1
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Dhahri H, Saintilnord WN, Chandler D, Fondufe-Mittendorf YN. Beyond the Usual Suspects: Examining the Role of Understudied Histone Variants in Breast Cancer. Int J Mol Sci 2024; 25:6788. [PMID: 38928493 PMCID: PMC11203562 DOI: 10.3390/ijms25126788] [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: 05/21/2024] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
The incorporation of histone variants has structural ramifications on nucleosome dynamics and stability. Due to their unique sequences, histone variants can alter histone-histone or histone-DNA interactions, impacting the folding of DNA around the histone octamer and the overall higher-order structure of chromatin fibers. These structural modifications alter chromatin compaction and accessibility of DNA by transcription factors and other regulatory proteins to influence gene regulatory processes such as DNA damage and repair, as well as transcriptional activation or repression. Histone variants can also generate a unique interactome composed of histone chaperones and chromatin remodeling complexes. Any of these perturbations can contribute to cellular plasticity and the progression of human diseases. Here, we focus on a frequently overlooked group of histone variants lying within the four human histone gene clusters and their contribution to breast cancer.
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Affiliation(s)
- Hejer Dhahri
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA or (H.D.); (W.N.S.)
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA;
| | - Wesley N. Saintilnord
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA or (H.D.); (W.N.S.)
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA;
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- The Edison Family Center of Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Darrell Chandler
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA;
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2
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Schmidt A, Zhang H, Schmitt S, Rausch C, Popp O, Chen J, Cmarko D, Butter F, Dittmar G, Lermyte F, Cardoso MC. The Proteomic Composition and Organization of Constitutive Heterochromatin in Mouse Tissues. Cells 2024; 13:139. [PMID: 38247831 PMCID: PMC10814525 DOI: 10.3390/cells13020139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Pericentric heterochromatin (PCH) forms spatio-temporarily distinct compartments and affects chromosome organization and stability. Albeit some of its components are known, an elucidation of its proteome and how it differs between tissues in vivo is lacking. Here, we find that PCH compartments are dynamically organized in a tissue-specific manner, possibly reflecting compositional differences. As the mouse brain and liver exhibit very different PCH architecture, we isolated native PCH fractions from these tissues, analyzed their protein compositions using quantitative mass spectrometry, and compared them to identify common and tissue-specific PCH proteins. In addition to heterochromatin-enriched proteins, the PCH proteome includes RNA/transcription and membrane-related proteins, which showed lower abundance than PCH-enriched proteins. Thus, we applied a cut-off of PCH-unspecific candidates based on their abundance and validated PCH-enriched proteins. Amongst the hits, MeCP2 was classified into brain PCH-enriched proteins, while linker histone H1 was not. We found that H1 and MeCP2 compete to bind to PCH and regulate PCH organization in opposite ways. Altogether, our workflow of unbiased PCH isolation, quantitative mass spectrometry, and validation-based analysis allowed the identification of proteins that are common and tissue-specifically enriched at PCH. Further investigation of selected hits revealed their opposing role in heterochromatin higher-order architecture in vivo.
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Affiliation(s)
- Annika Schmidt
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Hui Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Stephanie Schmitt
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Cathia Rausch
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Oliver Popp
- Proteomics Platform, Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Jiaxuan Chen
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Dusan Cmarko
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic
| | - Falk Butter
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Gunnar Dittmar
- Proteomics Platform, Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Frederik Lermyte
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Department of Chemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
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3
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Zhang L, Ye B, Xu Z, Li X, D M C, Shao Z. Genome-wide identification of mammalian cell-cycle invariant and mitotic-specific macroH2A1 domains. Biosci Trends 2023; 17:393-400. [PMID: 37778979 DOI: 10.5582/bst.2023.01214] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
The histone variant macroH2A has been found to play important regulatory roles in genomic processes, especially in regulating transcriptomes. However, whether macroH2A nucleosomes are retained on mitotic chromosomes to enable maintenance of cell-specific transcriptomes is not known. Here, examining mouse embryonic fibroblast cells (NIH-3T3) with native chromatin immunoprecipitation and sequencing (nChIP-seq), we show that the overwhelming majority (~90%) of macroH2A1 domains identified at the G1/S stage are indeed stably retained on mitotic chromosomes. Unexpectedly though, we also find that there are a number of macroH2A domains that are specific for either mitotic or G1/S cells. Notably, more than 7,000 interphase expressed genes flanked by macroH2A1 domains are loaded with macroH2A1 nucleosomes on the mitotic chromosome to form extended domains. Overall, these results reveal that, while the majority of macroH2A1 domains are indeed faithfully transmitted through the mitotic chromosomes, there is a previously unknown cell-cycle dependent exchange of macroH2A1 nucleosomes at numerous genomic loci, indicating the existence of molecular machineries for this dynamically regulated process. We anticipate that these findings will prove to be essential for the integrity of mitotic progression and the maintenance of cellular identity.
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Affiliation(s)
- Le Zhang
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University, Shanghai, China
- Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Bishan Ye
- Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zeqian Xu
- Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xinhui Li
- Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Czajkowsky D M
- Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zhifeng Shao
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University, Shanghai, China
- Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
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4
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Mandemaker IK, Fessler E, Corujo D, Kotthoff C, Wegerer A, Rouillon C, Buschbeck M, Jae LT, Mattiroli F, Ladurner AG. The histone chaperone ANP32B regulates chromatin incorporation of the atypical human histone variant macroH2A. Cell Rep 2023; 42:113300. [PMID: 37858472 DOI: 10.1016/j.celrep.2023.113300] [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: 02/03/2023] [Revised: 08/25/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023] Open
Abstract
All vertebrate genomes encode for three large histone H2A variants that have an additional metabolite-binding globular macrodomain module, macroH2A. MacroH2A variants impact heterochromatin organization and transcription regulation and establish a barrier for cellular reprogramming. However, the mechanisms of how macroH2A is incorporated into chromatin and the identity of any chaperones required for histone deposition remain elusive. Here, we develop a split-GFP-based assay for chromatin incorporation and use it to conduct a genome-wide mutagenesis screen in haploid human cells to identify proteins that regulate macroH2A dynamics. We show that the histone chaperone ANP32B is a regulator of macroH2A deposition. ANP32B associates with macroH2A in cells and in vitro binds to histones with low nanomolar affinity. In vitro nucleosome assembly assays show that ANP32B stimulates deposition of macroH2A-H2B and not of H2A-H2B onto tetrasomes. In cells, depletion of ANP32B strongly affects global macroH2A chromatin incorporation, revealing ANP32B as a macroH2A histone chaperone.
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Affiliation(s)
- Imke K Mandemaker
- Biomedical Center (BMC), Department of Physiological Chemistry, Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany; Hubrecht Institute, Uppsalalaan 8, 3584CT Utrecht, the Netherlands.
| | - Evelyn Fessler
- Gene Center and Department of Biochemistry, LMU Munich, 81377 Munich, Germany
| | - David Corujo
- Applied Epigenetics Program, Myeloid Neoplasm Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, 08916 Badalona, Barcelona, Spain; Germans Trias I Pujol Research Institute (IGTP), 08916 Badalona, Barcelona, Spain
| | - Christiane Kotthoff
- Biomedical Center (BMC), Department of Physiological Chemistry, Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Andreas Wegerer
- Biomedical Center (BMC), Department of Physiological Chemistry, Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Clément Rouillon
- Hubrecht Institute, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
| | - Marcus Buschbeck
- Applied Epigenetics Program, Myeloid Neoplasm Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, 08916 Badalona, Barcelona, Spain; Germans Trias I Pujol Research Institute (IGTP), 08916 Badalona, Barcelona, Spain
| | - Lucas T Jae
- Gene Center and Department of Biochemistry, LMU Munich, 81377 Munich, Germany
| | | | - Andreas G Ladurner
- Biomedical Center (BMC), Department of Physiological Chemistry, Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany; Eisbach Bio GmbH, 82152 Planegg-Martinsried, Germany.
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5
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Lewis HC, Kelnhofer-Millevolte LE, Brinkley MR, Arbach HE, Arnold EA, Sanders S, Bosse JB, Ramachandran S, Avgousti DC. HSV-1 exploits host heterochromatin for nuclear egress. J Cell Biol 2023; 222:e202304106. [PMID: 37516914 PMCID: PMC10373338 DOI: 10.1083/jcb.202304106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/31/2023] Open
Abstract
Herpes simplex virus (HSV-1) progeny form in the nucleus and exit to successfully infect other cells. Newly formed capsids navigate complex chromatin architecture to reach the inner nuclear membrane (INM) and egress. Here, we demonstrate by transmission electron microscopy (TEM) that HSV-1 capsids traverse heterochromatin associated with trimethylation on histone H3 lysine 27 (H3K27me3) and the histone variant macroH2A1. Through chromatin profiling during infection, we revealed global redistribution of these marks whereby massive host genomic regions bound by macroH2A1 and H3K27me3 correlate with decreased host transcription in active compartments. We found that the loss of these markers resulted in significantly lower viral titers but did not impact viral genome or protein accumulation. Strikingly, we discovered that loss of macroH2A1 or H3K27me3 resulted in nuclear trapping of capsids. Finally, by live-capsid tracking, we quantified this decreased capsid movement. Thus, our work demonstrates that HSV-1 takes advantage of the dynamic nature of host heterochromatin formation during infection for efficient nuclear egress.
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Affiliation(s)
- Hannah C Lewis
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology, Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Laurel E Kelnhofer-Millevolte
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology, Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- UW Medical Scientist Training Program , Seattle, WA, USA
| | - Mia R Brinkley
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hannah E Arbach
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Edward A Arnold
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Microbiology Graduate Program, University of Washington , Seattle, WA, USA
| | - Saskia Sanders
- Institute of Virology, Hannover Medical School , Hannover, Germany
- Leibniz Institute of Virology (LIV) , Hamburg, Germany
- Centre for Structural Systems Biology , Hamburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School , Hannover, Germany
| | - Jens B Bosse
- Institute of Virology, Hannover Medical School , Hannover, Germany
- Leibniz Institute of Virology (LIV) , Hamburg, Germany
- Centre for Structural Systems Biology , Hamburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School , Hannover, Germany
| | - Srinivas Ramachandran
- RNA Bioscience Initiative, University of Colorado School of Medicine , Aurora, CO, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Daphne C Avgousti
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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6
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Filipescu D, Carcamo S, Agarwal A, Tung N, Humblin É, Goldberg MS, Vyas NS, Beaumont KG, Demircioglu D, Sridhar S, Ghiraldini FG, Capparelli C, Aplin AE, Salmon H, Sebra R, Kamphorst AO, Merad M, Hasson D, Bernstein E. MacroH2A restricts inflammatory gene expression in melanoma cancer-associated fibroblasts by coordinating chromatin looping. Nat Cell Biol 2023; 25:1332-1345. [PMID: 37605008 PMCID: PMC10495263 DOI: 10.1038/s41556-023-01208-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/20/2023] [Indexed: 08/23/2023]
Abstract
MacroH2A has established tumour suppressive functions in melanoma and other cancers, but an unappreciated role in the tumour microenvironment. Using an autochthonous, immunocompetent mouse model of melanoma, we demonstrate that mice devoid of macroH2A variants exhibit increased tumour burden compared with wild-type counterparts. MacroH2A-deficient tumours accumulate immunosuppressive monocytes and are depleted of functional cytotoxic T cells, characteristics consistent with a compromised anti-tumour response. Single cell and spatial transcriptomics identify increased dedifferentiation along the neural crest lineage of the tumour compartment and increased frequency and activation of cancer-associated fibroblasts following macroH2A loss. Mechanistically, macroH2A-deficient cancer-associated fibroblasts display increased myeloid chemoattractant activity as a consequence of hyperinducible expression of inflammatory genes, which is enforced by increased chromatin looping of their promoters to enhancers that gain H3K27ac. In summary, we reveal a tumour suppressive role for macroH2A variants through the regulation of chromatin architecture in the tumour stroma with potential implications for human melanoma.
