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Qin B, Lu G, Chen X, Zheng C, Lin H, Liu Q, Shang J, Feng G. H2B oncohistones cause homologous recombination defect and genomic instability through reducing H2B monoubiquitination in Schizosaccharomyces pombe. J Biol Chem 2024; 300:107345. [PMID: 38718864 PMCID: PMC11167522 DOI: 10.1016/j.jbc.2024.107345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 06/02/2024] Open
Abstract
Canonical oncohistones are histone H3 mutations in the N-terminal tail associated with tumors and affect gene expression by altering H3 post-translational modifications (PTMs) and the epigenetic landscape. Noncanonical oncohistone mutations occur in both tails and globular domains of all four core histones and alter gene expression by perturbing chromatin remodeling. However, the effects and mechanisms of noncanonical oncohistones remain largely unknown. Here we characterized 16 noncanonical H2B oncohistones in the fission yeast Schizosaccharomyces pombe. We found that seven of them exhibited temperature sensitivities and 11 exhibited genotoxic sensitivities. A detailed study of two of these onco-mutants H2BG52D and H2BP102L revealed that they were defective in homologous recombination (HR) repair with compromised histone eviction and Rad51 recruitment. Interestingly, their genotoxic sensitivities and HR defects were rescued by the inactivation of the H2BK119 deubiquitination function of Ubp8 in the Spt-Ada-Gcn5-Acetyltransferase (SAGA) complex. The levels of H2BK119 monoubiquitination (H2Bub) in the H2BG52D and H2BP102L mutants are reduced in global genome and at local DNA break sites presumably due to enhanced recruitment of Ubp8 onto nucleosomes and are recovered upon loss of H2B deubiquitination function of the SAGA complex. Moreover, H2BG52D and H2BP102L heterozygotes exhibit genotoxic sensitivities and reduced H2Bub in cis. We therefore conclude that H2BG52D and H2BP102L oncohistones affect HR repair and genome stability via the reduction of H2Bub and propose that other noncanonical oncohistones may also affect histone PTMs to cause diseases.
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Affiliation(s)
- Bingxin Qin
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guangchun Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xuejin Chen
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Chenhua Zheng
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Huanteng Lin
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Qi Liu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jinjie Shang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Gang Feng
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China; School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
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2
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Aydin A, Klenk C, Nemec K, Işbilir A, Martin LM, Zauber H, Rrustemi T, Toka HR, Schuster H, Gong M, Stricker S, Bock A, Bähring S, Selbach M, Lohse MJ, Luft FC. ADAM19 cleaves the PTH receptor and associates with brachydactyly type E. Life Sci Alliance 2024; 7:e202302400. [PMID: 38331475 PMCID: PMC10853454 DOI: 10.26508/lsa.202302400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/10/2024] Open
Abstract
Brachydactyly type E (BDE), shortened metacarpals, metatarsals, cone-shaped epiphyses, and short stature commonly occurs as a sole phenotype. Parathyroid hormone-like protein (PTHrP) has been shown to be responsible in all forms to date, either directly or indirectly. We used linkage and then whole genome sequencing in a small pedigree, to elucidate BDE and identified a truncated disintegrin-and-metalloproteinase-19 (ADAM19) allele in all affected family members, but not in nonaffected persons. Since we had shown earlier that the extracellular domain of the parathyroid hormone receptor (PTHR1) is subject to an unidentified metalloproteinase cleavage, we tested the hypothesis that ADAM19 is a sheddase for PTHR1. WT ADAM19 cleaved PTHR1, while mutated ADAM-19 did not. We mapped the cleavage site that we verified with mass spectrometry between amino acids 64-65. ADAM-19 cleavage increased Gq and decreased Gs activation. Moreover, perturbed PTHR1 cleavage by ADAM19 increased ß-arrestin2 recruitment, while cAMP accumulation was not altered. We suggest that ADAM19 serves as a regulatory element for PTHR1 and could be responsible for BDE. This sheddase may affect other PTHrP or PTH-related functions.
