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Behrens LMP, Gasparotto J, Rampelotto PH, Escalona MAR, da Silva LDS, Carazza-Kessler FG, Barbosa CP, Campos MS, Dorn M, Gelain DP, Moreira JCF. Sodium propionate oral supplementation ameliorates depressive-like behavior through gut microbiome and histone 3 epigenetic regulation. J Nutr Biochem 2024; 130:109660. [PMID: 38685283 DOI: 10.1016/j.jnutbio.2024.109660] [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: 12/31/2023] [Revised: 03/30/2024] [Accepted: 04/23/2024] [Indexed: 05/02/2024]
Abstract
Major depressive disorder (MDD) is a global health concern, affecting over 250 million individuals worldwide. In recent years, the gut-brain axis has emerged as a promising field for understanding the pathophysiology of MDD. Microbial metabolites, such as short-chain fatty acids (SCFAs)-acetate, butyrate, and propionate-, have gained attention for their potential to influence epigenetic modifications within the host brain. However, the precise mechanisms through which these metabolites participate in MDD pathophysiology remain elusive. This study was designed to investigate the effects of oral SCFA supplementation in adult male Wistar rats subjected to chronic unpredictable mild stress (CUMS). A subset of control and CUMS-exposed rats received different supplementations: sodium acetate (NaOAc) at a concentration of 60 mM, sodium butyrate (NaB) at 40 mM, sodium propionate (NaP) at 50 mM, or a mixture of these SCFAs. The gut microbiome was assessed through 16S rRNA sequencing, and epigenetic profiling was performed using Western blot analysis. Results demonstrated that NaP supplementation significantly alleviated anhedonia in stressed animals, as evidenced by improved performance in the sucrose consumption test. This ameliorative effect was potentially associated with the modulation of gut bacterial communities, accompanied by the attenuation of the region-specific epigenetic dysregulation in the brain of the animals exposed to chronic stress. These findings suggest a potential association between gut dysbiosis and stress response, and NaP could be a promising target for future MDD interventions. However, further studies are needed to fully elucidate the underlying mechanisms of these effects.
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Affiliation(s)
- Luiza Marques Prates Behrens
- Center of Oxidative Stress Studies, Department of Biochemistry, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre 90035-003, Brazil; Graduate Program in Biological Sciences: Biochemistry, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre 90035-003, Brazil; Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre 91501-970, Brazil.
| | - Juciano Gasparotto
- Center of Oxidative Stress Studies, Department of Biochemistry, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre 90035-003, Brazil
| | - Pabulo Henrique Rampelotto
- Bioinformatics and Biostatistics Core Facility, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre 91501-907, Brazil
| | - Manuel Adrian Riveros Escalona
- Graduate Program in Veterinary Sciences, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre 91540-000, Brazil
| | - Lucas Dos Santos da Silva
- Center of Oxidative Stress Studies, Department of Biochemistry, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre 90035-003, Brazil; Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre 91501-970, Brazil
| | - Flávio Gabriel Carazza-Kessler
- Center of Oxidative Stress Studies, Department of Biochemistry, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre 90035-003, Brazil; Graduate Program in Biological Sciences: Biochemistry, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre 90035-003, Brazil
| | - Camila Pocharski Barbosa
- Center of Oxidative Stress Studies, Department of Biochemistry, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre 90035-003, Brazil
| | - Marlene Soares Campos
- Center of Oxidative Stress Studies, Department of Biochemistry, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre 90035-003, Brazil
| | - Márcio Dorn
- Department of Theoretical Informatics, Institute of Informatics, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre 91501-970, Brazil; Center of Biotechnology, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre 91501-970, Brazil
| | - Daniel Pens Gelain
- Center of Oxidative Stress Studies, Department of Biochemistry, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre 90035-003, Brazil; Department of Biochemistry, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre 90035-003, Brazil
| | - José Cláudio Fonseca Moreira
- Center of Oxidative Stress Studies, Department of Biochemistry, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre 90035-003, Brazil; Department of Biochemistry, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre 90035-003, Brazil
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2
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Harel T, Spicher C, Scheer E, Buchan JG, Cech J, Folland C, Frey T, Holtz AM, Innes AM, Keren B, Macken WL, Marcelis C, Otten CE, Paolucci SA, Petit F, Pfundt R, Pitceathly RDS, Rauch A, Ravenscroft G, Sanchev R, Steindl K, Tammer F, Tyndall A, Devys D, Vincent SD, Elpeleg O, Tora L. De novo variants in ATXN7L3 lead to developmental delay, hypotonia and distinctive facial features. Brain 2024; 147:2732-2744. [PMID: 38753057 DOI: 10.1093/brain/awae160] [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: 11/06/2023] [Revised: 03/02/2024] [Accepted: 04/08/2024] [Indexed: 08/02/2024] Open