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Affiliation(s)
- Dan Filipescu
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Saul Carcamo
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Bioinformatics for Next Generation Sequencing Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aman Agarwal
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Bioinformatics for Next Generation Sequencing Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Navpreet Tung
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Étienne Humblin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew S Goldberg
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nikki S Vyas
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristin G Beaumont
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Deniz Demircioglu
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Bioinformatics for Next Generation Sequencing Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Subhasree Sridhar
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Flavia G Ghiraldini
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Claudia Capparelli
- Department of Pharmacology, Physiology and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Andrew E Aplin
- Department of Pharmacology, Physiology and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Hélène Salmon
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institut Curie, INSERM, U932, and PSL Research University, Paris, France
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alice O Kamphorst
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Bioinformatics for Next Generation Sequencing Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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7
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Aggeletopoulou I, Kalafateli M, Tsounis EP, Triantos C. Epigenetic Regulation in Lean Nonalcoholic Fatty Liver Disease. Int J Mol Sci 2023; 24:12864. [PMID: 37629043 PMCID: PMC10454848 DOI: 10.3390/ijms241612864] [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: 07/31/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD), the most prominent cause of chronic liver disease worldwide, is a rapidly growing epidemic. It consists of a wide range of liver diseases, from steatosis to nonalcoholic steatohepatitis, and predisposes patients to liver fibrosis, cirrhosis, and even hepatocellular carcinoma. NAFLD is strongly correlated with obesity; however, it has been extensively reported among lean/nonobese individuals in recent years. Although lean patients demonstrate a lower prevalence of diabetes mellitus, central obesity, dyslipidemia, hypertension, and metabolic syndrome, a percentage of these patients may develop steatohepatitis, advanced liver fibrosis, and cardiovascular disease, and have increased all-cause mortality. The pathophysiological mechanisms of lean NAFLD remain vague. Studies have reported that lean NAFLD demonstrates a close association with environmental factors, genetic predisposition, and epigenetic modifications. In this review, we aim to discuss and summarize the epigenetic mechanisms involved in lean NAFLD and to introduce the interaction between epigenetic patterns and genetic or non genetic factors. Several epigenetic mechanisms have been implicated in the regulation of lean NAFLD. These include DNA methylation, histone modifications, and noncoding-RNA-mediated gene regulation. Epigenetics is an area of special interest in the setting of lean NAFLD as it could provide new insights into the therapeutic options and noninvasive biomarkers that target this under-recognized and challenging disorder.
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Affiliation(s)
- Ioanna Aggeletopoulou
- Division of Gastroenterology, Department of Internal Medicine, University Hospital of Patras, 26504 Patras, Greece; (I.A.); (E.P.T.)
| | - Maria Kalafateli
- Department of Gastroenterology, General Hospital of Patras, 26332 Patras, Greece;
| | - Efthymios P. Tsounis
- Division of Gastroenterology, Department of Internal Medicine, University Hospital of Patras, 26504 Patras, Greece; (I.A.); (E.P.T.)
| | - Christos Triantos
- Division of Gastroenterology, Department of Internal Medicine, University Hospital of Patras, 26504 Patras, Greece; (I.A.); (E.P.T.)
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8
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Nikolic A, Maule F, Bobyn A, Ellestad K, Paik S, Marhon SA, Mehdipour P, Lun X, Chen HM, Mallard C, Hay AJ, Johnston MJ, Gafuik CJ, Zemp FJ, Shen Y, Ninkovic N, Osz K, Labit E, Berger ND, Brownsey DK, Kelly JJ, Biernaskie J, Dirks PB, Derksen DJ, Jones SJM, Senger DL, Chan JA, Mahoney DJ, De Carvalho DD, Gallo M. macroH2A2 antagonizes epigenetic programs of stemness in glioblastoma. Nat Commun 2023; 14:3062. [PMID: 37244935 DOI: 10.1038/s41467-023-38919-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/22/2023] [Indexed: 05/29/2023] Open
Abstract
Self-renewal is a crucial property of glioblastoma cells that is enabled by the choreographed functions of chromatin regulators and transcription factors. Identifying targetable epigenetic mechanisms of self-renewal could therefore represent an important step toward developing effective treatments for this universally lethal cancer. Here we uncover an epigenetic axis of self-renewal mediated by the histone variant macroH2A2. With omics and functional assays deploying patient-derived in vitro and in vivo models, we show that macroH2A2 shapes chromatin accessibility at enhancer elements to antagonize transcriptional programs of self-renewal. macroH2A2 also sensitizes cells to small molecule-mediated cell death via activation of a viral mimicry response. Consistent with these results, our analyses of clinical cohorts indicate that high transcriptional levels of this histone variant are associated with better prognosis of high-grade glioma patients. Our results reveal a targetable epigenetic mechanism of self-renewal controlled by macroH2A2 and suggest additional treatment approaches for glioblastoma patients.
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Affiliation(s)
- Ana Nikolic
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Francesca Maule
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Anna Bobyn
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Katrina Ellestad
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Seungil Paik
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Parinaz Mehdipour
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Xueqing Lun
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Huey-Miin Chen
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Claire Mallard
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Alexander J Hay
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Michael J Johnston
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Christopher J Gafuik
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Franz J Zemp
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Nicoletta Ninkovic
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Katalin Osz
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Elodie Labit
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Compararive Biology and Experimental Medicine, Faculty of Veterinary Medicine, and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - N Daniel Berger
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Duncan K Brownsey
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Chemistry, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - John J Kelly
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jeff Biernaskie
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Compararive Biology and Experimental Medicine, Faculty of Veterinary Medicine, and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Peter B Dirks
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Darren J Derksen
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Chemistry, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Donna L Senger
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jennifer A Chan
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Douglas J Mahoney
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, Faculty of Science, University of Toronto, Toronto, ON, Canada
| | - Marco Gallo
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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9
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Dasovich M, Leung AKL. PARPs and ADP-ribosylation: Deciphering the complexity with molecular tools. Mol Cell 2023; 83:1552-1572. [PMID: 37119811 PMCID: PMC10202152 DOI: 10.1016/j.molcel.2023.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/07/2023] [Accepted: 04/05/2023] [Indexed: 05/01/2023]
Abstract
PARPs catalyze ADP-ribosylation-a post-translational modification that plays crucial roles in biological processes, including DNA repair, transcription, immune regulation, and condensate formation. ADP-ribosylation can be added to a wide range of amino acids with varying lengths and chemical structures, making it a complex and diverse modification. Despite this complexity, significant progress has been made in developing chemical biology methods to analyze ADP-ribosylated molecules and their binding proteins on a proteome-wide scale. Additionally, high-throughput assays have been developed to measure the activity of enzymes that add or remove ADP-ribosylation, leading to the development of inhibitors and new avenues for therapy. Real-time monitoring of ADP-ribosylation dynamics can be achieved using genetically encoded reporters, and next-generation detection reagents have improved the precision of immunoassays for specific forms of ADP-ribosylation. Further development and refinement of these tools will continue to advance our understanding of the functions and mechanisms of ADP-ribosylation in health and disease.
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Affiliation(s)
- Morgan Dasovich
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Molecular Biology and Genetics, Department of Oncology, and Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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10
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Oberdoerffer P, Miller KM. Histone H2A variants: Diversifying chromatin to ensure genome integrity. Semin Cell Dev Biol 2023; 135:59-72. [PMID: 35331626 PMCID: PMC9489817 DOI: 10.1016/j.semcdb.2022.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/12/2022]
Abstract
Histone variants represent chromatin components that diversify the structure and function of the genome. The variants of H2A, primarily H2A.X, H2A.Z and macroH2A, are well-established participants in DNA damage response (DDR) pathways, which function to protect the integrity of the genome. Through their deposition, post-translational modifications and unique protein interaction networks, these variants guard DNA from endogenous threats including replication stress and genome fragility as well as from DNA lesions inflicted by exogenous sources. A growing body of work is now providing a clearer picture on the involvement and mechanistic basis of H2A variant contribution to genome integrity. Beyond their well-documented role in gene regulation, we review here how histone H2A variants promote genome stability and how alterations in these pathways contribute to human diseases including cancer.
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Affiliation(s)
- Philipp Oberdoerffer
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA.
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA.
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11
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The Role of PARP1 and PAR in ATP-Independent Nucleosome Reorganisation during the DNA Damage Response. Genes (Basel) 2022; 14:genes14010112. [PMID: 36672853 PMCID: PMC9859207 DOI: 10.3390/genes14010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
The functioning of the eukaryotic cell genome is mediated by sophisticated protein-nucleic-acid complexes, whose minimal structural unit is the nucleosome. After the damage to genomic DNA, repair proteins need to gain access directly to the lesion; therefore, the initiation of the DNA damage response inevitably leads to local chromatin reorganisation. This review focuses on the possible involvement of PARP1, as well as proteins acting nucleosome compaction, linker histone H1 and non-histone chromatin protein HMGB1. The polymer of ADP-ribose is considered the main regulator during the development of the DNA damage response and in the course of assembly of the correct repair complex.