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Affiliation(s)
- Atakan Aydin
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- https://ror.org/001w7jn25 Experimental and Clinical Research Center, A Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin, Berlin, Germany
| | - Christoph Klenk
- Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| | - Katarina Nemec
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
- Department of Structural Biology and Center of Excellence for Data-Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ali Işbilir
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| | - Lisa M Martin
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Henrik Zauber
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Trendelina Rrustemi
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Hakan R Toka
- https://ror.org/001w7jn25 Experimental and Clinical Research Center, A Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin, Berlin, Germany
| | - Herbert Schuster
- https://ror.org/001w7jn25 Experimental and Clinical Research Center, A Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin, Berlin, Germany
| | - Maolian Gong
- https://ror.org/001w7jn25 Experimental and Clinical Research Center, A Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin, Berlin, Germany
| | - Sigmar Stricker
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Andreas Bock
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Rudolf-Boehm-Institute of Pharmacology and Toxicology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Sylvia Bähring
- https://ror.org/001w7jn25 Experimental and Clinical Research Center, A Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin, Berlin, Germany
| | - Matthias Selbach
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Martin J Lohse
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- ISAR Bioscience Institute, Munich, Germany
| | - Friedrich C Luft
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- https://ror.org/001w7jn25 Experimental and Clinical Research Center, A Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin, Berlin, Germany
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3
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Navasatli SA, Vahdati SN, Arjmand TF, Mohammadi far M, Behboudi H. New insight into the role of the ADAM protease family in breast carcinoma progression. Heliyon 2024; 10:e24805. [PMID: 38317965 PMCID: PMC10839977 DOI: 10.1016/j.heliyon.2024.e24805] [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: 08/13/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 02/07/2024] Open
Abstract
Protease and adhesion molecules play a very emphasized role in the occurrence or progression of metastasis in many types of cancers. In this context, a molecule that contains both protease and adhesion functions play a crucial role in metastasis. ADAMs (a disintegrin and metalloprotease) are molecules with this special characteristic. Recently, a lot of attention has been attracted to various ADAM molecules and researchers have tried to elucidate the role of ADAMs in breast cancer occurrence and progression. Disrupting ADAMs protease and adhesion capabilities can lead to the discovery of worthy therapeutic targets in breast cancer treatment. In this review, we intend to discuss the mechanism of action of various ADAM molecules, their relation to pathogenic processes of breast cancer, and their potential as possible targets for breast cancer treatment.
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Affiliation(s)
- Sepideh Aliniaye Navasatli
- Institute of Biochemistry and Biophysics, Department of Biochemistry, University of Tehran, Tehran, Iran
| | - Saeed Niazi Vahdati
- Institute of Biochemistry and Biophysics, Department of Biochemistry, University of Tehran, Tehran, Iran
| | - Tahura Fayeghi Arjmand
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Marjan Mohammadi far
- Institute of Biochemistry and Biophysics, Department of Biochemistry, University of Tehran, Tehran, Iran
| | - Hossein Behboudi
- Department of Biology, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran
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Zhang X, Li X, Tan X, Deng L, Zhong L, Wei C, Ruan H, Lu Y, Pang L. miR-146b-5p downregulates IRAK1 and ADAM19 to suppress trophoblast proliferation, invasion, and migration in miscarriage†. Biol Reprod 2023; 109:938-953. [PMID: 37676254 DOI: 10.1093/biolre/ioad112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/27/2023] [Accepted: 09/05/2023] [Indexed: 09/08/2023] Open
Abstract
A large proportion of miscarriages are classified as unexplained miscarriages since no cause is identified. No reliable biomarkers or treatments are available for these pregnancy losses. While our transcriptomic sequencing has revealed substantial upregulation of miR-146b-5p in unexplained miscarriage villous tissues, its role and associated molecular processes have yet to be fully characterized. Our work revealed that relative to samples from normal pregnancy, miR-146b-5p was significantly elevated in villous tissues from unexplained miscarriage patients and displayed promising diagnostic potential. Moreover, miR-146b-5p agomir contributed to higher rates of embryonic resorption in ICR mice. When overexpressed in HTR-8/SVneo cells, miR-146b-5p attenuated the proliferative, invasive, and migratory activity of these cells while suppressing the expression of MMP9 and immune inflammation-associated cytokines, including IL1B, IL11, CXCL1, CXCL8, and CXCL12. Conversely, inhibition of its expression enhanced proliferation, migration, and invasion abilities. Mechanistically, IL-1 receptor-associated kinase-1 and a disintegrin and metalloproteinase 19 were identified as miR-146b-5p targets regulating trophoblast function, and silencing IL-1 receptor-associated kinase-1 had similar effects as miR-146b-5p overexpression, while IL-1 receptor-associated kinase-1 overexpression could partially reverse the inhibitory impact of this microRNA on trophoblasts. miR-146b-5p may inhibit trophoblast proliferation, migration, invasion, and implantation-associated inflammation by downregulating IL-1 receptor-associated kinase-1 and a disintegrin and metalloproteinase 19, participating in the pathogenesis of miscarriage and providing a critical biomarker and a promising therapeutic target for unexplained miscarriage.