Abstract
Deubiquitination is crucial for the proper functioning of numerous biological pathways, such as DNA repair, cell cycle progression, transcription, signal transduction and autophagy. Accordingly, pathogenic variants in deubiquitinating enzymes (DUBs) have been implicated in neurodevelopmental disorders and congenital abnormalities. ATXN7L3 is a component of the DUB module of the Spt-Ada-Gcn5 acetyltransferase (SAGA) complex and two other related DUB modules, and it serves as an obligate adaptor protein of three ubiquitin-specific proteases (USP22, USP27X or USP51). Through exome sequencing and by using GeneMatcher, we identified nine individuals with heterozygous variants in ATXN7L3. The core phenotype included global motor and language developmental delay, hypotonia and distinctive facial characteristics, including hypertelorism, epicanthal folds, blepharoptosis, a small nose and mouth, and low-set, posteriorly rotated ears. To assess pathogenicity, we investigated the effects of a recurrent nonsense variant [c.340C>T; p.(Arg114Ter)] in fibroblasts of an affected individual. ATXN7L3 protein levels were reduced, and deubiquitylation was impaired, as indicated by an increase in histone H2Bub1 levels. This is consistent with the previous observation of increased H2Bub1 levels in Atxn7l3-null mouse embryos, which have developmental delay and embryonic lethality. In conclusion, we present clinical information and biochemical characterization supporting ATXN7L3 variants in the pathogenesis of a rare syndromic neurodevelopmental disorder.
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Affiliation(s)
- Tamar Harel
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel, 9112001
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel, 9112001
| | - Camille Spicher
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Jillian G Buchan
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195-7110, USA
| | - Jennifer Cech
- University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Chiara Folland
- Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Tanja Frey
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
| | - Alexander M Holtz
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - A Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Boris Keren
- Department of Genetics and Referral Center for Intellectual Disabilities of Rare Causes, AP-HP, Sorbonne Université, Assistance Publique-Hopitaux de Paris, Pitié-Salpêtrière Hospital, 75013, Paris, France
| | - William L Macken
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Carlo Marcelis
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 HR, Nijmegen, The Netherlands
| | - Catherine E Otten
- University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Sarah A Paolucci
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195-7110, USA
| | - Florence Petit
- CHU Lille, Clinique de génétique Guy Fontaine, F-59000 Lille, France
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 HR, Nijmegen, The Netherlands
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Anita Rauch
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
- University Children's Hospital Zurich, 8032 Zurich, Switzerland
- University of Zurich Research Priority Program ITINERARE: Innovative Therapies in Rare Diseases, 8032 Zurich, Switzerland
- University of Zurich Research Priority Program AdaBD: Adaptive Brain Circuits in Development and Learning, 8057 Zurich, Switzerland
| | - Gianina Ravenscroft
- Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Rani Sanchev
- Centre for Clinical Genetics, Sydney Children's Hospitals Network-Randwick, Sydney, NSW 2031, Australia
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
| | - Femke Tammer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 HR, Nijmegen, The Netherlands
| | - Amanda Tyndall
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Stéphane D Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel, 9112001
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel, 9112001
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
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3
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Komera I, Chen X, Liu L, Gao C. Microbial Synthetic Epigenetic Tools Design and Applications. ACS Synth Biol 2024; 13:1621-1632. [PMID: 38758631 DOI: 10.1021/acssynbio.4c00125] [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] [Indexed: 05/19/2024]
Abstract
Microbial synthetic epigenetics offers significant opportunities for the design of synthetic biology tools by leveraging reversible gene control mechanisms without altering DNA sequences. However, limited understanding and a lack of technologies for thorough analysis of the mechanisms behind epigenetic modifications have hampered their utilization in biotechnological applications. In this review, we explore advancements in developing epigenetic-based synthetic gene regulatory tools at both transcriptional and post-transcriptional levels. Furthermore, we examine strategies developed to construct epigenetic-based circuits that provide controllable and stable gene regulation, aiming to boost the performance of microbial chassis cells. Finally, we discuss the current challenges and perspectives in the development of synthetic epigenetic tools.