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12
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Bai L, Dermadi D, Kalesinskas L, Dvorak M, Chang SE, Ganesan A, Rubin SJS, Kuo A, Cheung P, Donato M, Utz PJ, Habtezion A, Khatri P. Mass-cytometry-based quantitation of global histone post-translational modifications at single-cell resolution across peripheral immune cells in IBD. J Crohns Colitis 2022; 17:804-815. [PMID: 36571819 PMCID: PMC10155749 DOI: 10.1093/ecco-jcc/jjac194] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Indexed: 01/26/2023]
Abstract
BACKGROUND AND AIMS Current understanding of histone post-translational modifications (histone modifications) across immune cell types in patients with inflammatory bowel disease (IBD) during remission and flare is limited. The study aimed to quantify histone modifications at a single-cell resolution in IBD patients during remission and flare and how they differ compared to healthy controls. METHODS We performed a case-control study of 94 subjects (83 IBD patients and 11 healthy controls). IBD patients had either UC (n=38) or CD (n=45) in clinical remission or flare. We used epigenetic profiling by time-of-flight (EpiTOF) to investigate changes in histone modifications within peripheral blood mononuclear cells from IBD patients. RESULTS We discovered substantial heterogeneity in histone modifications across multiple immune cell types in IBD patients. They had a higher proportion of less differentiated CD34 + hematopoietic progenitors, and a subset of CD56 bright NK cells and γδ T cells characterized by distinct histone modifications associated with the gene transcription. The subset of CD56 bright NK cells had increased several histone acetylations. An epigenetically defined subset of NK was associated with higher levels of CRP in peripheral blood. CD14+ monocytes from IBD patients had significantly decreased cleaved H3T22, suggesting they were epigenetically primed for macrophage differentiation. CONCLUSION We describe the first systems-level quantification of histone modifications across immune cells from IBD patients at a single-cell resolution revealing the increased epigenetic heterogeneity that is not possible with traditional ChIP-seq profiling. Our data open new directions in investigating the association between histone modifications and IBD pathology using other epigenomic tools.
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Affiliation(s)
- Lawrence Bai
- Immunology Program, Stanford University School of Medicine, 1215 Welch Road, Modular B, Stanford, CA 94305 USA
| | - Denis Dermadi
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Laurynas Kalesinskas
- Biomedical Informatics Training Program, Stanford University School of Medicine, 1265 Welch Road, MSOB X-343, Stanford, CA 94305 USA
| | - Mai Dvorak
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.,Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah E Chang
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.,Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ananthakrishnan Ganesan
- Computational and Mathematical Engineering, Stanford University, 475 Via Ortega, Suite B060, Stanford, CA 94305 USA
| | - Samuel J S Rubin
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, United States
| | - Alex Kuo
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.,Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peggie Cheung
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.,Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Paul J Utz
- Immunology Program, Stanford University School of Medicine, 1215 Welch Road, Modular B, Stanford, CA 94305 USA.,Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.,Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aida Habtezion
- Immunology Program, Stanford University School of Medicine, 1215 Welch Road, Modular B, Stanford, CA 94305 USA.,Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.,Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, United States
| | - Purvesh Khatri
- Immunology Program, Stanford University School of Medicine, 1215 Welch Road, Modular B, Stanford, CA 94305 USA.,Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
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13
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Lin JMG, Kourtis S, Ghose R, Pardo Lorente N, Kubicek S, Sdelci S. Metabolic modulation of transcription: The role of one-carbon metabolism. Cell Chem Biol 2022; 29:S2451-9456(22)00415-9. [PMID: 36513079 DOI: 10.1016/j.chembiol.2022.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 10/05/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022]
Abstract
While it is well known that expression levels of metabolic enzymes regulate the metabolic state of the cell, there is mounting evidence that the converse is also true, that metabolite levels themselves can modulate gene expression via epigenetic modifications and transcriptional regulation. Here we focus on the one-carbon metabolic pathway, which provides the essential building blocks of many classes of biomolecules, including purine nucleotides, thymidylate, serine, and methionine. We review the epigenetic roles of one-carbon metabolic enzymes and their associated metabolites and introduce an interactive computational resource that places enzyme essentiality in the context of metabolic pathway topology. Therefore, we briefly discuss examples of metabolic condensates and higher-order complexes of metabolic enzymes downstream of one-carbon metabolism. We speculate that they may be required to the formation of transcriptional condensates and gene expression control. Finally, we discuss new ways to exploit metabolic pathway compartmentalization to selectively target these enzymes in cancer.
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Affiliation(s)
- Jung-Ming G Lin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Vienna 1090, Austria
| | - Savvas Kourtis
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Ritobrata Ghose
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Natalia Pardo Lorente
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Vienna 1090, Austria
| | - Sara Sdelci
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain.
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14
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Zong W, Gong Y, Sun W, Li T, Wang ZQ. PARP1: Liaison of Chromatin Remodeling and Transcription. Cancers (Basel) 2022; 14:cancers14174162. [PMID: 36077699 PMCID: PMC9454564 DOI: 10.3390/cancers14174162] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation) is a covalent post-translational modification and plays a key role in the immediate response of cells to stress signals. Poly(ADP-ribose) polymerase 1 (PARP1), the founding member of the PARP superfamily, synthesizes long and branched polymers of ADP-ribose (PAR) onto acceptor proteins, thereby modulating their function and their local surrounding. PARP1 is the most prominent of the PARPs and is responsible for the production of about 90% of PAR in the cell. Therefore, PARP1 and PARylation play a pleotropic role in a wide range of cellular processes, such as DNA repair and genomic stability, cell death, chromatin remodeling, inflammatory response and gene transcription. PARP1 has DNA-binding and catalytic activities that are important for DNA repair, yet also modulate chromatin conformation and gene transcription, which can be independent of DNA damage response. PARP1 and PARylation homeostasis have also been implicated in multiple diseases, including inflammation, stroke, diabetes and cancer. Studies of the molecular action and biological function of PARP1 and PARylation provide a basis for the development of pharmaceutic strategies for clinical applications. This review focuses primarily on the role of PARP1 in the regulation of chromatin remodeling and transcriptional activation.
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Affiliation(s)
- Wen Zong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Correspondence: (W.Z.); or (Z.-Q.W.)
| | - Yamin Gong
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany
- College of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen 518055, China
| | - Wenli Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Tangliang Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Zhao-Qi Wang
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich-Schiller-University of Jena, 07743 Jena, Germany
- Correspondence: (W.Z.); or (Z.-Q.W.)
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15
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Longarini EJ, Matic I. The fast-growing business of Serine ADP-ribosylation. DNA Repair (Amst) 2022; 118:103382. [DOI: 10.1016/j.dnarep.2022.103382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/03/2022]
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16
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Corujo D, Malinverni R, Carrillo-Reixach J, Meers O, Garcia-Jaraquemada A, Le Pannérer MM, Valero V, Pérez A, Del Río-Álvarez Á, Royo L, Pérez-González B, Raurell H, Acemel RD, Santos-Pereira JM, Garrido-Pontnou M, Gómez-Skarmeta JL, Pasquali L, Manyé J, Armengol C, Buschbeck M. MacroH2As regulate enhancer-promoter contacts affecting enhancer activity and sensitivity to inflammatory cytokines. Cell Rep 2022; 39:110988. [PMID: 35732123 DOI: 10.1016/j.celrep.2022.110988] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 04/04/2022] [Accepted: 05/31/2022] [Indexed: 11/18/2022] Open
Abstract
MacroH2A histone variants have a function in gene regulation that is poorly understood at the molecular level. We report that macroH2A1.2 and macroH2A2 modulate the transcriptional ground state of cancer cells and how they respond to inflammatory cytokines. Removal of macroH2A1.2 and macroH2A2 in hepatoblastoma cells affects the contact frequency of promoters and distal enhancers coinciding with changes in enhancer activity or preceding them in response to the cytokine tumor necrosis factor alpha. Although macroH2As regulate genes in both directions, they globally facilitate the nuclear factor κB (NF-κB)-mediated response. In contrast, macroH2As suppress the response to the pro-inflammatory cytokine interferon gamma. MacroH2A2 has a stronger contribution to gene repression than macroH2A1.2. Taken together, our results suggest that macroH2As have a role in regulating the response of cancer cells to inflammatory signals on the level of chromatin structure. This is likely relevant for the interaction of cancer cells with immune cells of their microenvironment.
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Affiliation(s)
- David Corujo
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, Badalona, Barcelona 08916, Spain; Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Barcelona 08916, Spain
| | - Roberto Malinverni
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, Badalona, Barcelona 08916, Spain
| | - Juan Carrillo-Reixach
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Barcelona 08916, Spain; Childhood Liver Oncology Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona 08916, Spain
| | - Oliver Meers
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, Badalona, Barcelona 08916, Spain; Doctoral Programme in Biomedicine, Universitat de Barcelona, Facultat de Farmàcia i Ciències de l'Alimentació, Barcelona 08028, Spain
| | - Arce Garcia-Jaraquemada
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona 08916, Spain
| | - Marguerite-Marie Le Pannérer
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, Badalona, Barcelona 08916, Spain; PhD Programme in Biomedicine, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Vanesa Valero
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, Badalona, Barcelona 08916, Spain
| | - Ainhoa Pérez
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, Badalona, Barcelona 08916, Spain
| | - Álvaro Del Río-Álvarez
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Barcelona 08916, Spain; Childhood Liver Oncology Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona 08916, Spain
| | - Laura Royo
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Barcelona 08916, Spain; Childhood Liver Oncology Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona 08916, Spain
| | - Beatriz Pérez-González
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Helena Raurell
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Rafael D Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla 41013, Spain
| | - José M Santos-Pereira
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla 41013, Spain
| | | | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla 41013, Spain
| | - Lorenzo Pasquali
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Josep Manyé
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona 08916, Spain; Liver and Digestive Diseases Networking Biomedical Research Centre (CIBEREHD), Madrid 28029, Spain
| | - Carolina Armengol
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Barcelona 08916, Spain; Childhood Liver Oncology Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona 08916, Spain; Liver and Digestive Diseases Networking Biomedical Research Centre (CIBEREHD), Madrid 28029, Spain.
| | - Marcus Buschbeck
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, Badalona, Barcelona 08916, Spain; Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Barcelona 08916, Spain.
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17
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Guberovic I, Farkas M, Corujo D, Buschbeck M. Evolution, structure and function of divergent macroH2A1 splice isoforms. Semin Cell Dev Biol 2022; 135:43-49. [PMID: 35422391 DOI: 10.1016/j.semcdb.2022.03.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/29/2022] [Indexed: 12/13/2022]
Abstract
The replacement of replication-coupled histones with non-canonical histone variants provides chromatin with additional properties and contributes to the plasticity of the epigenome. MacroH2A histone variants are counterparts of the replication-coupled histone H2A. They are characterized by a unique tripartite structure, consisting of a histone fold, an unstructured linker, and a globular macrodomain. MacroH2A1.1 and macroH2A1.2 are the result of alternative splicing of the MACROH2A1 gene and can have opposing biological functions. Here, we discuss the structural differences between the macrodomains of the two isoforms, resulting in differential ligand binding. We further discuss how this modulates gene regulation by the two isoforms, in cases resulting in opposing role of macroH2A1.1 and macroH2A1.2 in development and differentiation. Finally, we share recent insight in the evolution of macroH2As. Taken together, in this review, we aim to discuss in unprecedented detail distinct properties and functions of the fascinating macroH2A1 splice isoforms.
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Affiliation(s)
- Iva Guberovic
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, Badalona, Spain
| | - Marina Farkas
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, Badalona, Spain
| | - David Corujo
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, Badalona, Spain
| | - Marcus Buschbeck
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, Badalona, Spain; Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain.
