novel epigenetic targets. In this study, we employed mass spectrometry-based approaches to comprehensively profile histone H3 PTMs in a panel of normal and tumoral tissues for different cancer types, identifying various changes, some of which appear to be a consequence of the increased proliferation rate of tumors, while others are cell-cycle independent. Histone PTM changes found in tumors partially correlate with alterations of the gene expression profiles of HMEs obtained from publicly available data and are generally lost in culture conditions. Through this analysis, we identified tumor- and subtype-specific histone PTM changes, but also widespread changes in the levels of histone H3 K9me3 and K14ac marks. In particular, H3K14ac showed a cell-cycle independent decrease in all the seven tumor/tumor subtype models tested and could represent a novel epigenetic hallmark of cancer. .
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18
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Kim JE. Bookmarking by histone methylation ensures chromosomal integrity during mitosis. Arch Pharm Res 2019; 42:466-480. [PMID: 31020544 DOI: 10.1007/s12272-019-01156-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/19/2019] [Indexed: 12/22/2022]
Abstract
The cell cycle is an orchestrated process that replicates DNA and transmits genetic information to daughter cells. Cell cycle progression is governed by diverse histone modifications that control gene transcription in a timely fashion. Histone modifications also regulate cell cycle progression by marking specific chromatic regions. While many reviews have covered histone phosphorylation and acetylation as regulators of the cell cycle, little attention has been paid to the roles of histone methylation in the faithful progression of mitosis. Indeed, specific histone methylations occurring before, during, or after mitosis affect kinetochore assembly and chromosome condensation and segregation. In addition to timing, histone methylations specify the chromatin regions such as chromosome arms, pericentromere, and centromere. Therefore, spatiotemporal programming of histone methylations ensures epigenetic inheritance through mitosis. This review mainly discusses histone methylations and their relevance to mitotic progression.
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Affiliation(s)
- Ja-Eun Kim
- Department of Pharmacology, School of Medicine, Kyung Hee University, Seoul, 02447, Republic of Korea.
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19
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Hoedt E, Zhang G, Neubert TA. Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) for Quantitative Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:531-539. [PMID: 31347069 DOI: 10.1007/978-3-030-15950-4_31] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Stable isotope labeling by amino acids in cell culture (SILAC) is a powerful approach for high-throughput quantitative proteomics. SILAC allows highly accurate protein quantitation through metabolic encoding of whole cell proteomes using stable isotope labeled amino acids. Since its introduction in 2002, SILAC has become increasingly popular. In this chapter we review the methodology and application of SILAC, with an emphasis on three research areas: dynamics of posttranslational modifications, protein-protein interactions, and protein turnover.
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Affiliation(s)
- Esthelle Hoedt
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Guoan Zhang
- Proteomics and Metabolomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
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20
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Bártová E, Lochmanová G, Legartová S, Suchánková J, Fedr R, Krejčí J, Zdráhal Z. Irradiation by γ-rays reduces the level of H3S10 phosphorylation and weakens the G2 phase-dependent interaction between H3S10 phosphorylation and γH2AX. Biochimie 2018; 154:86-98. [DOI: 10.1016/j.biochi.2018.07.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 07/31/2018] [Indexed: 10/28/2022]
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21
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Zhao B, Xu W, Rong B, Chen G, Ye X, Dai R, Li W, Chen J, Cai J, Song L, Luo ZQ, Zeng R, Shi Y, Han JDJ, Lan F. H3K14me3 genomic distributions and its regulation by KDM4 family demethylases. Cell Res 2018; 28:1118-1120. [PMID: 30337684 DOI: 10.1038/s41422-018-0095-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 08/20/2018] [Accepted: 09/04/2018] [Indexed: 12/13/2022] Open
Affiliation(s)
- Bin Zhao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Epigenetics and Metabolism, Ministry of Science and Technology, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Wenqi Xu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Epigenetics and Metabolism, Ministry of Science and Technology, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Bowen Rong
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Epigenetics and Metabolism, Ministry of Science and Technology, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Guoyu Chen
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Xuanjia Ye
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Epigenetics and Metabolism, Ministry of Science and Technology, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Ruofei Dai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Epigenetics and Metabolism, Ministry of Science and Technology, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Wenjing Li
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Epigenetics and Metabolism, Ministry of Science and Technology, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Jiajia Chen
- Institutes of Biomedical Sciences and Department of Systems Biology for Medicine, Basic Medical College, Fudan University, Shanghai, 20032, China
| | - Jiajun Cai
- Department of Neurosurgery Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Lei Song
- Department of Respiratory Medicine, Center of Infection and Immunity, The First Hospital, Jilin University, Changchun, Jilin, 130001, China
| | - Zhao-Qing Luo
- Department of Respiratory Medicine, Center of Infection and Immunity, The First Hospital, Jilin University, Changchun, Jilin, 130001, China
| | - Rong Zeng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yang Shi
- Newborn Medicine Division, Boston Children's Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jing-Dong J Han
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Fei Lan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Epigenetics and Metabolism, Ministry of Science and Technology, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
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22
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Basilicata MF, Bruel AL, Semplicio G, Valsecchi CIK, Aktaş T, Duffourd Y, Rumpf T, Morton J, Bache I, Szymanski WG, Gilissen C, Vanakker O, Õunap K, Mittler G, van der Burgt I, El Chehadeh S, Cho MT, Pfundt R, Tan TY, Kirchhoff M, Menten B, Vergult S, Lindstrom K, Reis A, Johnson DS, Fryer A, McKay V, Fisher RB, Thauvin-Robinet C, Francis D, Roscioli T, Pajusalu S, Radtke K, Ganesh J, Brunner HG, Wilson M, Faivre L, Kalscheuer VM, Thevenon J, Akhtar A. De novo mutations in MSL3 cause an X-linked syndrome marked by impaired histone H4 lysine 16 acetylation. Nat Genet 2018; 50:1442-1451. [PMID: 30224647 PMCID: PMC7398719 DOI: 10.1038/s41588-018-0220-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 08/01/2018] [Indexed: 12/15/2022]
Abstract
The etiological spectrum of ultra-rare developmental disorders remains to be fully defined. Chromatin regulatory mechanisms maintain cellular identity and function, where misregulation may lead to developmental defects. Here, we report pathogenic variations in MSL3, which encodes a member of the chromatin-associated male-specific lethal (MSL) complex responsible for bulk histone H4 lysine 16 acetylation (H4K16ac) in flies and mammals. These variants cause an X-linked syndrome affecting both sexes. Clinical features of the syndrome include global developmental delay, progressive gait disturbance, and recognizable facial dysmorphism. MSL3 mutations affect MSL complex assembly and activity, accompanied by a pronounced loss of H4K16ac levels in vivo. Patient-derived cells display global transcriptome alterations of pathways involved in morphogenesis and cell migration. Finally, we use histone deacetylase inhibitors to rebalance acetylation levels, alleviating some of the molecular and cellular phenotypes of patient cells. Taken together, we characterize a syndrome that allowed us to decipher the developmental importance of MSL3 in humans.