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Affiliation(s)
- Irene Komera
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
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4
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Navabpour S, Farrell K, Kincaid SE, Omar N, Musaus M, Lin Y, Xie H, Jarome TJ. Monoubiquitination of histone H2B is a crucial regulator of the transcriptome during memory formation. Learn Mem 2024; 31:a053912. [PMID: 38580378 PMCID: PMC11000578 DOI: 10.1101/lm.053912.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/07/2024] [Indexed: 04/07/2024]
Abstract
Posttranslational modification of histone proteins is critical for memory formation. Recently, we showed that monoubiquitination of histone H2B at lysine 120 (H2Bub) is critical for memory formation in the hippocampus. However, the transcriptome controlled by H2Bub remains unknown. Here, we found that fear conditioning in male rats increased or decreased the expression of 86 genes in the hippocampus but, surprisingly, siRNA-mediated knockdown of the H2Bub ligase, Rnf20, abolished changes in all but one of these genes. These findings suggest that monoubiquitination of histone H2B is a crucial regulator of the transcriptome during memory formation.
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Affiliation(s)
- Shaghayegh Navabpour
- Translational Biology, Medicine and Health Graduate Program, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Kayla Farrell
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Shannon E Kincaid
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Nour Omar
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Madeline Musaus
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Yu Lin
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia 24061, USA
| | - Hehuang Xie
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia 24061, USA
- Fralin Life Science Institute at Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Timothy J Jarome
- Translational Biology, Medicine and Health Graduate Program, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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5
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Gu M, Ren B, Fang Y, Ren J, Liu X, Wang X, Zhou F, Xiao R, Luo X, You L, Zhao Y. Epigenetic regulation in cancer. MedComm (Beijing) 2024; 5:e495. [PMID: 38374872 PMCID: PMC10876210 DOI: 10.1002/mco2.495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/21/2024] Open
Abstract
Epigenetic modifications are defined as heritable changes in gene activity that do not involve changes in the underlying DNA sequence. The oncogenic process is driven by the accumulation of alterations that impact genome's structure and function. Genetic mutations, which directly disrupt the DNA sequence, are complemented by epigenetic modifications that modulate gene expression, thereby facilitating the acquisition of malignant characteristics. Principals among these epigenetic changes are shifts in DNA methylation and histone mark patterns, which promote tumor development and metastasis. Notably, the reversible nature of epigenetic alterations, as opposed to the permanence of genetic changes, positions the epigenetic machinery as a prime target in the discovery of novel therapeutics. Our review delves into the complexities of epigenetic regulation, exploring its profound effects on tumor initiation, metastatic behavior, metabolic pathways, and the tumor microenvironment. We place a particular emphasis on the dysregulation at each level of epigenetic modulation, including but not limited to, the aberrations in enzymes responsible for DNA methylation and histone modification, subunit loss or fusions in chromatin remodeling complexes, and the disturbances in higher-order chromatin structure. Finally, we also evaluate therapeutic approaches that leverage the growing understanding of chromatin dysregulation, offering new avenues for cancer treatment.