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18
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Phillips EO, Gunjan A. Histone Variants: The Unsung Guardians of the Genome. DNA Repair (Amst) 2022; 112:103301. [DOI: 10.1016/j.dnarep.2022.103301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 02/01/2022] [Accepted: 02/12/2022] [Indexed: 12/15/2022]
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19
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Wootton J, Soutoglou E. Chromatin and Nuclear Dynamics in the Maintenance of Replication Fork Integrity. Front Genet 2022; 12:773426. [PMID: 34970302 PMCID: PMC8712883 DOI: 10.3389/fgene.2021.773426] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Replication of the eukaryotic genome is a highly regulated process and stringent control is required to maintain genome integrity. In this review, we will discuss the many aspects of the chromatin and nuclear environment that play key roles in the regulation of both unperturbed and stressed replication. Firstly, the higher order organisation of the genome into A and B compartments, topologically associated domains (TADs) and sub-nuclear compartments has major implications in the control of replication timing. In addition, the local chromatin environment defined by non-canonical histone variants, histone post-translational modifications (PTMs) and enrichment of factors such as heterochromatin protein 1 (HP1) plays multiple roles in normal S phase progression and during the repair of replicative damage. Lastly, we will cover how the spatial organisation of stalled replication forks facilitates the resolution of replication stress.
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Affiliation(s)
- Jack Wootton
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Evi Soutoglou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
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20
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Sowa ST, Galera-Prat A, Wazir S, Alanen HI, Maksimainen MM, Lehtiö L. A molecular toolbox for ADP-ribosyl binding proteins. CELL REPORTS METHODS 2021; 1:100121. [PMID: 34786571 PMCID: PMC8580838 DOI: 10.1016/j.crmeth.2021.100121] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/29/2021] [Accepted: 11/04/2021] [Indexed: 12/24/2022]
Abstract
Proteins interacting with ADP-ribosyl groups are often involved in disease-related pathways or viral infections, making them attractive drug targets. We present a robust and accessible assay applicable to both hydrolyzing or non-hydrolyzing binders of mono- and poly-ADP-ribosyl groups. This technology relies on a C-terminal tag based on a Gi protein alpha subunit peptide (GAP), which allows for site-specific introduction of cysteine-linked mono- and poly-ADP-ribosyl groups or analogs. By fusing the GAP-tag and ADP-ribosyl binders to fluorescent proteins, we generate robust FRET partners and confirm the interaction with 22 known ADP-ribosyl binders. The applicability for high-throughput screening of inhibitors is demonstrated with the SARS-CoV-2 nsp3 macrodomain, for which we identify suramin as a moderate-affinity yet non-specific inhibitor. High-affinity ADP-ribosyl binders fused to nanoluciferase complement this technology, enabling simple blot-based detection of ADP-ribosylated proteins. All these tools can be produced in Escherichia coli and will help in ADP-ribosylation research and drug discovery.
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Affiliation(s)
- Sven T. Sowa
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Albert Galera-Prat
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Sarah Wazir
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Heli I. Alanen
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Mirko M. Maksimainen
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Lari Lehtiö
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
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21
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Evolution of a histone variant involved in compartmental regulation of NAD metabolism. Nat Struct Mol Biol 2021; 28:1009-1019. [PMID: 34887560 DOI: 10.1038/s41594-021-00692-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022]
Abstract
NAD metabolism is essential for all forms of life. Compartmental regulation of NAD+ consumption, especially between the nucleus and the mitochondria, is required for energy homeostasis. However, how compartmental regulation evolved remains unclear. In the present study, we investigated the evolution of the macrodomain-containing histone variant macroH2A1.1, an integral chromatin component that limits nuclear NAD+ consumption by inhibiting poly(ADP-ribose) polymerase 1 in vertebrate cells. We found that macroH2A originated in premetazoan protists. The crystal structure of the macroH2A macrodomain from the protist Capsaspora owczarzaki allowed us to identify highly conserved principles of ligand binding and pinpoint key residue substitutions, selected for during the evolution of the vertebrate stem lineage. Metabolic characterization of the Capsaspora lifecycle suggested that the metabolic function of macroH2A was associated with nonproliferative stages. Taken together, we provide insight into the evolution of a chromatin element involved in compartmental NAD regulation, relevant for understanding its metabolism and potential therapeutic applications.
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22
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Huang Y, Huang S, Ma L, Wang Y, Wang X, Xiao L, Qin W, Li L, Yuan X. Exploring the Prognostic Value, Immune Implication and Biological Function of H2AFY Gene in Hepatocellular Carcinoma. Front Immunol 2021; 12:723293. [PMID: 34899687 PMCID: PMC8651705 DOI: 10.3389/fimmu.2021.723293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 11/02/2021] [Indexed: 12/09/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is an extremely malignant cancer with poor survival. H2AFY gene encodes for a variant of H2A histone, and it has been found to be dysregulated in various tumors. However, the clinical value, biological functions and correlations with immune infiltration of H2AFY in HCC remain unclear. Methods We analyzed the expression and clinical significance of H2AFY in HCC using multiple databases, including Oncomine, HCCDB, TCGA, ICGC, and so on. The genetic alterations of H2AFY were analyzed by cBioPortal and COSMIC databases. Co-expression networks of H2AFY and its regulators were investigated by LinkedOmics. The correlations between H2AFY and tumor immune infiltration were explored using TIMER, TISIDB databases, and CIBERSORT method. Finally, H2AFY was knocked down with shRNA lentiviruses in HCC cell lines for functional assays in vitro. Results H2AFY expression was upregulated in the HCC tissues and cells. Kaplan-Meier and Cox regression analyses revealed that high H2AFY expression was an independent prognostic factor for poor survival in HCC patients. Functional network analysis indicated that H2AFY and its co-expressed genes regulates cell cycle, mitosis, spliceosome and chromatin assembly through pathways involving many cancer-related kinases and E2F family. Furthermore, we observed significant correlations between H2AFY expression and immune infiltration in HCC. H2AFY knockdown suppressed the cell proliferation and migration, promoted cycle arrest, and apoptosis of HCC cells in vitro. Conclusion Our study revealed that H2AFY is a potential biomarker for unfavorable prognosis and correlates with immune infiltration in HCC.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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23
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Apelt K, Lans H, Schärer OD, Luijsterburg MS. Nucleotide excision repair leaves a mark on chromatin: DNA damage detection in nucleosomes. Cell Mol Life Sci 2021; 78:7925-7942. [PMID: 34731255 PMCID: PMC8629891 DOI: 10.1007/s00018-021-03984-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/27/2021] [Accepted: 10/15/2021] [Indexed: 11/28/2022]
Abstract
Global genome nucleotide excision repair (GG-NER) eliminates a broad spectrum of DNA lesions from genomic DNA. Genomic DNA is tightly wrapped around histones creating a barrier for DNA repair proteins to access DNA lesions buried in nucleosomal DNA. The DNA-damage sensors XPC and DDB2 recognize DNA lesions in nucleosomal DNA and initiate repair. The emerging view is that a tight interplay between XPC and DDB2 is regulated by post-translational modifications on the damage sensors themselves as well as on chromatin containing DNA lesions. The choreography between XPC and DDB2, their interconnection with post-translational modifications such as ubiquitylation, SUMOylation, methylation, poly(ADP-ribos)ylation, acetylation, and the functional links with chromatin remodelling activities regulate not only the initial recognition of DNA lesions in nucleosomes, but also the downstream recruitment and necessary displacement of GG-NER factors as repair progresses. In this review, we highlight how nucleotide excision repair leaves a mark on chromatin to enable DNA damage detection in nucleosomes.
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Affiliation(s)
- Katja Apelt
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea.,Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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24
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Phosphorylation within Intrinsic Disordered Region Discriminates Histone Variant macroH2A1 Splicing Isoforms-macroH2A1.1 and macroH2A1.2. BIOLOGY 2021; 10:biology10070659. [PMID: 34356514 PMCID: PMC8301376 DOI: 10.3390/biology10070659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 01/02/2023]
Abstract
Simple Summary MacroH2A1, a histone H2A variant, is present as two alternative splicing isoforms, macroH2A1.1 and macroH2A1.2, which are finely regulated through several mechanisms, including post-translational modifications (PTM). In this article, the authors provide the PTM pattern of macroH2A1.1 and macroH2A1.2 in the same experimental setting through mass spec analysis. They report a different phosphorylation level in their intrinsically disordered linker region, which can be responsible for their different biological role, as computational analysis shows. Abstract Background: Gene expression in eukaryotic cells can be governed by histone variants, which replace replication-coupled histones, conferring unique chromatin properties. MacroH2A1 is a histone H2A variant containing a domain highly similar to H2A and a large non-histone (macro) domain. MacroH2A1, in turn, is present in two alternatively exon-spliced isoforms: macroH2A1.1 and macroH2A1.2, which regulate cell plasticity and proliferation in a remarkably distinct manner. The N-terminal and the C-terminal tails of H2A histones stem from the nucleosome core structure and can be target sites for several post-translational modifications (PTMs). MacroH2A1.1 and macroH2A1.2 isoforms differ only in a few amino acids and their ability to bind NAD-derived metabolites, a property allegedly conferring their different functions in vivo. Some of the modifications on the macroH2A1 variant have been identified, such as phosphorylation (T129, S138) and methylation (K18, K123, K239). However, no study to our knowledge has analyzed extensively, and in parallel, the PTM pattern of macroH2A1.1 and macroH2A1.2 in the same experimental setting, which could facilitate the understanding of their distinct biological functions in health and disease. Methods: We used a mass spectrometry-based approach to identify the sites for phosphorylation, acetylation, and methylation in green fluorescent protein (GFP)-tagged macroH2A1.1 and macroH2A1.2 expressed in human hepatoma cells. The impact of selected PTMs on macroH2A1.1 and macroH2A1.2 structure and function are demonstrated using computational analyses. Results: We identified K7 as a new acetylation site in both macroH2A1 isoforms. Quantitative comparison of histone marks between the two isoforms revealed significant differences in the levels of phosphorylated T129 and S170. Our computational analysis provided evidence that the phosphorylation status in the intrinsically disordered linker region in macroH2A1 isoforms might represent a key regulatory element contributing to their distinct biological responses. Conclusions: Taken together, our results report different PTMs on the two macroH2A1 splicing isoforms as responsible for their distinct features and distribution in the cell.
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25
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DNA methylation and histone variants in aging and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:1-110. [PMID: 34507780 DOI: 10.1016/bs.ircmb.2021.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aging-related diseases such as cancer can be traced to the accumulation of molecular disorder including increased DNA mutations and epigenetic drift. We provide a comprehensive review of recent results in mice and humans on modifications of DNA methylation and histone variants during aging and in cancer. Accumulated errors in DNA methylation maintenance lead to global decreases in DNA methylation with relaxed repression of repeated DNA and focal hypermethylation blocking the expression of tumor suppressor genes. Epigenetic clocks based on quantifying levels of DNA methylation at specific genomic sites is proving to be a valuable metric for estimating the biological age of individuals. Histone variants have specialized functions in transcriptional regulation and genome stability. Their concentration tends to increase in aged post-mitotic chromatin, but their effects in cancer are mainly determined by their specialized functions. Our increased understanding of epigenetic regulation and their modifications during aging has motivated interventions to delay or reverse epigenetic modifications using the epigenetic clocks as a rapid readout for efficacity. Similarly, the knowledge of epigenetic modifications in cancer is suggesting new approaches to target these modifications for cancer therapy.