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Affiliation(s)
- M Felicia Basilicata
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Ange-Line Bruel
- Inserm UMR 1231 GAD, Genetics of Developmental disorders and Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs FHU TRANSLAD, Université de Bourgogne-Franche Comté, Dijon, France
| | - Giuseppe Semplicio
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | | | - Tuğçe Aktaş
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Yannis Duffourd
- Inserm UMR 1231 GAD, Genetics of Developmental disorders and Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs FHU TRANSLAD, Université de Bourgogne-Franche Comté, Dijon, France
| | - Tobias Rumpf
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Jenny Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's Hospital NHS Foundation Trust, Birmingham, UK
| | - Iben Bache
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Witold G Szymanski
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Olivier Vanakker
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital and Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Ineke van der Burgt
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Salima El Chehadeh
- Inserm UMR 1231 GAD, Genetics of Developmental disorders and Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs FHU TRANSLAD, Université de Bourgogne-Franche Comté, Dijon, France
- Service de Génétique Médicale, Hôpital de Hautepierre, Strasbourg, France
| | | | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne Department of Paediatrics, Parkville, VIC, Australia
| | - Maria Kirchhoff
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Kristin Lindstrom
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Diana S Johnson
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Alan Fryer
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Victoria McKay
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Richard B Fisher
- Northern Genetics Service, Teesside Genetics Unit, The James Cook University Hospital, Middlesbrough, UK
| | - Christel Thauvin-Robinet
- Inserm UMR 1231 GAD, Genetics of Developmental disorders and Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs FHU TRANSLAD, Université de Bourgogne-Franche Comté, Dijon, France
| | - David Francis
- Cytogenetic Laboratory, Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Tony Roscioli
- Neuroscience Research Australia, Sydney, New South Wales, Australia
- Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
- Department of Medical Genetics, Sydney Children's Hospital, Sydney, New South Wales, Australia
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital and Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Kelly Radtke
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Jaya Ganesh
- Division of Genetics, Cooper University Hospital and Cooper Medical School at Rowan University, Camden, NJ, USA
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Meredith Wilson
- Department of Clinical Genetics, Children's Hospital at Westmead, Disciplines of Genetic Medicine and Child and Adolescent Health, University of Sydney, Sydney, New South Wales, Australia
| | - Laurence Faivre
- Inserm UMR 1231 GAD, Genetics of Developmental disorders and Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs FHU TRANSLAD, Université de Bourgogne-Franche Comté, Dijon, France
| | - Vera M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Julien Thevenon
- Inserm UMR 1231 GAD, Genetics of Developmental disorders and Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs FHU TRANSLAD, Université de Bourgogne-Franche Comté, Dijon, France.
- CNRS UMR 5309, INSERM, U1209, Institute of Advanced Biosciences, Université Grenoble-Alpes CHU Grenoble, Grenoble, France.
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
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24
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Noberini R, Osti D, Miccolo C, Richichi C, Lupia M, Corleone G, Hong SP, Colombo P, Pollo B, Fornasari L, Pruneri G, Magnani L, Cavallaro U, Chiocca S, Minucci S, Pelicci G, Bonaldi T. Extensive and systematic rewiring of histone post-translational modifications in cancer model systems. Nucleic Acids Res 2018; 46:3817-3832. [PMID: 29618087 PMCID: PMC5934616 DOI: 10.1093/nar/gky224] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 03/09/2018] [Accepted: 03/16/2018] [Indexed: 01/04/2023] Open
Abstract
Histone post-translational modifications (PTMs) generate a complex combinatorial code that regulates gene expression and nuclear functions, and whose deregulation has been documented in different types of cancers. Therefore, the availability of relevant culture models that can be manipulated and that retain the epigenetic features of the tissue of origin is absolutely crucial for studying the epigenetic mechanisms underlying cancer and testing epigenetic drugs. In this study, we took advantage of quantitative mass spectrometry to comprehensively profile histone PTMs in patient tumor tissues, primary cultures and cell lines from three representative tumor models, breast cancer, glioblastoma and ovarian cancer, revealing an extensive and systematic rewiring of histone marks in cell culture conditions, which includes a decrease of H3K27me2/me3, H3K79me1/me2 and H3K9ac/K14ac, and an increase of H3K36me1/me2. While some changes occur in short-term primary cultures, most of them are instead time-dependent and appear only in long-term cultures. Remarkably, such changes mostly revert in cell line- and primary cell-derived in vivo xenograft models. Taken together, these results support the use of xenografts as the most representative models of in vivo epigenetic processes, suggesting caution when using cultured cells, in particular cell lines and long-term primary cultures, for epigenetic investigations.