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Affiliation(s)
- Minzhi Gu
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Bo Ren
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Yuan Fang
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Jie Ren
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Xiaohong Liu
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Xing Wang
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Feihan Zhou
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Ruiling Xiao
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Xiyuan Luo
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Lei You
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Yupei Zhao
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
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Schnee P, Pleiss J, Jeltsch A. Approaching the catalytic mechanism of protein lysine methyltransferases by biochemical and simulation techniques. Crit Rev Biochem Mol Biol 2024; 59:20-68. [PMID: 38449437 DOI: 10.1080/10409238.2024.2318547] [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: 10/24/2023] [Accepted: 02/10/2024] [Indexed: 03/08/2024]
Abstract
Protein lysine methyltransferases (PKMTs) transfer up to three methyl groups to the side chains of lysine residues in proteins and fulfill important regulatory functions by controlling protein stability, localization and protein/protein interactions. The methylation reactions are highly regulated, and aberrant methylation of proteins is associated with several types of diseases including neurologic disorders, cardiovascular diseases, and various types of cancer. This review describes novel insights into the catalytic machinery of various PKMTs achieved by the combined application of biochemical experiments and simulation approaches during the last years, focusing on clinically relevant and well-studied enzymes of this group like DOT1L, SMYD1-3, SET7/9, G9a/GLP, SETD2, SUV420H2, NSD1/2, different MLLs and EZH2. Biochemical experiments have unraveled many mechanistic features of PKMTs concerning their substrate and product specificity, processivity and the effects of somatic mutations observed in PKMTs in cancer cells. Structural data additionally provided information about the substrate recognition, enzyme-substrate complex formation, and allowed for simulations of the substrate peptide interaction and mechanism of PKMTs with atomistic resolution by molecular dynamics and hybrid quantum mechanics/molecular mechanics methods. These simulation technologies uncovered important mechanistic details of the PKMT reaction mechanism including the processes responsible for the deprotonation of the target lysine residue, essential conformational changes of the PKMT upon substrate binding, but also rationalized regulatory principles like PKMT autoinhibition. Further developments are discussed that could bring us closer to a mechanistic understanding of catalysis of this important class of enzymes in the near future. The results described here illustrate the power of the investigation of enzyme mechanisms by the combined application of biochemical experiments and simulation technologies.
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Affiliation(s)
- Philipp Schnee
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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7
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Robert F, Jeronimo C. Transcription-coupled nucleosome assembly. Trends Biochem Sci 2023; 48:978-992. [PMID: 37657993 DOI: 10.1016/j.tibs.2023.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/21/2023] [Accepted: 08/04/2023] [Indexed: 09/03/2023]
Abstract
Eukaryotic transcription occurs on chromatin, where RNA polymerase II encounters nucleosomes during elongation. These nucleosomes must unravel for the DNA to enter the active site. However, in most transcribed genes, nucleosomes remain intact due to transcription-coupled chromatin assembly mechanisms. These mechanisms primarily involve the local reassembly of displaced nucleosomes to prevent (epi)genomic instability and the emergence of cryptic transcription. As a fail-safe mechanism, cells can assemble nucleosomes de novo, particularly in highly transcribed genes, but this may result in the loss of epigenetic information. This review examines transcription-coupled chromatin assembly, with an emphasis on studies in yeast and recent structural studies. These studies shed light on how elongation factors and histone chaperones coordinate to enable nucleosome recycling during transcription.
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Affiliation(s)
- François Robert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, QC H3T 1J4, Canada; Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC H3A 1A3, Canada.
| | - Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
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8
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Nakamura R, Nakayama JI. Regulation of the SUV39H Family Methyltransferases: Insights from Fission Yeast. Biomolecules 2023; 13:biom13040593. [PMID: 37189341 DOI: 10.3390/biom13040593] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Histones, which make up nucleosomes, undergo various post-translational modifications, such as acetylation, methylation, phosphorylation, and ubiquitylation. In particular, histone methylation serves different cellular functions depending on the location of the amino acid residue undergoing modification, and is tightly regulated by the antagonistic action of histone methyltransferases and demethylases. The SUV39H family of histone methyltransferases (HMTases) are evolutionarily conserved from fission yeast to humans and play an important role in the formation of higher-order chromatin structures called heterochromatin. The SUV39H family HMTases catalyzes the methylation of histone H3 lysine 9 (H3K9), and this modification serves as a binding site for heterochromatin protein 1 (HP1) to form a higher-order chromatin structure. While the regulatory mechanism of this family of enzymes has been extensively studied in various model organisms, Clr4, a fission yeast homologue, has made an important contribution. In this review, we focus on the regulatory mechanisms of the SUV39H family of proteins, in particular, the molecular mechanisms revealed by the studies of the fission yeast Clr4, and discuss their generality in comparison to other HMTases.