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26
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Hsu CJ, Meers O, Buschbeck M, Heidel FH. The Role of MacroH2A Histone Variants in Cancer. Cancers (Basel) 2021; 13:cancers13123003. [PMID: 34203934 PMCID: PMC8232725 DOI: 10.3390/cancers13123003] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/07/2021] [Accepted: 06/14/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary The structural unit of chromatin is the nucleosome that is composed of DNA wrapped around a core of eight histone proteins. Histone variants can replace ‘standard’ histones at specific sites of the genome. Thus, histone variants modulate all functions in the context of chromatin, such as gene expression. Here, we provide a concise review on a group of histone variants termed macroH2A. They contain two additional domains that contribute to their increased size. We discuss how these domains mediate molecular functions in normal cells and the role of macroH2As in gene expression and cancer. Abstract The epigenome regulates gene expression and provides a molecular memory of cellular events. A growing body of evidence has highlighted the importance of epigenetic regulation in physiological tissue homeostasis and malignant transformation. Among epigenetic mechanisms, the replacement of replication-coupled histones with histone variants is the least understood. Due to differences in protein sequence and genomic distribution, histone variants contribute to the plasticity of the epigenome. Here, we focus on the family of macroH2A histone variants that are particular in having a tripartite structure consisting of a histone fold, an intrinsically disordered linker and a globular macrodomain. We discuss how these domains mediate different molecular functions related to chromatin architecture, transcription and DNA repair. Dysregulated expression of macroH2A histone variants has been observed in different subtypes of cancer and has variable prognostic impact, depending on cellular context and molecular background. We aim to provide a concise review regarding the context- and isoform-dependent contributions of macroH2A histone variants to cancer development and progression.
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Affiliation(s)
- Chen-Jen Hsu
- Internal Medicine C, Greifswald University Medicine, 17475 Greifswald, Germany;
| | - Oliver Meers
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, 08916 Badalona, Spain;
| | - Marcus Buschbeck
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, 08916 Badalona, Spain;
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Campus Can Ruti, 08916 Badalona, Spain
- Correspondence: (M.B.); (F.H.H.); Tel.: +34-935-572-800 (M.B.); +49-383-486-6698 (F.H.H.); Fax: +49-383-486-6713 (F.H.H.)
| | - Florian H. Heidel
- Internal Medicine C, Greifswald University Medicine, 17475 Greifswald, Germany;
- Leibniz Institute on Aging, Fritz-Lipmann Institute, 07745 Jena, Germany
- Correspondence: (M.B.); (F.H.H.); Tel.: +34-935-572-800 (M.B.); +49-383-486-6698 (F.H.H.); Fax: +49-383-486-6713 (F.H.H.)
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27
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Schmücker A, Lei B, Lorković ZJ, Capella M, Braun S, Bourguet P, Mathieu O, Mechtler K, Berger F. Crosstalk between H2A variant-specific modifications impacts vital cell functions. PLoS Genet 2021; 17:e1009601. [PMID: 34086674 PMCID: PMC8208582 DOI: 10.1371/journal.pgen.1009601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/16/2021] [Accepted: 05/14/2021] [Indexed: 12/15/2022] Open
Abstract
Selection of C-terminal motifs participated in evolution of distinct histone H2A variants. Hybrid types of variants combining motifs from distinct H2A classes are extremely rare. This suggests that the proximity between the motif cases interferes with their function. We studied this question in flowering plants that evolved sporadically a hybrid H2A variant combining the SQ motif of H2A.X that participates in the DNA damage response with the KSPK motif of H2A.W that stabilizes heterochromatin. Our inventory of PTMs of H2A.W variants showed that in vivo the cell cycle-dependent kinase CDKA phosphorylates the KSPK motif of H2A.W but only in absence of an SQ motif. Phosphomimicry of KSPK prevented DNA damage response by the SQ motif of the hybrid H2A.W/X variant. In a synthetic yeast expressing the hybrid H2A.W/X variant, phosphorylation of KSPK prevented binding of the BRCT-domain protein Mdb1 to phosphorylated SQ and impaired response to DNA damage. Our findings illustrate that PTMs mediate interference between the function of H2A variant specific C-terminal motifs. Such interference could explain the mutual exclusion of motifs that led to evolution of H2A variants.
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Affiliation(s)
- Anna Schmücker
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Bingkun Lei
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Zdravko J. Lorković
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Matías Capella
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Sigurd Braun
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
- International Max Planck Research School for Molecular and Cellular Life Sciences, Planegg-Martinsried, Germany
| | - Pierre Bourguet
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
- CNRS, Université Clermont Auvergne, Inserm, Génétique Reproduction et Développement, Clermont-Ferrand, France
| | - Olivier Mathieu
- CNRS, Université Clermont Auvergne, Inserm, Génétique Reproduction et Développement, Clermont-Ferrand, France
| | - Karl Mechtler
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
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28
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Ma H, Su L, Xia W, Wang W, Tan G, Jiao J. MacroH2A1.2 deficiency leads to neural stem cell differentiation defects and autism-like behaviors. EMBO Rep 2021; 22:e52150. [PMID: 34046991 DOI: 10.15252/embr.202052150] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 02/06/2023] Open
Abstract
The development of the nervous system requires precise regulation. Any disturbance in the regulation process can lead to neurological developmental diseases, such as autism and schizophrenia. Histone variants are important components of epigenetic regulation. The function and mechanisms of the macroH2A (mH2A) histone variant during brain development are unknown. Here, we show that deletion of the mH2A isoform mH2A1.2 interferes with neural stem cell differentiation in mice. Deletion of mH2A1.2 affects neurodevelopment, enhances neural progenitor cell (NPC) proliferation, and reduces NPC differentiation in the developing mouse brain. mH2A1.2-deficient mice exhibit autism-like behaviors, such as deficits in social behavior and exploratory abilities. We identify NKX2.2 as an important downstream effector gene and show that NKX2.2 expression is reduced after mH2A1.2 deletion and that overexpression of NKX2.2 rescues neuronal abnormalities caused by mH2A1.2 loss. Our study reveals that mH2A1.2 reduces the proliferation of neural progenitors and enhances neuronal differentiation during embryonic neurogenesis and that these effects are at least in part mediated by NKX2.2. These findings provide a basis for studying the relationship between mH2A1.2 and neurological disorders.
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Affiliation(s)
- Hongyan Ma
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Libo Su
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenlong Xia
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenwen Wang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Guohe Tan
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Guangxi Key Laboratory of Regenerative Medicine, School of Basic Medical Sciences and Center for Translational Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Jianwei Jiao
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
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29
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Kumbhar R, Sanchez A, Perren J, Gong F, Corujo D, Medina F, Devanathan SK, Xhemalce B, Matouschek A, Buschbeck M, Buck-Koehntop BA, Miller KM. Poly(ADP-ribose) binding and macroH2A mediate recruitment and functions of KDM5A at DNA lesions. J Cell Biol 2021; 220:212163. [PMID: 34003252 PMCID: PMC8135068 DOI: 10.1083/jcb.202006149] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 03/15/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
The histone demethylase KDM5A erases histone H3 lysine 4 methylation, which is involved in transcription and DNA damage responses (DDRs). While DDR functions of KDM5A have been identified, how KDM5A recognizes DNA lesion sites within chromatin is unknown. Here, we identify two factors that act upstream of KDM5A to promote its association with DNA damage sites. We have identified a noncanonical poly(ADP-ribose) (PAR)–binding region unique to KDM5A. Loss of the PAR-binding region or treatment with PAR polymerase (PARP) inhibitors (PARPi’s) blocks KDM5A–PAR interactions and DNA repair functions of KDM5A. The histone variant macroH2A1.2 is also specifically required for KDM5A recruitment and function at DNA damage sites, including homology-directed repair of DNA double-strand breaks and repression of transcription at DNA breaks. Overall, this work reveals the importance of PAR binding and macroH2A1.2 in KDM5A recognition of DNA lesion sites that drive transcriptional and repair activities at DNA breaks within chromatin that are essential for maintaining genome integrity.
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Affiliation(s)
- Ramhari Kumbhar
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Anthony Sanchez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Jullian Perren
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Fade Gong
- Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX
| | - David Corujo
- Cancer and Leukemia Epigenetics and Biology Program, Josep Carreras Leukaemia Cancer Institute, Barcelona, Spain
| | - Frank Medina
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Sravan K Devanathan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Blerta Xhemalce
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Marcus Buschbeck
- Cancer and Leukemia Epigenetics and Biology Program, Josep Carreras Leukaemia Cancer Institute, Barcelona, Spain.,Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute, Badalona, Spain
| | | | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX
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30
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Control of the chromatin response to DNA damage: Histone proteins pull the strings. Semin Cell Dev Biol 2021; 113:75-87. [DOI: 10.1016/j.semcdb.2020.07.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/29/2020] [Accepted: 07/01/2020] [Indexed: 12/20/2022]
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31
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Abstract
Cancer is a complex disease characterized by loss of cellular homeostasis through genetic and epigenetic alterations. Emerging evidence highlights a role for histone variants and their dedicated chaperones in cancer initiation and progression. Histone variants are involved in processes as diverse as maintenance of genome integrity, nuclear architecture and cell identity. On a molecular level, histone variants add a layer of complexity to the dynamic regulation of transcription, DNA replication and repair, and mitotic chromosome segregation. Because these functions are critical to ensure normal proliferation and maintenance of cellular fate, cancer cells are defined by their capacity to subvert them. Hijacking histone variants and their chaperones is emerging as a common means to disrupt homeostasis across a wide range of cancers, particularly solid tumours. Here we discuss histone variants and histone chaperones as tumour-promoting or tumour-suppressive players in the pathogenesis of cancer.