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Affiliation(s)
- Xiaoli Zhang
- Department of Prenatal Diagnosis and Genetic Diseases, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xueyu Li
- Department of Prenatal Diagnosis and Genetic Diseases, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Reproductive Medicine Center, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
| | - Xuemei Tan
- Department of Prenatal Diagnosis and Genetic Diseases, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Lingjie Deng
- Department of Prenatal Diagnosis and Genetic Diseases, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Linlin Zhong
- Department of Prenatal Diagnosis and Genetic Diseases, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Changqiang Wei
- Department of Prenatal Diagnosis and Genetic Diseases, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Heyun Ruan
- Department of Prenatal Diagnosis and Genetic Diseases, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yebin Lu
- Department of Prenatal Diagnosis and Genetic Diseases, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Lihong Pang
- Department of Prenatal Diagnosis and Genetic Diseases, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High-Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, Guangxi, China
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5
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Zhang X, Fawwal DV, Spangle JM, Corbett AH, Jones CY. Exploring the Molecular Underpinnings of Cancer-Causing Oncohistone Mutants Using Yeast as a Model. J Fungi (Basel) 2023; 9:1187. [PMID: 38132788 PMCID: PMC10744705 DOI: 10.3390/jof9121187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
Understanding the molecular basis of cancer initiation and progression is critical in developing effective treatment strategies. Recently, mutations in genes encoding histone proteins that drive oncogenesis have been identified, converting these essential proteins into "oncohistones". Understanding how oncohistone mutants, which are commonly single missense mutations, subvert the normal function of histones to drive oncogenesis requires defining the functional consequences of such changes. Histones genes are present in multiple copies in the human genome with 15 genes encoding histone H3 isoforms, the histone for which the majority of oncohistone variants have been analyzed thus far. With so many wildtype histone proteins being expressed simultaneously within the oncohistone, it can be difficult to decipher the precise mechanistic consequences of the mutant protein. In contrast to humans, budding and fission yeast contain only two or three histone H3 genes, respectively. Furthermore, yeast histones share ~90% sequence identity with human H3 protein. Its genetic simplicity and evolutionary conservation make yeast an excellent model for characterizing oncohistones. The power of genetic approaches can also be exploited in yeast models to define cellular signaling pathways that could serve as actionable therapeutic targets. In this review, we focus on the value of yeast models to serve as a discovery tool that can provide mechanistic insights and inform subsequent translational studies in humans.
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Affiliation(s)
- Xinran Zhang
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
| | - Dorelle V. Fawwal
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - Jennifer M. Spangle
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Anita H. Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Celina Y. Jones
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
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6
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Espinoza Pereira KN, Shan J, Licht JD, Bennett RL. Histone mutations in cancer. Biochem Soc Trans 2023; 51:1749-1763. [PMID: 37721138 PMCID: PMC10657182 DOI: 10.1042/bst20210567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/19/2023]
Abstract
Genes encoding histone proteins are recurrently mutated in tumor samples, and these mutations may impact nucleosome stability, histone post-translational modification, or chromatin dynamics. The prevalence of histone mutations across diverse cancer types suggest that normal chromatin structure is a barrier to tumorigenesis. Oncohistone mutations disrupt chromatin structure and gene regulatory mechanisms, resulting in aberrant gene expression and the development of cancer phenotypes. Examples of oncohistones include the histone H3 K27M mutation found in pediatric brain cancers that blocks post-translational modification of the H3 N-terminal tail and the histone H2B E76K mutation found in some solid tumors that disrupts nucleosome stability. Oncohistones may comprise a limited fraction of the total histone pool yet cause global effects on chromatin structure and drive cancer phenotypes. Here, we survey histone mutations in cancer and review their function and role in tumorigenesis.