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9
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Zhou Q, Xiong J, Zhu B. Menin, the COMPASS to locate H3K79 dimethylation. Sci Bull (Beijing) 2023; 68:565-567. [PMID: 36894384 DOI: 10.1016/j.scib.2023.02.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Affiliation(s)
- Qinchao Zhou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Xiong
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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10
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Chou KY, Lee JY, Kim KB, Kim E, Lee HS, Ryu HY. Histone modification in Saccharomyces cerevisiae: A review of the current status. Comput Struct Biotechnol J 2023; 21:1843-1850. [PMID: 36915383 PMCID: PMC10006725 DOI: 10.1016/j.csbj.2023.02.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
The budding yeast Saccharomyces cerevisiae is a well-characterized and popular model system for investigating histone modifications and the inheritance of chromatin states. The data obtained from this model organism have provided essential and critical information for understanding the complexity of epigenetic interactions and regulation in eukaryotes. Recent advances in biotechnology have facilitated the detection and quantitation of protein post-translational modification (PTM), including acetylation, methylation, phosphorylation, ubiquitylation, sumoylation, and acylation, and led to the identification of several novel modification sites in histones. Determining the cellular function of these new histone markers is essential for understanding epigenetic mechanisms and their impact on various biological processes. In this review, we describe recent advances and current views on histone modifications and their effects on chromatin dynamics in S. cerevisiae.
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Key Words
- AdoMet, S-adenosylmethionine
- CAF-1, chromatin assembly factor-1
- CTD, C-terminal domain
- DSB, double-strand break
- E Glu, glutamic acid
- HAT, histone acetyltransferase
- HDAC, histone deacetylase
- Histone acetylation
- Histone acylation
- Histone methylation
- Histone phosphorylation
- Histone sumoylation
- Histone ubiquitylation
- JMJC, Jumonji C
- K Lys, lysine
- PTM, post-translational modification
- R Arg, arginine
- S, serine
- SAGA, Spt-Ada-Gcn5 acetyltransferase
- STUbL, SUMO-targeted ubiquitin ligase
- SUMO, small ubiquitin-like modifier
- T, threonine
- Y, tyrosine
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Affiliation(s)
- Kwon Young Chou
- School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jun-Yeong Lee
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kee-Beom Kim
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Eunjeong Kim
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyun-Shik Lee
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hong-Yeoul Ryu
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
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11
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Cai Q, Guo H, Fang R, Hua Y, Zhu Y, Zheng X, Yan J, Wang J, Hu Y, Zhang C, Zhang C, Duan R, Kong F, Zhang S, Chen D, Ji S. A Toll-dependent Bre1/Rad6-cact feedback loop in controlling host innate immune response. Cell Rep 2022; 41:111795. [PMID: 36516751 DOI: 10.1016/j.celrep.2022.111795] [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: 12/27/2021] [Revised: 10/19/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022] Open
Abstract
The Toll signaling pathway was initially identified for its involvement in the control of early embryogenesis. It was later shown to be also part of a major innate immune pathway controlling the expression of anti-microbial peptides in many eukaryotes including humans; cactus, the essential negative regulator of this pathway in flies, was found to be induced in parallel to the Toll-dependent activation process during immune defenses. We were interested in the mechanisms of this dual effect and provide here evidence that upon pathogenic stimuli, dorsal, one of the transcription factors of the fly Toll pathway, can induce the expression of the E3 ligase Bre1. We further show that Bre1 complexes with the E2 Rad6 to mono-ubiquitinate histone H2B and to promote the transcription of cactus to achieve homeostasis of the Toll immune response. Our studies characterize a Toll signal-dependent regulatory machinery in governing the Toll pathway in Drosophila.