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Affiliation(s)
| | - Dan Filipescu
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
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32
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Eleazer R, Fondufe‐Mittendorf YN. The multifaceted role of PARP1 in RNA biogenesis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1617. [PMID: 32656996 PMCID: PMC7856298 DOI: 10.1002/wrna.1617] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/11/2020] [Accepted: 06/17/2020] [Indexed: 12/31/2022]
Abstract
Poly(ADP-ribose) polymerases (PARPs) are abundant nuclear proteins that synthesize ADP ribose polymers (pADPr) and catalyze the addition of (p)ADPr to target biomolecules. PARP1, the most abundant and well-studied PARP, is a multifunctional enzyme that participates in numerous critical cellular processes. A considerable amount of PARP research has focused on PARP1's role in DNA damage. However, an increasing body of evidence outlines more routine roles for PARP and PARylation in nearly every step of RNA biogenesis and metabolism. PARP1's involvement in these RNA processes is pleiotropic and has been ascribed to PARP1's unique flexible domain structures. PARP1 domains are modular self-arranged enabling it to recognize structurally diverse substrates and to act simultaneously through multiple discrete mechanisms. These mechanisms include direct PARP1-protein binding, PARP1-nucleic acid binding, covalent PARylation of target molecules, covalent autoPARylation, and induction of noncovalent interactions with PAR molecules. A combination of these mechanisms has been implicated in PARP1's context-specific regulation of RNA biogenesis and metabolism. We examine the mechanisms of PARP1 regulation in transcription initiation, elongation and termination, co-transcriptional splicing, RNA export, and post-transcriptional RNA processing. Finally, we consider promising new investigative avenues for PARP1 involvement in these processes with an emphasis on PARP1 regulation of subcellular condensates. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Rebekah Eleazer
- Department of Molecular and Cellular Biochemistry and Markey Cancer CenterUniversity of KentuckyLexingtonKentuckyUSA
| | - Yvonne N. Fondufe‐Mittendorf
- Department of Molecular and Cellular Biochemistry and Markey Cancer CenterUniversity of KentuckyLexingtonKentuckyUSA
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Abstract
Adenosine diphosphate (ADP)-ribosylation is a unique post-translational modification that regulates many biological processes, such as DNA damage repair. During DNA repair, ADP-ribosylation needs to be reversed by ADP-ribosylhydrolases. A group of ADP-ribosylhydrolases have a catalytic domain, namely the macrodomain, which is conserved in evolution from prokaryotes to humans. Not all macrodomains remove ADP-ribosylation. One set of macrodomains loses enzymatic activity and only binds to ADP-ribose (ADPR). Here, we summarize the biological functions of these macrodomains in DNA damage repair and compare the structure of enzymatically active and inactive macrodomains. Moreover, small molecular inhibitors have been developed that target macrodomains to suppress DNA damage repair and tumor growth. Macrodomain proteins are also expressed in pathogens, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, these domains may not be directly involved in DNA damage repair in the hosts or pathogens. Instead, they play key roles in pathogen replication. Thus, by targeting macrodomains it may be possible to treat pathogen-induced diseases, such as coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Lily Yu
- Westridge School, Pasadena, California 91105, USA
| | - Xiuhua Liu
- Institute of Life Science and Green Development, College of Life Science, Hebei University, Baoding 071002, China.
| | - Xiaochun Yu
- School of Life Sciences, Westlake University, Hangzhou 310024, China.
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Lei B, Capella M, Montgomery SA, Borg M, Osakabe A, Goiser M, Muhammad A, Braun S, Berger F. A Synthetic Approach to Reconstruct the Evolutionary and Functional Innovations of the Plant Histone Variant H2A.W. Curr Biol 2021; 31:182-191.e5. [PMID: 33096036 DOI: 10.1016/j.cub.2020.09.080] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/28/2020] [Accepted: 09/28/2020] [Indexed: 12/11/2022]
Abstract
Diversification of histone variants is marked by the acquisition of distinct motifs and functional properties through convergent evolution.1-4 H2A variants are distinguished by specific C-terminal motifs and tend to be segregated within defined domains of the genome.5,6 Whether evolution of these motifs pre-dated the evolution of segregation mechanisms or vice versa has remained unclear. A suitable model to address this question is the variant H2A.W, which evolved in plants through acquisition of a KSPK motif7 and is tightly associated with heterochromatin.4 We used fission yeast, where chromatin is naturally devoid of H2A.W, to study the impact of engineered chimeras combining yeast H2A with the KSPK motif. Biochemical assays showed that the KSPK motif conferred nucleosomes with specific properties. Despite uniform incorporation of the engineered H2A chimeras in the yeast genome, the KSPK motif specifically affected heterochromatin composition and function. We conclude that the KSPK motif promotes chromatin properties in yeast that are comparable to the properties and function of H2A.W in plant heterochromatin. We propose that the selection of functional motifs confer histone variants with properties that impact primarily a specific chromatin state. The association between a new histone variant and a preferred chromatin state can thus provide a setting for the evolution of mechanisms that segregate the new variant to this state, thereby enhancing the impact of the selected properties of the variant on genome activity.
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Affiliation(s)
- Bingkun Lei
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Matías Capella
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Großhaderner Straße 9, 82152 Planegg-Martinsried, Germany
| | - Sean A Montgomery
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Michael Borg
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Akihisa Osakabe
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Malgorzata Goiser
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Abubakar Muhammad
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Großhaderner Straße 9, 82152 Planegg-Martinsried, Germany; International Max Planck Research School for Molecular and Cellular Life Sciences, Am Klopferspitz 18, 82152 Planegg-Martinsried, Germany
| | - Sigurd Braun
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Großhaderner Straße 9, 82152 Planegg-Martinsried, Germany; International Max Planck Research School for Molecular and Cellular Life Sciences, Am Klopferspitz 18, 82152 Planegg-Martinsried, Germany.
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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Boeren J, Gribnau J. Xist-mediated chromatin changes that establish silencing of an entire X chromosome in mammals. Curr Opin Cell Biol 2020; 70:44-50. [PMID: 33360102 DOI: 10.1016/j.ceb.2020.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/17/2020] [Accepted: 11/22/2020] [Indexed: 12/19/2022]
Abstract
X chromosome inactivation (XCI) ensures an equal gene dosage between the sexes in placental mammals. Xist, a modular multi-domain X-encoded long non-coding RNA coats the X chromosome in cis during XCI. Xist recruits chromatin remodelers and repressor complexes ensuring silencing of the inactive X (Xi). Here, we review the recent work focused on the role of Xist functional repeats and interacting RNA-binding factors in the establishment of the silent state. Xist orchestrates recruitment of remodelers and repressors that first facilitate removal of the active chromatin landscape and subsequently direct the transition into a repressive heterochromatic environment. Some of these factors affect silencing on a chromosome-wide scale, while others display gene-specific silencing defects. The temporal order of recruitment shows each silencing step is party dependent on one another. After the Xi is established, many of the factors are dispensable, and a different repertoire of proteins ensure the silenced Xi is maintained and propagated.
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Affiliation(s)
- Jeffrey Boeren
- Department of Developmental Biology, Erasmus University Medical Center, the Netherlands; Oncode Institute, Erasmus University Medical Center, the Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus University Medical Center, the Netherlands; Oncode Institute, Erasmus University Medical Center, the Netherlands.
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36
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Lone IN, Sengez B, Hamiche A, Dimitrov S, Alotaibi H. The Role of Histone Variants in the Epithelial-To-Mesenchymal Transition. Cells 2020; 9:cells9112499. [PMID: 33213091 PMCID: PMC7698467 DOI: 10.3390/cells9112499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/13/2020] [Accepted: 11/14/2020] [Indexed: 11/16/2022] Open
Abstract
The epithelial-to-mesenchymal transition (EMT) is a physiological process activated during early embryogenesis, which continues to shape tissues and organs later on. It is also hijacked by tumor cells during metastasis. The regulation of EMT has been the focus of many research groups culminating in the last few years and resulting in an elaborate transcriptional network buildup. However, the implication of epigenetic factors in the control of EMT is still in its infancy. Recent discoveries pointed out that histone variants, which are key epigenetic players, appear to be involved in EMT control. This review summarizes the available data on histone variants' function in EMT that would contribute to a better understanding of EMT itself and EMT-related diseases.
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Affiliation(s)
- Imtiaz Nisar Lone
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey; (I.N.L.); (B.S.); (S.D.)
| | - Burcu Sengez
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey; (I.N.L.); (B.S.); (S.D.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir 35340, Turkey
| | - Ali Hamiche
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, 67400 Illkirch, France;
| | - Stefan Dimitrov
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey; (I.N.L.); (B.S.); (S.D.)
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé-Allée des Alpes, 38700 La Tronche, France
| | - Hani Alotaibi
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey; (I.N.L.); (B.S.); (S.D.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir 35340, Turkey
- Correspondence: ; Tel.: +90-232-299-4100 (ext. 5071)
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Rother MB, Pellegrino S, Smith R, Gatti M, Meisenberg C, Wiegant WW, Luijsterburg MS, Imhof R, Downs JA, Vertegaal ACO, Huet S, Altmeyer M, van Attikum H. CHD7 and 53BP1 regulate distinct pathways for the re-ligation of DNA double-strand breaks. Nat Commun 2020; 11:5775. [PMID: 33188175 PMCID: PMC7666215 DOI: 10.1038/s41467-020-19502-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 10/15/2020] [Indexed: 01/16/2023] Open
Abstract
Chromatin structure is dynamically reorganized at multiple levels in response to DNA double-strand breaks (DSBs). Yet, how the different steps of chromatin reorganization are coordinated in space and time to differentially regulate DNA repair pathways is insufficiently understood. Here, we identify the Chromodomain Helicase DNA Binding Protein 7 (CHD7), which is frequently mutated in CHARGE syndrome, as an integral component of the non-homologous end-joining (NHEJ) DSB repair pathway. Upon recruitment via PARP1-triggered chromatin remodeling, CHD7 stimulates further chromatin relaxation around DNA break sites and brings in HDAC1/2 for localized chromatin de-acetylation. This counteracts the CHD7-induced chromatin expansion, thereby ensuring temporally and spatially controlled 'chromatin breathing' upon DNA damage, which we demonstrate fosters efficient and accurate DSB repair by controlling Ku and LIG4/XRCC4 activities. Loss of CHD7-HDAC1/2-dependent cNHEJ reinforces 53BP1 assembly at the damaged chromatin and shifts DSB repair to mutagenic NHEJ, revealing a backup function of 53BP1 when cNHEJ fails.
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Grants
- 25715 Cancer Research UK
- 714326 European Research Council
- MR/N02155X/2 Medical Research Council
- MR/N02155X/1 Medical Research Council
- This research was financially supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (ERC-StG 714326 to M.A.; ERC-StG 310913 to A.C.O.V.; ERC-CoG 50364 to H.v.A), the Swiss National Science Foundation (grants 150690 and 179057 to M.A.), grants from the Danish Research Council (DFF 1333-00037B and 1331-00732B to M.A.), NWO-VENI (863.11.007) and NWO-VIDI (016.161.320) grants to M.S.L., People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/ 2007-2013) under REA grant agreement [(PCOFUND-GA-2013-609102), through the PRESTIGE program coordinated by Campus France (PRESTIGE-2017-2-0042), the Université Bretagne-Loire and the Fondation ARC pour la recherche sur le cancer (PDF20181208405) to R.S., the Ligue contre le Cancer du Grand-Ouest (committees 22 and 35), the Fondation ARC pour la recherche sur le cancer (20161204883), the Agence Nationale de la Recherche (PRC-2018 REPAIRCHROM) and the Institut Universitaire de France to S.H., and the Medical Research Council (MR/N02155X/1) to C.M. and J.A.D..