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Affiliation(s)
| | - Jixiu Shan
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, U.S.A
| | - Jonathan D. Licht
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, U.S.A
| | - Richard L. Bennett
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, U.S.A
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7
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Dhamdhere MR, Spiegelman DV, Schneper L, Erbe AK, Sondel PM, Spiegelman VS. Generation of Novel Immunocompetent Mouse Cell Lines to Model Experimental Metastasis of High-Risk Neuroblastoma. Cancers (Basel) 2023; 15:4693. [PMID: 37835389 PMCID: PMC10571844 DOI: 10.3390/cancers15194693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
NB, being a highly metastatic cancer, is one of the leading causes of cancer-related deaths in children. Increased disease recurrence and clinical resistance in patients with metastatic high-risk NBs (HR-NBs) result in poor outcomes and lower overall survival. However, the paucity of appropriate in vivo models for HR-NB metastasis has limited investigations into the underlying biology of HR-NB metastasis. This study was designed to address this limitation and develop suitable immunocompetent models for HR-NB metastasis. Here, we developed several highly metastatic immunocompetent murine HR-NB cell lines. Our newly developed cell lines show 100% efficiency in modeling experimental metastasis in C57BL6 mice and feature metastasis to the sites frequently observed in humans with HR-NB (liver and bone). In vivo validation demonstrated their specifically gained metastatic phenotype. The in vitro characterization of the cell lines showed increased cell invasion, acquired anchorage-independent growth ability, and resistance to MHC-I induction upon IFN-γ treatment. Furthermore, RNA-seq analysis of the newly developed cells identified a differentially regulated gene signature and an enrichment of processes consistent with their acquired metastatic phenotype, including extracellular matrix remodeling, angiogenesis, cell migration, and chemotaxis. The presented newly developed cell lines are, thus, suitable and promising tools for HR-NB metastasis and microenvironment studies in an immunocompetent system.
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Affiliation(s)
- Mayura R. Dhamdhere
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Dan V. Spiegelman
- Department of Human Oncology, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53792, USA; (D.V.S.); (P.M.S.)
| | - Lisa Schneper
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Amy K. Erbe
- Department of Human Oncology, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53792, USA; (D.V.S.); (P.M.S.)
| | - Paul M. Sondel
- Department of Human Oncology, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53792, USA; (D.V.S.); (P.M.S.)
| | - Vladimir S. Spiegelman
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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Zhang S, Yang F, Huang Y, He L, Li Y, Wan YCE, Ding Y, Chan KM, Xie T, Sun H, Wang H. ATF3 induction prevents precocious activation of skeletal muscle stem cell by regulating H2B expression. Nat Commun 2023; 14:4978. [PMID: 37591871 PMCID: PMC10435463 DOI: 10.1038/s41467-023-40465-w] [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: 08/21/2022] [Accepted: 07/27/2023] [Indexed: 08/19/2023] Open
Abstract
Skeletal muscle stem cells (also called satellite cells, SCs) are important for maintaining muscle tissue homeostasis and damage-induced regeneration. However, it remains poorly understood how SCs enter cell cycle to become activated upon injury. Here we report that AP-1 family member ATF3 (Activating Transcription Factor 3) prevents SC premature activation. Atf3 is rapidly and transiently induced in SCs upon activation. Short-term deletion of Atf3 in SCs accelerates acute injury-induced regeneration, however, its long-term deletion exhausts the SC pool and thus impairs muscle regeneration. The Atf3 loss also provokes SC activation during voluntary exercise and enhances the activation during endurance exercise. Mechanistically, ATF3 directly activates the transcription of Histone 2B genes, whose reduction accelerates nucleosome displacement and gene transcription required for SC activation. Finally, the ATF3-dependent H2B expression also prevents genome instability and replicative senescence in SCs. Therefore, this study has revealed a previously unknown mechanism for preserving the SC population by actively suppressing precocious activation, in which ATF3 is a key regulator.
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Affiliation(s)
- Suyang Zhang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
- Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, New Territories, Hong Kong SAR, China
| | - Feng Yang
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yile Huang
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Liangqiang He
- Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuying Li
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yi Ching Esther Wan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518172, China
| | - Yingzhe Ding
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kui Ming Chan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518172, China
| | - Ting Xie
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China.
- Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, New Territories, Hong Kong SAR, China.
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9
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Huang D, Edwards AD, Gong X, Kraus WL. Functional Analysis of Histone ADP-Ribosylation In Vitro and in Cells. Methods Mol Biol 2023; 2609:157-192. [PMID: 36515836 DOI: 10.1007/978-1-0716-2891-1_11] [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] [Indexed: 12/15/2022]
Abstract
Gene regulation in the nucleus requires precise control of the molecular processes that dictate how, when, and which genes are transcribed. The posttranslational modification (PTM) of histones in chromatin is an effective means to link cellular signaling to gene expression outcomes. The repertoire of histone PTMs includes phosphorylation, acetylation, methylation, ubiquitylation, and ADP-ribosylation (ADPRylation). ADPRylation is a reversible PTM that results in the covalent transfer of ADP-ribose units derived from NAD+ to substrate proteins on glutamate, aspartate, serine, and other amino acids. Histones were the first substrate proteins identified for ADPRylation, over five decades ago. Since that time, histone ADPRylation has been shown to be a widespread and critical regulator of chromatin structure and function during transcription, DNA repair, and replication. Here, we describe a set of protocols that allow the user to investigate site-specific histone ADPRylation and its functional consequences in biochemical assays and in cells in a variety of biological systems. With the recent discovery that some cancer-causing histone mutations (i.e., oncohistone mutations) occur at functional sites of regulatory ADPRylation, these protocols may have additional utility in studies of oncology.
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Affiliation(s)
- Dan Huang
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cardiology, Clinical Center for Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China.
| | - Andrea D Edwards
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xuan Gong
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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10
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Mitchener MM, Muir TW. Oncohistones: Exposing the nuances and vulnerabilities of epigenetic regulation. Mol Cell 2022; 82:2925-2938. [PMID: 35985302 PMCID: PMC9482148 DOI: 10.1016/j.molcel.2022.07.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/20/2022] [Accepted: 07/14/2022] [Indexed: 12/19/2022]
Abstract
Work over the last decade has uncovered a new layer of epigenetic dysregulation. It is now appreciated that somatic missense mutations in histones, the packaging agents of genomic DNA, are often associated with human pathologies, especially cancer. Although some of these "oncohistone" mutations are thought to be key drivers of cancer, the impacts of the majority of them on disease onset and progression remain to be elucidated. Here, we survey this rapidly expanding research field with particular emphasis on how histone mutants, even at low dosage, can corrupt chromatin states. This work is unveiling the remarkable intricacies of epigenetic control mechanisms. Throughout, we highlight how studies of oncohistones have leveraged, and in some cases fueled, the advances in our ability to manipulate and interrogate chromatin at the molecular level.
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Affiliation(s)
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
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11
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Lemon LD, Kannan S, Mo KW, Adams M, Choi HG, Gulka AOD, Withers ES, Nurelegne HT, Gomez V, Ambrocio RE, Tumminkatti R, Lee RS, Wan M, Fasken MB, Spangle JM, Corbett AH. A Saccharomyces cerevisiae model and screen to define the functional consequences of oncogenic histone missense mutations. G3 GENES|GENOMES|GENETICS 2022; 12:6585874. [PMID: 35567477 PMCID: PMC9258546 DOI: 10.1093/g3journal/jkac120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/06/2022] [Indexed: 11/17/2022]
Abstract
Somatic missense mutations in histone genes turn these essential proteins into oncohistones, which can drive oncogenesis. Understanding how missense mutations alter histone function is challenging in mammals as mutations occur in a single histone gene. For example, described oncohistone mutations predominantly occur in the histone H3.3 gene, despite the human genome encoding 15 H3 genes. To understand how oncogenic histone missense mutations alter histone function, we leveraged the budding yeast model, which contains only 2 H3 genes, to explore the functional consequences of oncohistones H3K36M, H3G34W, H3G34L, H3G34R, and H3G34V. Analysis of cells that express each of these variants as the sole copy of H3 reveals that H3K36 mutants show different drug sensitivities compared to H3G34 mutants. This finding suggests that changes to proximal amino acids in the H3 N-terminal tail alter distinct biological pathways. We exploited the caffeine-sensitive growth of H3K36-mutant cells to perform a high copy suppressor screen. This screen identified genes linked to histone function and transcriptional regulation, including Esa1, a histone H4/H2A acetyltransferase; Tos4, a forkhead-associated domain-containing gene expression regulator; Pho92, an N6-methyladenosine RNA-binding protein; and Sgv1/Bur1, a cyclin-dependent kinase. We show that the Esa1 lysine acetyltransferase activity is critical for suppression of the caffeine-sensitive growth of H3K36R-mutant cells while the previously characterized binding interactions of Tos4 and Pho92 are not required for suppression. This screen identifies pathways that could be altered by oncohistone mutations and highlights the value of yeast genetics to identify pathways altered by such mutations.