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Affiliation(s)
- Roberta Noberini
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Milan 20139, Italy
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Daniela Osti
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Claudia Miccolo
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Cristina Richichi
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Michela Lupia
- Unit of Gynecological Oncology Research, European Institute of Oncology, Milan 20141, Italy
| | - Giacomo Corleone
- Department of Surgery and Cancer, Imperial College Hammersmith, London W12, UK
| | - Sung-Pil Hong
- Department of Surgery and Cancer, Imperial College Hammersmith, London W12, UK
| | - Piergiuseppe Colombo
- Department of Pathology, Humanitas Clinical and Research Center, Rozzano, Milan 20089, Italy
| | - Bianca Pollo
- Department of Neuropathology, IRCCS Foundation Neurological Institute 'C. Besta', Milan 20133, Italy
| | - Lorenzo Fornasari
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Giancarlo Pruneri
- Biobank for Translational Medicine Unit, Department of Pathology, European Institute of Oncology, Milano 20141, Italy
- School of Medicine, University of Milan, Milan 20122, Italy
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College Hammersmith, London W12, UK
| | - Ugo Cavallaro
- Unit of Gynecological Oncology Research, European Institute of Oncology, Milan 20141, Italy
| | - Susanna Chiocca
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Saverio Minucci
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
- New Drugs Program, European Institute of Oncology, Milan 20139, Italy
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Giuliana Pelicci
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
- Department of Translational Medicine, Piemonte Orientale University 'Amedeo Avogadro', Novara 28100, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
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Kurita K, Sakamoto T, Yagi N, Sakamoto Y, Ito A, Nishino N, Sako K, Yoshida M, Kimura H, Seki M, Matsunaga S. Live imaging of H3K9 acetylation in plant cells. Sci Rep 2017; 7:45894. [PMID: 28418019 PMCID: PMC5394682 DOI: 10.1038/srep45894] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 03/07/2017] [Indexed: 12/23/2022] Open
Abstract
Proper regulation of histone acetylation is important in development and cellular responses to environmental stimuli. However, the dynamics of histone acetylation at the single-cell level remains poorly understood. Here we established a transgenic plant cell line to track histone H3 lysine 9 acetylation (H3K9ac) with a modification-specific intracellular antibody (mintbody). The H3K9ac-specific mintbody fused to the enhanced green fluorescent protein (H3K9ac-mintbody-GFP) was introduced into tobacco BY-2 cells. We successfully demonstrated that H3K9ac-mintbody-GFP interacted with H3K9ac in vivo. The ratio of nuclear/cytoplasmic H3K9ac-mintbody-GFP detected in quantitative analysis reflected the endogenous H3K9ac levels. Under chemically induced hyperacetylation conditions with histone deacetylase inhibitors including trichostatin A, Ky-2 and Ky-14, significant enhancement of H3K9ac was detected by H3K9ac-mintbody-GFP dependent on the strength of inhibitors. Conversely, treatment with a histone acetyltransferase inhibitor, C646 caused a reduction in the nuclear to cytoplasmic ratio of H3K9ac-mintbody-GFP. Using this system, we assessed the environmental responses of H3K9ac and found that cold and salt stresses enhanced H3K9ac in tobacco BY-2 cells. In addition, a combination of H3K9ac-mintbody-GFP with 5-ethynyl-2'-deoxyuridine labelling confirmed that H3K9ac level is constant during interphase.
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Affiliation(s)
- Kazuki Kurita
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Noriyoshi Yagi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Yuki Sakamoto
- Imaging Frontier Center, Organization for Research Advancement, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Akihiro Ito
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Norikazu Nishino
- Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, 808-0196, Japan
| | - Kaori Sako
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hiroshi Kimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- Imaging Frontier Center, Organization for Research Advancement, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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Noberini R, Bonaldi T. A Super-SILAC Strategy for the Accurate and Multiplexed Profiling of Histone Posttranslational Modifications. Methods Enzymol 2016; 586:311-332. [PMID: 28137569 DOI: 10.1016/bs.mie.2016.09.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Histone posttranslational modifications (hPTMs) generate a complex combinatorial code that plays a critical role in the regulation of gene activity and nuclear architecture during physiological and pathological processes. Mass spectrometry (MS) offers an unbiased, comprehensive, and quantitative view on hPTM patterns, and has emerged as a powerful tool in epigenetic research. Stable isotope labeling by amino acid in cell culture (SILAC) is a MS-based quantitative method that relies on the metabolic labeling of cell populations, which has been widely applied in global proteomic studies and can also be exploited for the accurate quantitation of hPTM changes among distinct functional states. However, the classical SILAC strategy has two main limits: it cannot be applied to more than three cell populations at the time and excludes samples that cannot be metabolically labeled, such as clinical samples. These limitations can be overcome by using a super-SILAC strategy, where a mix of heavy-labeled cell lines is used as a spike-in to analyze any types of samples with high accuracy and high multiplexing capabilities. In this chapter, we will provide a detailed description of a protocol to set up a histone-focused super-SILAC strategy and exploit it to accurately profile hPTMs across multiple samples. As a case study, we will describe a breast cancer-focused super-SILAC approach, which we used in a recent publication to profile hPTMs in frozen and formalin-fixed paraffin-embedded human samples, revealing previously unknown marks that differentiate breast cancer subtypes.
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Affiliation(s)
- R Noberini
- Center for Genomic Science, Istituto Italiano di Tecnologia, Milano, Italy
| | - T Bonaldi
- European Institute of Oncology, Milano, Italy.
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Proteome Profiling of Urinary Exosomes Identifies Alpha 1-Antitrypsin and H2B1K as Diagnostic and Prognostic Biomarkers for Urothelial Carcinoma. Sci Rep 2016; 6:34446. [PMID: 27686150 PMCID: PMC5043375 DOI: 10.1038/srep34446] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/14/2016] [Indexed: 11/09/2022] Open
Abstract
MALDI-TOF spectrometry has not been used for urinary exosome analysis. We used it for determining UC biomarkers. From 2012 to 2015, we enrolled 129 consecutive patients with UC and 62 participants without UC. Exosomes from their urine were isolated, and analyzed through MALDI-TOF spectrometry. Immunohistochemical (IHC) analysis of another 122 UC and 26 non-UC tissues was conducted to verify the discovered biomarkers. Two peaks at m/z 5593 (fragmented peptide of alpha-1-antitrypsin; sensitivity, 50.4%; specificity, 96.9%) and m/z 5947 (fragmented peptide of histone H2B1K sensitivity, 62.0%; specificity, 92.3%) were identified as UC diagnosis exosome biomarkers. UC patients with detectable histone H2B1K showed 2.29- and 3.11-fold increased risks of recurrence and progression, respectively, compared with those with nondetectable histone H2B1K. Verification results of IHC staining revealed significantly higher expression of alpha 1-antitrypsin (p = 0.038) and H2B1K (p = 0.005) in UC tissues than in normal tissues. The expression of alpha 1-antitrypsin and H2B1K in UC tissues was significantly correlated with UC grades (p < 0.05). Urinary exosome proteins alpha 1-antitrypsin and histone H2B1K, which are identified through MALDI-TOF analysis, could facilitate rapid diagnosis and prognosis of UC.
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ElBashir R, Vanselow JT, Kraus A, Janzen CJ, Siegel TN, Schlosser A. Fragment ion patchwork quantification for measuring site-specific acetylation degrees. Anal Chem 2016; 87:9939-45. [PMID: 26335048 DOI: 10.1021/acs.analchem.5b02517] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We introduce fragment ion patchwork quantification as a new mass spectrometry-based approach for the highly accurate quantification of site-specific acetylation degrees. This method combines (13)C1-acetyl derivatization on the protein level, proteolysis by low-specificity proteases and quantification on the fragment ion level. Acetylation degrees are determined from the isotope patterns of acetylated b and y ions. We show that this approach allows to determine site-specific acetylation degrees of all lysine residues for all core histones of Trypanosoma brucei. In addition, we demonstrate how this approach can be used to identify substrate sites of histone acetyltransferases.