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Affiliation(s)
- Magdalena B Rother
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Stefania Pellegrino
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Rebecca Smith
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes)-UMR 6290, BIOSIT-UMS3480, F-35000, Rennes, France
| | - Marco Gatti
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | | | - Wouter W Wiegant
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Ralph Imhof
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Jessica A Downs
- The Institute of Cancer Research, Royal Cancer Hospital, London, UK
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes)-UMR 6290, BIOSIT-UMS3480, F-35000, Rennes, France
- Institut Universitaire de France, Paris, France
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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38
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LSH mediates gene repression through macroH2A deposition. Nat Commun 2020; 11:5647. [PMID: 33159050 PMCID: PMC7648012 DOI: 10.1038/s41467-020-19159-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
The human Immunodeficiency Centromeric Instability Facial Anomalies (ICF) 4 syndrome is a severe disease with increased mortality caused by mutation in the LSH gene. Although LSH belongs to a family of chromatin remodeling proteins, it remains unknown how LSH mediates its function on chromatin in vivo. Here, we use chemical-induced proximity to rapidly recruit LSH to an engineered locus and find that LSH specifically induces macroH2A1.2 and macroH2A2 deposition in an ATP-dependent manner. Tethering of LSH induces transcriptional repression and silencing is dependent on macroH2A deposition. Loss of LSH decreases macroH2A enrichment at repeat sequences and results in transcriptional reactivation. Likewise, reduction of macroH2A by siRNA interference mimicks transcriptional reactivation. ChIP-seq analysis confirmed that LSH is a major regulator of genome-wide macroH2A distribution. Tethering of ICF4 mutations fails to induce macroH2A deposition and ICF4 patient cells display reduced macroH2A deposition and transcriptional reactivation supporting a pathogenic role for altered marcoH2A deposition. We propose that LSH is a major chromatin modulator of the histone variant macroH2A and that its ability to insert marcoH2A into chromatin and transcriptionally silence is disturbed in the ICF4 syndrome. The human ICF 4 syndrome is caused by mutation of the chromatin remodeller LSH. Here, the authors show that LSH depletion disrupts the ability of histone variant macroH2A to insert into chromatin and silence transcription.
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Ferrand J, Rondinelli B, Polo SE. Histone Variants: Guardians of Genome Integrity. Cells 2020; 9:E2424. [PMID: 33167489 PMCID: PMC7694513 DOI: 10.3390/cells9112424] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022] Open
Abstract
Chromatin integrity is key for cell homeostasis and for preventing pathological development. Alterations in core chromatin components, histone proteins, recently came into the spotlight through the discovery of their driving role in cancer. Building on these findings, in this review, we discuss how histone variants and their associated chaperones safeguard genome stability and protect against tumorigenesis. Accumulating evidence supports the contribution of histone variants and their chaperones to the maintenance of chromosomal integrity and to various steps of the DNA damage response, including damaged chromatin dynamics, DNA damage repair, and damage-dependent transcription regulation. We present our current knowledge on these topics and review recent advances in deciphering how alterations in histone variant sequence, expression, and deposition into chromatin fuel oncogenic transformation by impacting cell proliferation and cell fate transitions. We also highlight open questions and upcoming challenges in this rapidly growing field.
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Affiliation(s)
| | | | - Sophie E. Polo
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université de Paris, 75013 Paris, France; (J.F.); (B.R.)
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40
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Martire S, Banaszynski LA. The roles of histone variants in fine-tuning chromatin organization and function. Nat Rev Mol Cell Biol 2020; 21:522-541. [PMID: 32665685 PMCID: PMC8245300 DOI: 10.1038/s41580-020-0262-8] [Citation(s) in RCA: 194] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2020] [Indexed: 12/15/2022]
Abstract
Histones serve to both package and organize DNA within the nucleus. In addition to histone post-translational modification and chromatin remodelling complexes, histone variants contribute to the complexity of epigenetic regulation of the genome. Histone variants are characterized by a distinct protein sequence and a selection of designated chaperone systems and chromatin remodelling complexes that regulate their localization in the genome. In addition, histone variants can be enriched with specific post-translational modifications, which in turn can provide a scaffold for recruitment of variant-specific interacting proteins to chromatin. Thus, through these properties, histone variants have the capacity to endow specific regions of chromatin with unique character and function in a regulated manner. In this Review, we provide an overview of recent advances in our understanding of the contribution of histone variants to chromatin function in mammalian systems. First, we discuss new molecular insights into chaperone-mediated histone variant deposition. Next, we discuss mechanisms by which histone variants influence chromatin properties such as nucleosome stability and the local chromatin environment both through histone variant sequence-specific effects and through their role in recruiting different chromatin-associated complexes. Finally, we focus on histone variant function in the context of both embryonic development and human disease, specifically developmental syndromes and cancer.
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Affiliation(s)
- Sara Martire
- Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Laura A Banaszynski
- Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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41
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Abstract
Histone variants regulate chromatin accessibility and gene transcription. Given their distinct properties and functions, histone varint substitutions allow for profound alteration of nucleosomal architecture and local chromatin landscape. Skeletal myogenesis driven by the key transcription factor MyoD is characterized by precise temporal regulation of myogenic genes. Timed substitution of variants within the nucleosomes provides a powerful means to ensure sequential expression of myogenic genes. Indeed, growing evidence has shown H3.3, H2A.Z, macroH2A, and H1b to be critical for skeletal myogenesis. However, the relative importance of various histone variants and their associated chaperones in myogenesis is not fully appreciated. In this review, we summarize the role that histone variants play in altering chromatin landscape to ensure proper muscle differentiation. The temporal regulation and cross talk between histones variants and their chaperones in conjunction with other forms of epigenetic regulation could be critical to understanding myogenesis and their involvement in myopathies.
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Affiliation(s)
- Nandini Karthik
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
| | - Reshma Taneja
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
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42
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The Histone Variant MacroH2A1 Regulates Key Genes for Myogenic Cell Fusion in a Splice-Isoform Dependent Manner. Cells 2020; 9:cells9051109. [PMID: 32365743 PMCID: PMC7290658 DOI: 10.3390/cells9051109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/21/2020] [Accepted: 04/23/2020] [Indexed: 12/16/2022] Open
Abstract
MacroH2A histone variants have functions in differentiation, somatic cell reprogramming and cancer. However, at present, it is not clear how macroH2As affect gene regulation to exert these functions. We have parted from the initial observation that loss of total macroH2A1 led to a change in the morphology of murine myotubes differentiated ex vivo. The fusion of myoblasts to myotubes is a key process in embryonic myogenesis and highly relevant for muscle regeneration after acute or chronic injury. We have focused on this physiological process, to investigate the functions of the two splice isoforms of macroH2A1. Individual perturbation of the two isoforms in myotubes forming in vitro from myogenic C2C12 cells showed an opposing phenotype, with macroH2A1.1 enhancing, and macroH2A1.2 reducing, fusion. Differential regulation of a subset of fusion-related genes encoding components of the extracellular matrix and cell surface receptors for adhesion correlated with these phenotypes. We describe, for the first time, splice isoform-specific phenotypes for the histone variant macroH2A1 in a physiologic process and provide evidence for a novel underlying molecular mechanism of gene regulation.
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43
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Leung AKL. Poly(ADP-ribose): A Dynamic Trigger for Biomolecular Condensate Formation. Trends Cell Biol 2020; 30:370-383. [PMID: 32302549 DOI: 10.1016/j.tcb.2020.02.002] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 02/01/2020] [Accepted: 02/03/2020] [Indexed: 01/18/2023]
Abstract
Poly(ADP-ribose) (PAR) is a nucleic acid-like protein modification that can seed the formation of microscopically visible cellular compartments that lack enveloping membranes, recently termed biomolecular condensates. These PAR-mediated condensates are linked to cancer, viral infection, and neurodegeneration. Recent data have shown the therapeutic potential of modulating PAR conjugation (PARylation): PAR polymerase (PARP) inhibitors can modulate the formation and dynamics of these condensates as well as the trafficking of their components - many of which are key disease factors. However, the way in which PARylation facilitates these functions remains unclear, partly because of our lack of understanding of the fundamental parameters of intracellular PARylation, including the sites that are conjugated, PAR chain length and structure, and the physicochemical properties of the conjugates. This review first introduces the role of PARylation in regulating biomolecular condensates, followed by discussion of current knowledge gaps, potential solutions, and therapeutic applications.
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Affiliation(s)
- Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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44
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Hurtado-Bagès S, Knobloch G, Ladurner AG, Buschbeck M. The taming of PARP1 and its impact on NAD + metabolism. Mol Metab 2020; 38:100950. [PMID: 32199820 PMCID: PMC7300387 DOI: 10.1016/j.molmet.2020.01.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/10/2020] [Accepted: 01/24/2020] [Indexed: 12/21/2022] Open
Abstract
Background Poly-ADP-ribose polymerases (PARPs) are key mediators of cellular stress response. They are intimately linked to cellular metabolism through the consumption of NAD+. PARP1/ARTD1 in the nucleus is the major NAD+ consuming activity and plays a key role in maintaining genomic integrity. Scope of review In this review, we discuss how different organelles are linked through NAD+ metabolism and how PARP1 activation in the nucleus can impact the function of distant organelles. We discuss how differentiated cells tame PARP1 function by upregulating an endogenous inhibitor, the histone variant macroH2A1.1. Major conclusions The presence of macroH2A1.1, particularly in differentiated cells, raises the threshold for the activation of PARP1 with consequences for DNA repair, gene transcription, and NAD+ homeostasis. Beyond DNA repair, PARP1 is essential for metabolic homeostasis. Epigenetic mechanisms prevent metabolic disorders through PARP1 taming. Beyond cancer, the development of PARP1 inhibitors offers diverse clinical potential.
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Affiliation(s)
- Sarah Hurtado-Bagès
- Josep Carreras Leukemia Research Institute, Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916, Badalona, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Gunnar Knobloch
- Biomedical Center Munich, Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Andreas G Ladurner
- Biomedical Center Munich, Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany; Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, 81377, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität München, 81377, Munich, Germany.
| | - Marcus Buschbeck
- Josep Carreras Leukemia Research Institute, Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916, Badalona, Spain; Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), 08916, Badalona, Spain.
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45
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Páhi ZG, Borsos BN, Pantazi V, Ujfaludi Z, Pankotai T. PARylation During Transcription: Insights into the Fine-Tuning Mechanism and Regulation. Cancers (Basel) 2020; 12:cancers12010183. [PMID: 31940791 PMCID: PMC7017041 DOI: 10.3390/cancers12010183] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/19/2019] [Accepted: 01/09/2020] [Indexed: 01/31/2023] Open
Abstract
Transcription is a multistep, tightly regulated process. During transcription initiation, promoter recognition and pre-initiation complex (PIC) formation take place, in which dynamic recruitment or exchange of transcription activators occur. The precise coordination of the recruitment and removal of transcription factors, as well as chromatin structural changes, are mediated by post-translational modifications (PTMs). Poly(ADP-ribose) polymerases (PARPs) are key players in this process, since they can modulate DNA-binding activities of specific transcription factors through poly-ADP-ribosylation (PARylation). PARylation can regulate the transcription at three different levels: (1) by directly affecting the recruitment of specific transcription factors, (2) by triggering chromatin structural changes during initiation and as a response to cellular stresses, or (3) by post-transcriptionally modulating the stability and degradation of specific mRNAs. In this review, we principally focus on these steps and summarise the recent findings, demonstrating the mechanisms through which PARylation plays a potential regulatory role during transcription and DNA repair.