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Affiliation(s)
- Laramie D Lemon
- Department of Biology, Emory University , Atlanta, GA 30322, USA
| | - Sneha Kannan
- Department of Biology, Emory University , Atlanta, GA 30322, USA
| | - Kim Wai Mo
- Department of Biology, Emory University , Atlanta, GA 30322, USA
| | - Miranda Adams
- Department of Biology, Emory University , Atlanta, GA 30322, USA
- Department of Radiation Oncology, Emory University , Atlanta, GA 30322, USA
- Graduate Program in Cancer Biology, Emory University , Atlanta, GA 30322, USA
| | - Haley G Choi
- Department of Biology, Emory University , Atlanta, GA 30322, USA
- Department of Radiation Oncology, Emory University , Atlanta, GA 30322, USA
| | - Alexander O D Gulka
- Department of Biology, Emory University , Atlanta, GA 30322, USA
- Graduate Program in Genetics and Molecular Biology, Emory University , Atlanta, GA 30322, USA
| | - Elise S Withers
- Department of Biology, Emory University , Atlanta, GA 30322, USA
| | | | - Valeria Gomez
- Department of Biology, Emory University , Atlanta, GA 30322, USA
| | - Reina E Ambrocio
- Department of Biology, Emory University , Atlanta, GA 30322, USA
| | - Rhea Tumminkatti
- Department of Biology, Emory University , Atlanta, GA 30322, USA
| | - Richard S Lee
- Department of Biology, Emory University , Atlanta, GA 30322, USA
- Department of Radiation Oncology, Emory University , Atlanta, GA 30322, USA
| | - Morris Wan
- Department of Biology, Emory University , Atlanta, GA 30322, USA
| | - Milo B Fasken
- Department of Biology, Emory University , Atlanta, GA 30322, USA
| | - Jennifer M Spangle
- Department of Radiation Oncology, Emory University , Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University , Atlanta, GA 30322, USA
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12
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Huang D, Camacho CV, Martire S, Nagari A, Setlem R, Gong X, Edwards AD, Chiu SP, Banaszynski LA, Kraus WL. Oncohistone Mutations Occur at Functional Sites of Regulatory ADP-Ribosylation. Cancer Res 2022; 82:2361-2377. [PMID: 35472077 PMCID: PMC9256803 DOI: 10.1158/0008-5472.can-22-0742] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 01/07/2023]
Abstract
Recent studies have identified cancer-associated mutations in histone genes that lead to the expression of mutant versions of core histones called oncohistones. Many oncohistone mutations occur at Asp and Glu residues, two amino acids known to be ADP-ribosylated (ADPRylated) by PARP1. We screened 25 Glu or Asp oncohistone mutants for their effects on cell growth in breast and ovarian cancer cells. Ectopic expression of six mutants of three different core histones (H2B, H3, and H4) altered cell growth in at least two different cell lines. Two of these sites, H2B-D51 and H4-D68, were indeed sites of ADPRylation in wild-type (unmutated) histones, and mutation of these sites inhibited ADPRylation. Mutation of H2B-D51 dramatically altered chromatin accessibility at enhancers and promoters, as well as gene expression outcomes, whereas mutation of H4-D68 did not. Additional biochemical, cellular, proteomic, and genomic analyses demonstrated that ADPRylation of H2B-D51 inhibits p300-mediated acetylation of H2B at many Lys residues. In breast cancer cell xenografts in mice, H2B-D51A promoted tumor growth, but did not confer resistance to the cytotoxic effects of PARP inhibition. Collectively, these results demonstrate that functional Asp and Glu ADPRylation sites on histones are mutated in cancers, allowing cancer cells to escape the growth-regulating effects of post-translational modifications via distinct mechanisms. SIGNIFICANCE This study identifies cancer-driving mutations in histones as sites of PARP1-mediated ADP-ribosylation in breast and ovarian cancers, providing a molecular pathway by which cancers may subvert the growth-regulating effects of PARP1.