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Affiliation(s)
| | | | | | - Christian J Janzen
- Department of Cell & Developmental Biology, Biocenter University of Wuerzburg , Am Hubland, 97074 Wuerzburg, Germany
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29
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Noberini R, Sigismondo G, Bonaldi T. The contribution of mass spectrometry-based proteomics to understanding epigenetics. Epigenomics 2016; 8:429-45. [DOI: 10.2217/epi.15.108] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Chromatin is a macromolecular complex composed of DNA and histones that regulate gene expression and nuclear architecture. The concerted action of DNA methylation, histone post-translational modifications and chromatin-associated proteins control the epigenetic regulation of the genome, ultimately determining cell fate and the transcriptional outputs of differentiated cells. Deregulation of this complex machinery leads to disease states, and exploiting epigenetic drugs is becoming increasingly attractive for therapeutic intervention. Mass spectrometry (MS)-based proteomics emerged as a powerful tool complementary to genomic approaches for epigenetic research, allowing the unbiased and comprehensive analysis of histone post-translational modifications and the characterization of chromatin constituents and chromatin-associated proteins. Furthermore, MS holds great promise for epigenetic biomarker discovery and represents a useful tool for deconvolution of epigenetic drug targets. Here, we will provide an overview of the applications of MS-based proteomics in various areas of chromatin biology.
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Affiliation(s)
- Roberta Noberini
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, via Adamello 16, Milano, Italy
| | - Gianluca Sigismondo
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, Milano, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, Milano, Italy
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Yu Y, Chen J, Gao Y, Gao J, Liao R, Wang Y, Oyang C, Li E, Zeng C, Zhou S, Yang P, Jin H, Yi W. Quantitative Profiling of Combinational K27/K36 Modifications on Histone H3 Variants in Mouse Organs. J Proteome Res 2016; 15:1070-9. [PMID: 26799478 DOI: 10.1021/acs.jproteome.5b01164] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The coexisting post-translational modifications (PTMs) on histone H3 N-terminal tails were known to crosstalk between each other, indicating their interdependency in the epigenetic regulation pathways. H3K36 methylation, an important activating mark, was recently reported to antagonize with PRC2-mediated H3K27 methylation with possible crosstalk mechanism during transcription regulation process. On the basis of our previous studies, we further integrated RP/HILIC liquid chromatography with MRM mass spectrometry to quantify histone PTMs from various mouse organs, especially the combinatorial K27/K36 marks for all three major histone H3 variants. Despite their subtle difference in physicochemical properties, we successfully obtained decent separation and high detection sensitivity for both histone H3.3 specific peptides and histone H3.1/3.2 specific peptides. In addition, the overall abundance of H3.3 can be quantified simultaneously. We applied this method to investigate the pattern of the combinatorial K27/K36 marks for all three major histone H3 variants across five mouse organs. Intriguing distribution differences were observed not only between different H3 variants but also between different organs. Our data shed the new insights into histone codes functions in epigenetic regulation during cell differentiation and developmental process.
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Affiliation(s)
- Yanyan Yu
- China Novartis Institutes for BioMedical Research Co. Ltd. , Building 8, Lane 898 Halei Road, Shanghai 201203, China
| | - Jiajia Chen
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University , 220 Handan Road, Shanghai 200433, China
| | - Yuan Gao
- China Novartis Institutes for BioMedical Research Co. Ltd. , Building 8, Lane 898 Halei Road, Shanghai 201203, China
| | - Jun Gao
- China Novartis Institutes for BioMedical Research Co. Ltd. , Building 8, Lane 898 Halei Road, Shanghai 201203, China
| | - Rijing Liao
- China Novartis Institutes for BioMedical Research Co. Ltd. , Building 8, Lane 898 Halei Road, Shanghai 201203, China
| | - Yi Wang
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University , 220 Handan Road, Shanghai 200433, China
| | - Counde Oyang
- China Novartis Institutes for BioMedical Research Co. Ltd. , Building 8, Lane 898 Halei Road, Shanghai 201203, China
| | - En Li
- China Novartis Institutes for BioMedical Research Co. Ltd. , Building 8, Lane 898 Halei Road, Shanghai 201203, China
| | - Chenhui Zeng
- China Novartis Institutes for BioMedical Research Co. Ltd. , Building 8, Lane 898 Halei Road, Shanghai 201203, China
| | - Shaolian Zhou
- China Novartis Institutes for BioMedical Research Co. Ltd. , Building 8, Lane 898 Halei Road, Shanghai 201203, China
| | - Pengyuan Yang
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University , 220 Handan Road, Shanghai 200433, China
| | - Hong Jin
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University , 220 Handan Road, Shanghai 200433, China
| | - Wei Yi
- China Novartis Institutes for BioMedical Research Co. Ltd. , Building 8, Lane 898 Halei Road, Shanghai 201203, China
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Mao H, Han G, Xu L, Zhu D, Lin H, Cao X, Yu Y, Chen CD. Cis-existence of H3K27me3 and H3K36me2 in mouse embryonic stem cells revealed by specific ions of isobaric modification chromatogram. Stem Cell Res Ther 2015. [PMID: 26194893 PMCID: PMC4533945 DOI: 10.1186/s13287-015-0131-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Introduction Histone H3 lysine 27 trimethylation (H3K27me3) and H3 lysine 36 trimethylation (H3K36me3) are important epigenetic modifications correlated with transcription repression and activation, respectively. These two opposing modifications rarely co-exist in the same H3 polypeptide. However, a small but significant amount of H3 tails are modified with 5 methyl groups on K27 and K36 in mouse embryonic stem cells (mESCs) and it is unclear how the trimethylation is distributed on K27 or K36. Methods A label-free, bottom-up mass spectrum method, named specific ions of isobaric modification chromatogram (SIMC), was established to quantify the relative abundance of K27me2-K36me3 and K27me3-K36me2 in the same histone H3 tail. Results By using this method, we demonstrated that the H3K27me3-K36me2 comprises about 85 % of the penta-methylated H3 tails at K27 and K36 in mESCs. Upon mESC differentiation, the abundance of H3K27me3-K36me2 significantly decreased, while the level of H3K27me2-K36me3 remains unchanged. Conclusion Our study not only revealed the cis-existence of H3K27me3-K36me2 in mESCs, but also suggested that this combinatorial histone modification may assume a specific regulatory function during differentiation. Electronic supplementary material The online version of this article (doi:10.1186/s13287-015-0131-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hailei Mao
- Department of Anesthesiology and Critical Care Medicine, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China. .,State Key Laboratory of Molecular Biology, and Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
| | - Gang Han
- State Key Laboratory of Molecular Biology, and Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
| | - Longyong Xu
- State Key Laboratory of Molecular Biology, and Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
| | - Duming Zhu
- Department of Anesthesiology and Critical Care Medicine, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.