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Affiliation(s)
- Qingshuang Cai
- Center for Developmental Biology, School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Huimin Guo
- Center for Biological Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Rong Fang
- Center for Developmental Biology, School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Yongzhi Hua
- Center for Developmental Biology, School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Yangyang Zhu
- Center for Developmental Biology, School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Xianrui Zheng
- Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou 363000, Fujian, China
| | - Jing Yan
- Center for Developmental Biology, School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Jiale Wang
- Center for Developmental Biology, School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Yixuan Hu
- Center for Developmental Biology, School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Chuchu Zhang
- Center for Developmental Biology, School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Chao Zhang
- Center for Developmental Biology, School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Renjie Duan
- Center for Developmental Biology, School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Fanrui Kong
- Center for Developmental Biology, School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Shikun Zhang
- Center for Developmental Biology, School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Di Chen
- Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou 511436, Guangdong, China.
| | - Shanming Ji
- Center for Developmental Biology, School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China.
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12
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Rahman S, Hoffmann NA, Worden EJ, Smith ML, Namitz KEW, Knutson BA, Cosgrove MS, Wolberger C. Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome. Proc Natl Acad Sci U S A 2022; 119:e2205691119. [PMID: 36095189 PMCID: PMC9499523 DOI: 10.1073/pnas.2205691119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/09/2022] [Indexed: 11/18/2022] Open
Abstract
The human Mixed Lineage Leukemia-1 (MLL1) complex methylates histone H3K4 to promote transcription and is stimulated by monoubiquitination of histone H2B. Recent structures of the MLL1-WRAD core complex, which comprises the MLL1 methyltransferase, WDR5, RbBp5, Ash2L, and DPY-30, have revealed variability in the docking of MLL1-WRAD on nucleosomes. In addition, portions of the Ash2L structure and the position of DPY30 remain ambiguous. We used an integrated approach combining cryoelectron microscopy (cryo-EM) and mass spectrometry cross-linking to determine a structure of the MLL1-WRAD complex bound to ubiquitinated nucleosomes. The resulting model contains the Ash2L intrinsically disordered region (IDR), SPRY insertion region, Sdc1-DPY30 interacting region (SDI-motif), and the DPY30 dimer. We also resolved three additional states of MLL1-WRAD lacking one or more subunits, which may reflect different steps in the assembly of MLL1-WRAD. The docking of subunits in all four states differs from structures of MLL1-WRAD bound to unmodified nucleosomes, suggesting that H2B-ubiquitin favors assembly of the active complex. Our results provide a more complete picture of MLL1-WRAD and the role of ubiquitin in promoting formation of the active methyltransferase complex.
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Affiliation(s)
- Sanim Rahman
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Niklas A. Hoffmann
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Evan J. Worden
- Department of Structural Biology, Van Andel Research Institute, Grand Rapids, MI 49503
| | - Marissa L. Smith
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Kevin E. W. Namitz
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Bruce A. Knutson
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Michael S. Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
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13
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Chen JJ, Stermer D, Tanny JC. Decoding histone ubiquitylation. Front Cell Dev Biol 2022; 10:968398. [PMID: 36105353 PMCID: PMC9464978 DOI: 10.3389/fcell.2022.968398] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Histone ubiquitylation is a critical part of both active and repressed transcriptional states, and lies at the heart of DNA damage repair signaling. The histone residues targeted for ubiquitylation are often highly conserved through evolution, and extensive functional studies of the enzymes that catalyze the ubiquitylation and de-ubiquitylation of histones have revealed key roles linked to cell growth and division, development, and disease in model systems ranging from yeast to human cells. Nonetheless, the downstream consequences of these modifications have only recently begun to be appreciated on a molecular level. Here we review the structure and function of proteins that act as effectors or “readers” of histone ubiquitylation. We highlight lessons learned about how ubiquitin recognition lends specificity and function to intermolecular interactions in the context of transcription and DNA repair, as well as what this might mean for how we think about histone modifications more broadly.