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Affiliation(s)
- Dan Huang
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Cardiology, Clinical Center for Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China.,Address correspondence to: Dan Huang: and W. Lee Kraus:
| | - Cristel V. Camacho
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sara Martire
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Laboratory of Chromatin Biology, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anusha Nagari
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Computational Core Facility, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rohit Setlem
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Computational Core Facility, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xuan Gong
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Andrea D. Edwards
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shu-Ping Chiu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Laura A. Banaszynski
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Laboratory of Chromatin Biology, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W. Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Address correspondence to: Dan Huang: and W. Lee Kraus:
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13
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Abstract
Chromatin dysfunction has been implicated in a growing number of cancers especially in children and young adults. In addition to chromatin modifying and remodeling enzymes, mutations in histone genes are linked to human cancers. Since the first reports of hotspot missense mutations affecting key residues at histone H3 tail, studies have revealed how these so-called "oncohistones" dominantly (H3K27M and H3K36M) or locally (H3.3G34R/W) inhibit corresponding histone methyltransferases and misregulate epigenome and transcriptome to promote tumorigenesis. More recently, widespread mutations in all four core histones are identified in diverse cancer types. Furthermore, an "oncohistone-like" protein EZHIP has been implicated in driving childhood ependymomas through a mechanism highly reminiscent of H3K27M mutation. We will review recent progresses on understanding the biochemical, molecular and biological mechanisms underlying the canonical and novel histone mutations. Importantly, these mechanistic insights have identified therapeutic opportunities for oncohistone-driven tumors.
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Affiliation(s)
- Varun Sahu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Chao Lu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA,Corresponding author: Chao Lu:
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14
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Genome-wide mapping of somatic mutation rates uncovers drivers of cancer. Nat Biotechnol 2022; 40:1634-1643. [PMID: 35726091 PMCID: PMC9646522 DOI: 10.1038/s41587-022-01353-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 05/10/2022] [Indexed: 01/12/2023]
Abstract
Identification of cancer driver mutations that confer a proliferative advantage is central to understanding cancer; however, searches have often been limited to protein-coding sequences and specific non-coding elements (for example, promoters) because of the challenge of modeling the highly variable somatic mutation rates observed across tumor genomes. Here we present Dig, a method to search for driver elements and mutations anywhere in the genome. We use deep neural networks to map cancer-specific mutation rates genome-wide at kilobase-scale resolution. These estimates are then refined to search for evidence of driver mutations under positive selection throughout the genome by comparing observed to expected mutation counts. We mapped mutation rates for 37 cancer types and applied these maps to identify putative drivers within intronic cryptic splice regions, 5' untranslated regions and infrequently mutated genes. Our high-resolution mutation rate maps, available for web-based exploration, are a resource to enable driver discovery genome-wide.
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15
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Histone H2B Mutations in Cancer. Biomedicines 2021; 9:biomedicines9060694. [PMID: 34205231 PMCID: PMC8235166 DOI: 10.3390/biomedicines9060694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/04/2021] [Accepted: 06/15/2021] [Indexed: 01/27/2023] Open
Abstract
Oncohistones have emerged as a new area in cancer epigenetics research. Recent efforts to catalogue histone mutations in cancer patients have revealed thousands of histone mutations across different types of cancer. In contrast to previously identified oncohistones (H3K27M, H3G34V/R, and H3K36M), where the mutations occur on the tail domain and affect histone post-translational modifications, the majority of the newly identified mutations are located within the histone fold domain and affect gene expression via distinct mechanisms. The recent characterization of the selected H2B has revealed previously unappreciated roles of oncohistones in nucleosome stability, chromatin accessibility, and chromatin remodeling. This review summarizes recent advances in the study of H2B oncohistones and other emerging oncohistones occurring on other types of histones, particularly those occurring on the histone fold domain.
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