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Volpari T, De Santis F, Bracken AP, Pupa SM, Buschbeck M, Wegner A, Di Cosimo S, Lisanti MP, Dotti G, Massaia M, Pruneri G, Anichini A, Fortunato O, De Braud F, Del Vecchio M, Di Nicola M. Anticancer innovative therapy: Highlights from the ninth annual meeting. Cytokine Growth Factor Rev 2019; 51:1-9. [PMID: 31862236 DOI: 10.1016/j.cytogfr.2019.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The Ninth Annual Conference of "Anticancer Innovative Therapy", organized by Fondazione IRCCS Istituto Nazionale dei Tumori di Milano (Fondazione IRCCS INT) and hosted by Hotel Michelangelo, was held in Milan on 25 January 2019. Cutting-edge science was presented in two main scientific sessions: i) pre-clinical evidences and new targets, and ii) clinical translation. The Keynote lecture entitled "Cancer stem cells (CSCs): metabolic strategies for their identification and eradication" presented by M. Lisanti, was one of the highlights of the conference. One key concept of the meeting was how the continuous advances in our knowledge about molecular mechanisms in various fields of research (cancer metabolism reprogramming, epigenetic regulation, transformation/invasiveness, and immunology, among others) are driving cancer research towards more effective personalized antineoplastic strategies. Specifically, recent preclinical data on the following topics were discussed: 1. Polycomb group proteins in cancer; 2. A d16HER2 splice variant is a flag of HER2 addiction across HER2-positive cancers; 3. Studying chromatin as a nexus between translational and basic research; 4. Metabolomic analysis in cancer patients; 5. CDK4-6 cyclin inhibitors: clinical activity and future perspectives as immunotherapy adjuvant; and 6. Cancer stem cells (CSCs): metabolic strategies for their identification and eradication. In terms of clinical translation, several novel approaches were presented: 1. Developing CAR-T cell therapies: an update of preclinical and clinical development at University of North Carolina; 2. Vγ9Vδ2 T-cell activation and immune suppression in multiple myeloma; 3. Predictive biomarkers for real-world immunotherapy: the cancer immunogram model in the clinical arena; and 4. Mechanisms of resistance to immune checkpoint blockade in solid tumors. Overall, the pre-clinical and clinical findings presented could pave the way to identify novel actionable therapeutic targets to significantly enhance the care of persons with cancer.
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Affiliation(s)
- T Volpari
- Immunotherapy and Innovative Therapeutics Unit, Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - F De Santis
- Immunotherapy and Innovative Therapeutics Unit, Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - A P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - S M Pupa
- Molecular Targeting Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - M Buschbeck
- Josep Carreras Leukemia Research Institute (IJC), Campus ICO-Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - A Wegner
- Technische Universiät Braunschweig, Department of Bioinfomatics and Biochemistry and Braunschweig Integrated Center of Systems Biology (BRICS), Rebenring 56, 38106, Braunschweig, Germany
| | - S Di Cosimo
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - M P Lisanti
- Translational Medicine, Biomedical Research Centre, School of Environment and Life Sciences, University of Salford, Greater Manchester, United Kingdom
| | - G Dotti
- Lineberger Comprehensive Cancer Center and Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, United States
| | - M Massaia
- Laboratorio di Immunologia dei Tumori del Sangue, Centro Interdipartimentale di Ricerca in Biologia Molecolare, Università degli Studi di Torino, Turin, Italy; SC Ematologia, AO S. Croce e Carle, Cuneo, Italy
| | - G Pruneri
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS - Istituto Nazionale dei Tumori, Milan, Italy
| | - A Anichini
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - O Fortunato
- Tumor Genomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - F De Braud
- Medical Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - M Del Vecchio
- Immunotherapy and Innovative Therapeutics Unit, Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Unit of Melanoma Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - M Di Nicola
- Immunotherapy and Innovative Therapeutics Unit, Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Medical Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
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MacroH2A1 Regulation of Poly(ADP-Ribose) Synthesis and Stability Prevents Necrosis and Promotes DNA Repair. Mol Cell Biol 2019; 40:MCB.00230-19. [PMID: 31636161 PMCID: PMC6908255 DOI: 10.1128/mcb.00230-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 10/08/2019] [Indexed: 12/16/2022] Open
Abstract
Through its ability to bind the ends of poly(ADP-ribose) (PAR) chains, the function of the histone variant macroH2A1.1, including its ability to regulate transcription, is coupled to PAR polymerases (PARPs). PARP1 also has a major role in DNA damage response (DDR) signaling, and our results show that macroH2A1 alters the kinetics of PAR accumulation following acute DNA damage by both suppressing PARP activity and simultaneously protecting PAR chains from degradation. Through its ability to bind the ends of poly(ADP-ribose) (PAR) chains, the function of the histone variant macroH2A1.1, including its ability to regulate transcription, is coupled to PAR polymerases (PARPs). PARP1 also has a major role in DNA damage response (DDR) signaling, and our results show that macroH2A1 alters the kinetics of PAR accumulation following acute DNA damage by both suppressing PARP activity and simultaneously protecting PAR chains from degradation. In this way, we demonstrate that macroH2A1 prevents cellular NAD+ depletion, subsequently preventing necrotic cell death that would otherwise occur due to PARP overactivation. We also show that macroH2A1-dependent PAR stabilization promotes efficient repair of oxidative DNA damage. While the role of PAR in recruiting and regulating macrodomain-containing proteins has been established, our results demonstrate that, conversely, macrodomain-containing proteins, and specifically those containing macroH2A1, can regulate PARP1 function through a novel mechanism that promotes both survival and efficient repair during DNA damage response.
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Zebrafish macroH2A variants have distinct embryo localization and function. Sci Rep 2019; 9:8632. [PMID: 31201343 PMCID: PMC6570772 DOI: 10.1038/s41598-019-45058-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/29/2019] [Indexed: 11/08/2022] Open
Abstract
Mouse and cell-based studies have shown that macroH2A histone variants predominantly associate with heterochromatin. Functional studies found that macroH2As are involved in gene repression, inhibiting the acquisition of pluripotency and preserving cell differentiation. However, only a few studies have analysed the role of macroH2A during early embryo development. We report the development of transgenic zebrafish lines expressing macroH2A isoforms (mH2A1 and mH2A2) fusion proteins (with GFP) under identified endogenous promoters. We found that mH2A1 and mH2A2 have different spatial and temporal expression patterns during embryonic development. mH2A1 is expressed mostly in the extraembryonic Yolk Syncytial Layer (YSL) starting before shield stage and decreasing once morphogenesis is completed. mH2A2 expression lags behind mH2A1, becoming evident at 24 hpf, within the whole body of the embryo proper. Our ChIP-seq analysis showed that mH2A1 and mH2A2 bind to different DNA regions, changing dramatically after gastrulation. We further analysed RNA-seq data and showed that there is not a general/unspecific repressing function of mH2A1 or mH2A2 associated with heterochromatin but a fine regulation depending on cell types and stage of development. mH2A1 downregulates DNA expression in specific cells and embryo stages and its effect is independent of heterochromatin formation but it is correlated with nucleus quiescence instead. Whereas mH2A2 DNA association correlates with upregulation of differentially expressed genes between 75% epiboly and 24 hpf stages. Our data provide information for underlying molecules that participate in crucial early developmental events, and open new venues to explore mH2A related mechanisms that involve cell proliferation, differentiation, migration and metabolism.
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Histone variant macroH2A: from chromatin deposition to molecular function. Essays Biochem 2019; 63:59-74. [DOI: 10.1042/ebc20180062] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 01/01/2023]
Abstract
Abstract
The eukaryotic genome is regulated in the context of chromatin. Specialized histones, known as histone variants, incorporate into chromatin to replace their canonical counterparts and represent an important layer of regulation to diversify the structural characteristics and functional outputs of chromatin. MacroH2A is an unusual histone variant with a bulky C-terminal non-histone domain that distinguishes it from all other histones. It is a critical player in stabilizing differentiated cell identity by posing as a barrier to somatic cell reprogramming toward pluripotency and acts as a tumor suppressor in a wide range of cancers. MacroH2A histones are generally regarded as repressive variants that are enriched at the inactive X chromosome (Xi) and broad domains across autosomal chromatin. Recent studies have shed light on to how macroH2A influences transcriptional outputs within distinct genomic contexts and revealed new intriguing molecular functions of macroH2A variants beyond transcriptional regulation. Furthermore, the mechanisms of its mysterious chromatin deposition are beginning to be unraveled, facilitating our understanding of its complex regulation of genome function.
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Bowerman S, Hickok RJ, Wereszczynski J. Unique Dynamics in Asymmetric macroH2A-H2A Hybrid Nucleosomes Result in Increased Complex Stability. J Phys Chem B 2019; 123:419-427. [PMID: 30557018 DOI: 10.1021/acs.jpcb.8b10668] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The fundamental unit of eukaryotic chromatin is the nucleosome core particle, a protein/DNA complex that binds ∼147 base pairs of DNA to a histone octamer. These histones-H3, H4, H2A, H2B-form the nucleosome core through a stacked interaction in which two H2A-H2B dimers flank the (H3-H4)2 tetramer. In vivo, genetic accessibility can be modulated by the substitution of canonical histones with variant proteins that contain the same structural motif but a different amino acid sequence, such as the transcriptional repression-associated macroH2A variant. Previously, Chakravarthy and Luger published a crystal study that showed that H2A substitution is not necessarily required of both H2A moieties, but that in vitro recombination of nucleosomes in the presence of both macroH2A and H2A histone folds results in a hybrid macroH2A-H2A nucleosome with one dimer of each type. Here, we present molecular dynamics simulations of this hybrid construct and compare the results to our previous study on homogeneous H2A- and macroH2A-containing nucleosomes. We find that the hybrid contains a unique set of dynamics that stabilize the interactions between protein constituents and create an altogether more stable nucleosome, both in terms of protein-DNA and protein-protein binding. While dimer-tetramer interactions are asymmetric, as the difference in moieties would suggest, we observe that it is the canonical dimer that is pulled further into the nucleosome core, resulting in more secure dimer-tetramer bonds and a more stable histone core, and we also find significantly more interaction between the dimer subunits. Together, these models provide evidence for hybrid H2A-macroH2A nucleosome formation being not only possible but actually energetically more favorable than a homogeneous construct, with dynamics that are unique from their homogeneous H2A or macroH2A nucleosome counterparts. These effects of hybrid substitution likely propagate into higher-order chromatin structures to hinder transcriptional activity.
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Affiliation(s)
- Samuel Bowerman
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , Chicago , Illinois 60616 , United States
| | - Robert J Hickok
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , Chicago , Illinois 60616 , United States
| | - Jeff Wereszczynski
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , Chicago , Illinois 60616 , United States
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