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14
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Khan SU, Khan MU, Kalsoom F, Khan MI, Gao S, Unar A, Zubair M, Bilal M. Mechanisms of gene regulation by histone degradation in adaptation of yeast: an overview of recent advances. Arch Microbiol 2022; 204:287. [PMID: 35482104 DOI: 10.1007/s00203-022-02897-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/12/2022] [Accepted: 04/04/2022] [Indexed: 02/07/2023]
Abstract
Histones are important component of eukaryotic cells chromatin and consist of arginine and lysine residues. Histones play an important role in the protection of DNA. Their contents significantly affect high-level chromatin structure formation, gene expression, DNA replication, and other important life activities. Protein degradation is an important regulatory mechanism of histone content. Recent studies have revealed that modification of amino acid sequence is directly related to histone breakdown. In addition, histone degradation is closely related to covalent modifications, such as ubiquitination and acetylation, which are considered to be driving factors in gene regulation. Gene regulation is an important mechanism in adaptation to the environment and survival of species. With the introduction of highly efficient technology, various mutations in histones have been identified in yeast. In the field of epigenetics and the transmission of chromatin states, two widely used model organisms are the budding yeast Saccharomyces cerevisiae and Schizosaccharomyces pombe. Higher eukaryotes can use their silent loci to maintain their epigenetic states and providing the base to investigate mechanisms underlying development. Therfore, both species have contributed a plethora of information on these mechanisms in both yeast and higher eukaryotes. This study focuses on the role of histone modifications in controlling telomeric silencing in Saccharomyces cerevisiae and centromeric silencing in S. pombe as examples of genetic loci that demonstrate epigenetic inheritance. In view of recent advances, this review focuses on the post-translational modification of histone amino acid residues and reviews the relationship between histone degradation and amino acid residue modification.
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Affiliation(s)
- Safir Ullah Khan
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Munir Ullah Khan
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China
| | - Fadia Kalsoom
- Department of Microbiology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
| | - Muhammad Imran Khan
- School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, People's Republic of China.
- Hefei National Laboratory for Physical Sciences at Microscale and the Center for Biomedical Engineering, University of Science and Technology of China, Hefei, 230027, People's Republic of China.
- Department of Pathology, District headquarters hospital, Jhang, 35200, Punjab Province, Islamic Republic of Pakistan.
| | - Shuang Gao
- School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Ahsanullah Unar
- School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Muhammad Zubair
- School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, People's Republic of China
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, People's Republic of China.
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15
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Li W, Jones K, Burke TJ, Hossain MA, Lariscy L. Epigenetic Regulation of Nucleotide Excision Repair. Front Cell Dev Biol 2022; 10:847051. [PMID: 35465333 PMCID: PMC9023881 DOI: 10.3389/fcell.2022.847051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 03/24/2022] [Indexed: 12/30/2022] Open
Abstract
Genomic DNA is constantly attacked by a plethora of DNA damaging agents both from endogenous and exogenous sources. Nucleotide excision repair (NER) is the most versatile repair pathway that recognizes and removes a wide range of bulky and/or helix-distorting DNA lesions. Even though the molecular mechanism of NER is well studied through in vitro system, the NER process inside the cell is more complicated because the genomic DNA in eukaryotes is tightly packaged into chromosomes and compacted into a nucleus. Epigenetic modifications regulate gene activity and expression without changing the DNA sequence. The dynamics of epigenetic regulation play a crucial role during the in vivo NER process. In this review, we summarize recent advances in our understanding of the epigenetic regulation of NER.
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16
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Ma T, Zhang L, Wang M, Li Y, Jian Y, Wu L, Kistler HC, Ma Z, Yin Y. Plant defense compound triggers mycotoxin synthesis by regulating H2B ub1 and H3K4 me2/3 deposition. THE NEW PHYTOLOGIST 2021; 232:2106-2123. [PMID: 34480757 PMCID: PMC9293436 DOI: 10.1111/nph.17718] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/30/2021] [Indexed: 05/05/2023]
Abstract
Fusarium graminearum produces the mycotoxin deoxynivalenol (DON) which promotes its expansion during infection on its plant host wheat. Conditional expression of DON production during infection is poorly characterized. Wheat produces the defense compound putrescine, which induces hypertranscription of DON biosynthetic genes (FgTRIs) and subsequently leads to DON accumulation during infection. Further, the regulatory mechanisms of FgTRIs hypertranscription upon putrescine treatment were investigated. The transcription factor FgAreA regulates putrescine-mediated transcription of FgTRIs by facilitating the enrichment of histone H2B monoubiquitination (H2B ub1) and histone 3 lysine 4 di- and trimethylations (H3K4 me2/3) on FgTRIs. Importantly, a DNA-binding domain (bZIP) specifically within the Fusarium H2B ub1 E3 ligase Bre1 othologs is identified, and the binding of this bZIP domain to FgTRIs depends on FgAreA-mediated chromatin rearrangement. Interestingly, H2B ub1 regulates H3K4 me2/3 via the methyltransferase complex COMPASS component FgBre2, which is different from Saccharomyces cerevisiae. Taken together, our findings reveal the molecular mechanisms by which host-generated putrescine induces DON production during F. graminearum infection. Our results also provide a novel insight into the role of putrescine during phytopathogen-host interactions and broaden our knowledge of H2B ub1 biogenesis and crosstalk between H2B ub1 and H3K4 me2/3 in eukaryotes.