| | - Hanqing Lin
- State Key Laboratory of Molecular Biology, and Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
| | - Xiongwen Cao
- State Key Laboratory of Molecular Biology, and Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
| | - Yi Yu
- State Key Laboratory of Molecular Biology, and Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
| | - Charlie Degui Chen
- State Key Laboratory of Molecular Biology, and Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
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32
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Chen X, Wei S, Ji Y, Guo X, Yang F. Quantitative proteomics using SILAC: Principles, applications, and developments. Proteomics 2015; 15:3175-92. [DOI: 10.1002/pmic.201500108] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/24/2015] [Accepted: 06/08/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Shasha Wei
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Yanlong Ji
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
- University of Chinese Academy of Sciences; Beijing P. R. China
| | - Xiaojing Guo
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
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Sharma AK, Khan SA, Sharda A, Reddy DV, Gupta S. MKP1 phosphatase mediates G1-specific dephosphorylation of H3Serine10P in response to DNA damage. Mutat Res 2015; 778:71-9. [PMID: 26111828 DOI: 10.1016/j.mrfmmm.2015.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/25/2015] [Accepted: 06/01/2015] [Indexed: 01/28/2023]
Abstract
Histone mark, H3S10 phosphorylation plays a dual role in a cell by maintaining relaxed chromatin for active transcription in interphase and condensed chromatin state in mitosis. The level of H3S10P has also been shown to alter on DNA damage; however, its cell cycle specific behavior and regulation during DNA damage response is largely unexplored. In the present study, we demonstrate G1 cell cycle phase specific reversible loss of H3S10P in response to IR-induced DNA damage is mediated by opposing activities of phosphatase, MKP1 and kinase, MSK1 of the MAP kinase pathway. We also show that the MKP1 recruits to the chromatin in response to DNA damage and correlates with the decrease of H3S10P, whereas MKP1 is released from chromatin during recovery phase of DDR. Furthermore, blocking of H3S10 dephosphorylation by MKP1 inhibition impairs DNA repair process and results in poor survival of WRL68 cells. Collectively, our data proposes a pathway regulating G1 cell cycle phase specific reversible reduction of H3S10P on IR induced DNA damage and also raises the possibility of combinatorial modulation of H3S10P with specific inhibitors to target the cancer cells in G1-phase of cell cycle.
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Affiliation(s)
- Ajit K Sharma
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai 410210 MH, India
| | - Shafqat A Khan
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai 410210 MH, India
| | - Asmita Sharda
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai 410210 MH, India
| | - Divya V Reddy
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai 410210 MH, India
| | - Sanjay Gupta
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai 410210 MH, India.
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Salzano M, Sanz-García M, Monsalve DM, Moura DS, Lazo PA. VRK1 chromatin kinase phosphorylates H2AX and is required for foci formation induced by DNA damage. Epigenetics 2015; 10:373-83. [PMID: 25923214 PMCID: PMC4623420 DOI: 10.1080/15592294.2015.1028708] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
All types of DNA damage cause a local alteration and relaxation of chromatin structure. Sensing and reacting to this initial chromatin alteration is a necessary trigger for any type of DNA damage response (DDR). In this context, chromatin kinases are likely candidates to participate in detection and reaction to a locally altered chromatin as a consequence of DNA damage and, thus, initiate the appropriate cellular response. In this work, we demonstrate that VRK1 is a nucleosomal chromatin kinase and that its depletion causes loss of histones H3 and H4 acetylation, which are required for chromatin relaxation, both in basal conditions and after DNA damage, independently of ATM. Moreover, VRK1 directly and stably interacts with histones H2AX and H3 in basal conditions. In response to DNA damage induced by ionizing radiation, histone H2AX is phosphorylated in Ser139 by VRK1. The phosphorylation of H2AX and the formation of γH2AX foci induced by ionizing radiation (IR), are prevented by VRK1 depletion and are rescued by kinase-active, but not kinase-dead, VRK1. In conclusion, we found that VRK1 is a novel chromatin component that reacts to its alterations and participates very early in DDR, functioning by itself or in cooperation with ATM.
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Affiliation(s)
- Marcella Salzano
- a Experimental Therapeutics and Translational Oncology Program; Instituto de Biología Molecular y Celular del Cáncer; Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Salamanca; Campus Miguel de Unamuno ; Salamanca , Spain
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35
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Reyes GX, Schmidt TT, Kolodner RD, Hombauer H. New insights into the mechanism of DNA mismatch repair. Chromosoma 2015; 124:443-62. [PMID: 25862369 DOI: 10.1007/s00412-015-0514-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 03/23/2015] [Accepted: 03/23/2015] [Indexed: 12/20/2022]
Abstract
The genome of all organisms is constantly being challenged by endogenous and exogenous sources of DNA damage. Errors like base:base mismatches or small insertions and deletions, primarily introduced by DNA polymerases during DNA replication are repaired by an evolutionary conserved DNA mismatch repair (MMR) system. The MMR system, together with the DNA replication machinery, promote repair by an excision and resynthesis mechanism during or after DNA replication, increasing replication fidelity by up-to-three orders of magnitude. Consequently, inactivation of MMR genes results in elevated mutation rates that can lead to increased cancer susceptibility in humans. In this review, we summarize our current understanding of MMR with a focus on the different MMR protein complexes, their function and structure. We also discuss how recent findings have provided new insights in the spatio-temporal regulation and mechanism of MMR.
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Affiliation(s)
- Gloria X Reyes
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Tobias T Schmidt
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Richard D Kolodner
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Moores-UCSD Cancer Center and Institute of Genomic Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA, 92093-0669, USA
| | - Hans Hombauer
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.
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36
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Nashun B, Hill PWS, Hajkova P. Reprogramming of cell fate: epigenetic memory and the erasure of memories past. EMBO J 2015; 34:1296-308. [PMID: 25820261 PMCID: PMC4491992 DOI: 10.15252/embj.201490649] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/18/2015] [Indexed: 12/24/2022] Open
Abstract
Cell identity is a reflection of a cell type-specific gene expression profile, and consequently, cell type-specific transcription factor networks are considered to be at the heart of a given cellular phenotype. Although generally stable, cell identity can be reprogrammed in vitro by forced changes to the transcriptional network, the most dramatic example of which was shown by the induction of pluripotency in somatic cells by the ectopic expression of defined transcription factors alone. Although changes to cell fate can be achieved in this way, the efficiency of such conversion remains very low, in large part due to specific chromatin signatures constituting an epigenetic barrier to the transcription factor-mediated reprogramming processes. Here we discuss the two-way relationship between transcription factor binding and chromatin structure during cell fate reprogramming. We additionally explore the potential roles and mechanisms by which histone variants, chromatin remodelling enzymes, and histone and DNA modifications contribute to the stability of cell identity and/or provide a permissive environment for cell fate change during cellular reprogramming.
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Affiliation(s)
- Buhe Nashun
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, UK
| | - Peter W S Hill
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, UK
| | - Petra Hajkova
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, UK
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37
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Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
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38
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Xu L, Chen J, Gao J, Yu H, Yang P. Crosstalk of homocysteinylation, methylation and acetylation on histone H3. Analyst 2015; 140:3057-63. [PMID: 25807213 DOI: 10.1039/c4an02355b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Homocysteinylation on histone H3 was first identified by LC-MS/MS, which affects methylation and acetylation levels of histone H3.
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Affiliation(s)
- Leilei Xu
- Minhang Hospital and Institutes of Biomedical Sciences
- Fudan University Shanghai Medical College
- Shanghai 200032
- China
| | - Jiajia Chen
- Minhang Hospital and Institutes of Biomedical Sciences
- Fudan University Shanghai Medical College
- Shanghai 200032
- China
| | - Jun Gao
- Minhang Hospital and Institutes of Biomedical Sciences
- Fudan University Shanghai Medical College
- Shanghai 200032
- China
| | - Hongxiu Yu
- Minhang Hospital and Institutes of Biomedical Sciences
- Fudan University Shanghai Medical College
- Shanghai 200032
- China
- Department of Systems Biology for Medicine
| | - Pengyuan Yang
- Minhang Hospital and Institutes of Biomedical Sciences
- Fudan University Shanghai Medical College
- Shanghai 200032
- China
- Department of Chemistry
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39
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Khan WA, Rogan PK, Knoll JHM. Localized, non-random differences in chromatin accessibility between homologous metaphase chromosomes. Mol Cytogenet 2014; 7:70. [PMID: 25520753 PMCID: PMC4269072 DOI: 10.1186/s13039-014-0070-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 10/06/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Condensation differences along the lengths of homologous, mitotic metaphase chromosomes are well known. This study reports molecular cytogenetic data showing quantifiable localized differences in condensation between homologs that are related to differences in accessibility (DA) of associated DNA probe targets. Reproducible DA was observed for ~10% of locus-specific, short (1.5-5 kb) single copy DNA probes used in fluorescence in situ hybridization. RESULTS Fourteen probes (from chromosomes 1, 5, 9, 11, 15, 17, 22) targeting genic and intergenic regions were developed and hybridized to cells from 10 individuals with cytogenetically-distinguishable homologs. Differences in hybridization between homologs were non-random for 8 genomic regions (RGS7, CACNA1B, GABRA5, SNRPN, HERC2, PMP22:IVS3, ADORA2B:IVS1, ACR) and were not unique to known imprinted domains or specific chromosomes. DNA probes within CCNB1, C9orf66, ADORA2B:Promoter-Ex1, PMP22:IVS4-Ex 5, and intergenic region 1p36.3 showed no DA (equivalent accessibility), while OPCML showed unbiased DA. To pinpoint probe locations, we performed 3D-structured illumination microscopy (3D-SIM). This showed that genomic regions with DA had 3.3-fold greater volumetric, integrated probe intensities and broad distributions of probe depths along axial and lateral axes of the 2 homologs, compared to a low copy probe target (NOMO1) with equivalent accessibility. Genomic regions with equivalent accessibility were also enriched for epigenetic marks of open interphase chromatin (DNase I HS, H3K27Ac, H3K4me1) to a greater extent than regions with DA. CONCLUSIONS This study provides evidence that DA is non-random and reproducible; it is locus specific, but not unique to known imprinted regions or specific chromosomes. Non-random DA was also shown to be heritable within a 2 generation family. DNA probe volume and depth measurements of hybridized metaphase chromosomes further show locus-specific chromatin accessibility differences by super-resolution 3D-SIM. Based on these data and the analysis of interphase epigenetic marks of genomic intervals with DA, we conclude that there are localized differences in compaction of homologs during mitotic metaphase and that these differences may arise during or preceding metaphase chromosome compaction. Our results suggest new directions for locus-specific structural analysis of metaphase chromosomes, motivated by the potential relationship of these findings to underlying epigenetic changes established during interphase.
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Affiliation(s)
- Wahab A Khan
- />Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON N6A 5C1 Canada
- />Cytognomix, Inc, London, ON N6G 4X8 Canada
| | - Peter K Rogan
- />Departments of Biochemistry and Computer Science, University of Western Ontario, London, ON N6A 5C1 Canada
- />Cytognomix, Inc, London, ON N6G 4X8 Canada
| | - Joan HM Knoll
- />Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON N6A 5C1 Canada
- />Cytognomix, Inc, London, ON N6G 4X8 Canada
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40
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Gao J, Liao R, Yu Y, Zhai H, Wang Y, Sack R, Peters AHFM, Chen J, Wu H, Huang Z, Hu M, Qi W, Lu C, Atadja P, Oyang C, Li E, Yi W, Zhou S. Absolute quantification of histone PTM marks by MRM-based LC-MS/MS. Anal Chem 2014; 86:9679-86. [PMID: 25166916 DOI: 10.1021/ac502333a] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The N-terminal tails of core histones harbor the sites of numerous post-translational modifications (PTMs) with important roles in the regulation of chromatin structure and function. Profiling histone PTM marks provides data that help understand the epigenetics events in cells and their connections with cancer and other diseases. Our previous study demonstrated that specific derivatization of histone peptides by NHS propionate significantly improved their chromatographic performance on reversed phase columns for LC/MS analysis. As a step forward, we recently developed a multiple reaction monitoring (MRM) based LC-MS/MS method to analyze 42 targeted histone peptides. By using stable isotopic labeled peptides as internal standards that are spiked into the reconstituted solutions, this method allows to measure absolute concentration of the tryptic peptides of H3 histone proteins extracted from cancer cell lines. The method was thoroughly validated for the accuracy and reproducibility through analyzing recombinant histone proteins and cellular samples. The linear dynamic range of the MRM assays was achieved in 3 orders of magnitude from 1 nM to 1 μM for all targeted peptides. Excellent intrabatch and interbatch reproducibility (<15% CV) was obtained. This method has been used to study translocated NSD2 (a histone lysine methyltransferase that catalyzes the histone lysine 36 methylation) function with its overexpression in KMS11 multiple myeloma cells. From the results we have successfully quantitated both individual and combinatorial histone marks in parental and NSD2 selective knockout KMS11 cells.
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Affiliation(s)
- Jun Gao
- China Novartis Institutes for BioMedical Research Co. Ltd. , Building 8, Lane 898 Halei Road, Shanghai 201203, China
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41
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Xu YM, Du JY, Lau ATY. Posttranslational modifications of human histone H3: an update. Proteomics 2014; 14:2047-60. [PMID: 25044606 DOI: 10.1002/pmic.201300435] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 05/30/2014] [Accepted: 07/04/2014] [Indexed: 02/05/2023]
Abstract
Histone proteins, the fundamental components of chromatin, are highly conserved proteins that present in eukaryotic nuclei. They organize genomic DNA to form nucleosomes, the basic units of chromatin. PTMs of histones play essential roles in many biological processes, such as chromatin condensation, gene expression, cell differentiation, and apoptosis. With the advancement of proteomic technology, a growing number of histone PTMs have been identified, including ADP-ribosylation, biotinylation, citrullination, crotonylation, O-GlcNAcylation, glutathionylation, succinylation, and so on. Because of the fast growing list of these PTMs in just a few years, the functions of these marks are being studied intensively. As histone H3 has the most number of PTMs among the histone members, in this review, we would like to present the overall concepts of the more familiar PTMs as well as discussing all the recently identified yet less well-known PTMs on human histone H3.
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Affiliation(s)
- Yan-Ming Xu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, P. R. China
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42
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Nguyen HT, Tian G, Murph MM. Molecular epigenetics in the management of ovarian cancer: are we investigating a rational clinical promise? Front Oncol 2014; 4:71. [PMID: 24782983 PMCID: PMC3986558 DOI: 10.3389/fonc.2014.00071] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 03/20/2014] [Indexed: 12/21/2022] Open
Abstract
Epigenetics is essentially a phenotypical change in gene expression without any alteration of the DNA sequence; the emergence of epigenetics in cancer research and mainstream oncology is fueling new hope. However, it is not yet known whether this knowledge will translate to improved clinical management of ovarian cancer. In this malignancy, women are still undergoing chemotherapy similar to what was approved in 1978, which to this day represents one of the biggest breakthroughs for treating ovarian cancer. Although liquid tumors are benefiting from epigenetically related therapies, solid tumors like ovarian cancer are not (yet?). Herein, we will review the science of molecular epigenetics, especially DNA methylation, histone modifications and microRNA, but also include transcription factors since they, too, are important in ovarian cancer. Pre-clinical and clinical research on the role of epigenetic modifications is also summarized. Unfortunately, ovarian cancer remains an idiopathic disease, for the most part, and there are many areas of patient management, which could benefit from improved technology. This review will also highlight the evidence suggesting that epigenetics may have pre-clinical utility in pharmacology and clinical applications for prognosis and diagnosis. Finally, drugs currently in clinical trials (i.e., histone deacetylase inhibitors) are discussed along with the promise for epigenetics in the exploitation of chemoresistance. Whether epigenetics will ultimately be the answer to better management in ovarian cancer is currently unknown; but we hope so in the future.
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Affiliation(s)
- Ha T Nguyen
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia College of Pharmacy , Athens, GA , USA
| | - Geng Tian
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia College of Pharmacy , Athens, GA , USA ; Department of Obstetrics and Gynecology, The Second Hospital of Jilin University , Changchun , China
| | - Mandi M Murph
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia College of Pharmacy , Athens, GA , USA
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43
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Soldi M, Bremang M, Bonaldi T. Biochemical systems approaches for the analysis of histone modification readout. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:657-68. [PMID: 24681439 DOI: 10.1016/j.bbagrm.2014.03.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 03/06/2014] [Accepted: 03/18/2014] [Indexed: 11/28/2022]
Abstract
Chromatin is the macromolecular nucleoprotein complex that governs the organization of genetic material in the nucleus of eukaryotic cells. In chromatin, DNA is packed with histone proteins into nucleosomes. Core histones are prototypes of hyper-modified proteins, being decorated by a large number of site-specific reversible and irreversible post-translational modifications (PTMs), which contribute to the maintenance and modulation of chromatin plasticity, gene activation, and a variety of other biological processes and disease states. The observations of the variety, frequency and co-occurrence of histone modifications in distinct patterns at specific genomic loci have led to the idea that hPTMs can create a molecular barcode, read by effector proteins that translate it into a specific transcriptional state, or process, on the underlying DNA. However, despite the fact that this histone-code hypothesis was proposed more than 10 years ago, the molecular details of its working mechanisms are only partially characterized. In particular, two questions deserve specific investigation: how the different modifications associate and synergize into patterns and how these PTM configurations are read and translated by multi-protein complexes into a specific functional outcome on the genome. Mass spectrometry (MS) has emerged as a versatile tool to investigate chromatin biology, useful for both identifying and validating hPTMs, and to dissect the molecular determinants of histone modification readout systems. We review here the MS techniques and the proteomics methods that have been developed to address these fundamental questions in epigenetics research, emphasizing approaches based on the proteomic dissection of distinct native chromatin regions, with a critical evaluation of their present challenges and future potential. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
- Monica Soldi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Michael Bremang
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.
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44
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Hoedt E, Zhang G, Neubert TA. Stable isotope labeling by amino acids in cell culture (SILAC) for quantitative proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:93-106. [PMID: 24952180 DOI: 10.1007/978-3-319-06068-2_5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Stable isotope labeling by amino acids in cell culture (SILAC) is a powerful approach for high-throughput quantitative proteomics. SILAC allows highly accurate protein quantitation through metabolic encoding of whole cell proteomes using stable isotope labeled amino acids. Since its introduction in 2002, SILAC has become increasingly popular. In this chapter we review the methodology and application of SILAC, with an emphasis on three research areas: dynamics of posttranslational modifications, protein-protein interactions, and protein turnover.
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Affiliation(s)
- Esthelle Hoedt
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 540 First Avenue, New York, NY, 10016, USA
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45
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Sevilla A, Binda O. Post-translational modifications of the histone variant H2AZ. Stem Cell Res 2014; 12:289-95. [PMID: 24316985 PMCID: PMC4671304 DOI: 10.1016/j.scr.2013.11.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 10/17/2013] [Accepted: 11/06/2013] [Indexed: 01/09/2023] Open
Affiliation(s)
- Ana Sevilla
- The New York Stem Cell Foundation Laboratory, New York, NY, 10032, USA
| | - Olivier Binda
- Newcastle Cancer Centre at the Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom.
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46
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Desvoyes B, Fernández-Marcos M, Sequeira-Mendes J, Otero S, Vergara Z, Gutierrez C. Looking at plant cell cycle from the chromatin window. FRONTIERS IN PLANT SCIENCE 2014; 5:369. [PMID: 25120553 PMCID: PMC4110626 DOI: 10.3389/fpls.2014.00369] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/11/2014] [Indexed: 05/03/2023]
Abstract
The cell cycle is defined by a series of complex events, finely coordinated through hormonal, developmental and environmental signals, which occur in a unidirectional manner and end up in producing two daughter cells. Accumulating evidence reveals that chromatin is not a static entity throughout the cell cycle. In fact, there are many changes that include nucleosome remodeling, histone modifications, deposition and exchange, among others. Interestingly, it is possible to correlate the occurrence of several of these chromatin-related events with specific processes necessary for cell cycle progression, e.g., licensing of DNA replication origins, the E2F-dependent transcriptional wave in G1, the activation of replication origins in S-phase, the G2-specific transcription of genes required for mitosis or the chromatin packaging occurring in mitosis. Therefore, an emerging view is that chromatin dynamics must be considered as an intrinsic part of cell cycle regulation. In this article, we review the main features of several key chromatin events that occur at defined times throughout the cell cycle and discuss whether they are actually controlling the transit through specific cell cycle stages.
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Affiliation(s)
| | | | | | | | | | - Crisanto Gutierrez
- *Correspondence: Crisanto Gutierrez, Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas, Universidad Autónoma de Madrid, Nicolas Cabrera 1, Cantoblanco, Madrid 28049, Spain e-mail:
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Dillinger S, Garea AV, Deutzmann R, Németh A. Analysis of histone posttranslational modifications from nucleolus-associated chromatin by mass spectrometry. Methods Mol Biol 2014; 1094:277-93. [PMID: 24162996 DOI: 10.1007/978-1-62703-706-8_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chromatin is unevenly distributed within the eukaryote nucleus and it contributes to the formation of morphologically and functionally distinct substructures, called chromatin domains and nuclear bodies. Here we describe an approach to assess specific chromatin features, the histone posttranslational modifications (PTMs), of the largest nuclear sub-compartment, the nucleolus. In this chapter, methods for the isolation of nucleolus-associated chromatin from native or formaldehyde-fixed cells and the effect of experimental procedures on the outcome of mass spectrometry analysis of histone PTMs are compared.
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Affiliation(s)
- Stefan Dillinger
- Biochemistry Center Regensburg, University of Regensburg, Regensburg, Germany
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48
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Karch KR, Denizio JE, Black BE, Garcia BA. Identification and interrogation of combinatorial histone modifications. Front Genet 2013; 4:264. [PMID: 24391660 PMCID: PMC3868920 DOI: 10.3389/fgene.2013.00264] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 11/15/2013] [Indexed: 11/13/2022] Open
Abstract
Histone proteins are dynamically modified to mediate a variety of cellular processes including gene transcription, DNA damage repair, and apoptosis. Regulation of these processes occurs through the recruitment of non-histone proteins to chromatin by specific combinations of histone post-translational modifications (PTMs). Mass spectrometry has emerged as an essential tool to discover and quantify histone PTMs both within and between samples in an unbiased manner. Developments in mass spectrometry that allow for characterization of large histone peptides or intact protein has made it possible to determine which modifications occur simultaneously on a single histone polypeptide. A variety of techniques from biochemistry, biophysics, and chemical biology have been employed to determine the biological relevance of discovered combinatorial codes. This review first describes advancements in the field of mass spectrometry that have facilitated histone PTM analysis and then covers notable approaches to probe the biological relevance of these modifications in their nucleosomal context.
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Affiliation(s)
- Kelly R Karch
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
| | - Jamie E Denizio
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
| | - Ben E Black
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
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49
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Li F, Mao G, Tong D, Huang J, Gu L, Yang W, Li GM. The histone mark H3K36me3 regulates human DNA mismatch repair through its interaction with MutSα. Cell 2013; 153:590-600. [PMID: 23622243 DOI: 10.1016/j.cell.2013.03.025] [Citation(s) in RCA: 432] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 02/13/2013] [Accepted: 03/18/2013] [Indexed: 12/23/2022]
Abstract
DNA mismatch repair (MMR) ensures replication fidelity by correcting mismatches generated during DNA replication. Although human MMR has been reconstituted in vitro, how MMR occurs in vivo is unknown. Here, we show that an epigenetic histone mark, H3K36me3, is required in vivo to recruit the mismatch recognition protein hMutSα (hMSH2-hMSH6) onto chromatin through direct interactions with the hMSH6 PWWP domain. The abundance of H3K36me3 in G1 and early S phases ensures that hMutSα is enriched on chromatin before mispairs are introduced during DNA replication. Cells lacking the H3K36 trimethyltransferase SETD2 display microsatellite instability (MSI) and an elevated spontaneous mutation frequency, characteristic of MMR-deficient cells. This work reveals that a histone mark regulates MMR in human cells and explains the long-standing puzzle of MSI-positive cancer cells that lack detectable mutations in known MMR genes.
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Affiliation(s)
- Feng Li
- Graduate Center for Toxicology, Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40506, USA
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50
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Abstract
Lysine methylation of histones and non-histone proteins has emerged in recent years as a posttranslational modification with wide-ranging cellular implications beyond epigenetic regulation. The molecular interactions between lysine methyltransferases and their substrates appear to be regulated by posttranslational modifications surrounding the lysine methyl acceptor. Two very interesting examples of this cross-talk between methyl-lysine sites are found in the SET (Su(var)3–9, Enhancer-of-zeste, Trithorax) domain-containing lysine methyltransferases SET7 and SETDB1, whereby the histone H3 trimethylated on lysine 4 (H3K4me3) modification prevents methylation by SETDB1 on H3 lysine 9 (H3K9) and the histone H3 trimethylated on lysine 9 (H3K9me3) modification prevents methylation by SET7 on H3K4. A similar cross-talk between posttranslational modifications regulates the functions of non-histone proteins such as the tumor suppressor p53 and the DNA methyltransferase DNMT1. Herein, in cis effects of acetylation, phosphorylation, as well as arginine and lysine methylation on lysine methylation events will be discussed.
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Affiliation(s)
- Olivier Binda
- Newcastle Cancer Centre at the Northern Institute for Cancer Research; Newcastle University, Newcastle upon Tyne, England.
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