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Affiliation(s)
- Tianling Ma
- State Key Laboratory of Rice BiologyInstitute of BiotechnologyZhejiang University866 Yuhangtang RoadHangzhou310058China
| | - Lixin Zhang
- State Key Laboratory of Rice BiologyInstitute of BiotechnologyZhejiang University866 Yuhangtang RoadHangzhou310058China
| | - Minhui Wang
- State Key Laboratory of Rice BiologyInstitute of BiotechnologyZhejiang University866 Yuhangtang RoadHangzhou310058China
| | - Yiqing Li
- State Key Laboratory of Rice BiologyInstitute of BiotechnologyZhejiang University866 Yuhangtang RoadHangzhou310058China
| | - Yunqing Jian
- State Key Laboratory of Rice BiologyInstitute of BiotechnologyZhejiang University866 Yuhangtang RoadHangzhou310058China
| | - Liang Wu
- Institute of Crop ScienceZhejiang University866 Yuhangtang RoadHangzhou310058China
| | - Harold Corby Kistler
- United States Department of AgricultureAgricultural Research Service1551 Lindig StreetSt PaulMN55108USA
| | - Zhonghua Ma
- State Key Laboratory of Rice BiologyInstitute of BiotechnologyZhejiang University866 Yuhangtang RoadHangzhou310058China
| | - Yanni Yin
- State Key Laboratory of Rice BiologyInstitute of BiotechnologyZhejiang University866 Yuhangtang RoadHangzhou310058China
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17
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Trans-tail regulation-mediated suppression of cryptic transcription. Exp Mol Med 2021; 53:1683-1688. [PMID: 34845331 PMCID: PMC8639711 DOI: 10.1038/s12276-021-00711-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 01/08/2023] Open
Abstract
Crosstalk between post-translational modifications of histone proteins influences the regulation of chromatin structure and gene expression. Among such crosstalk pathways, the best-characterized example is H2B monoubiquitination-mediated H3K4 and H3K79 methylation, which is referred to as trans-tail regulation. Although many studies have investigated the fragmentary effects of this pathway on silencing and transcription, its ultimate contribution to transcriptional control has remained unclear. Recent advances in molecular techniques and genomics have, however, revealed that the trans-tail crosstalk is linked to a more diverse cascade of histone modifications and has various functions in cotranscriptional processes. Furthermore, H2B monoubiquitination sequentially facilitates H3K4 dimethylation and histone sumoylation, thereby providing a binding platform for recruiting Set3 complex proteins, including two histone deacetylases, to restrict cryptic transcription from gene bodies. The removal of both ubiquitin and SUMO, small ubiquitin-like modifier, modifications from histones also facilitates a change in the phosphorylation pattern of the RNA polymerase II C-terminal domain that is required for subsequent transcriptional elongation. Therefore, this review describes recent findings regarding trans-tail regulation-driven processes to elaborate on their contribution to maintaining transcriptional fidelity. Crosstalk between different DNA-winding proteins, or histones, is a mechanism of molecular fidelity that helps prevent the initiation of aberrant gene expression, which may contribute to cancer and neurodegenerative disease. A team from South Korea, led by Jungmin Choi from the Korea University College of Medicine in Seoul and Hong-Yeoul Ryu from Kyungpook National University in Daegu, review the ways in which different histone proteins chemically modify parts of each other’s structure to regulate their functions. These modifications affect how histones interact with DNA, which in turn alters the dynamics of other factors implicated in gene expression. The correct interaction of histones is necessary to prevent the gene expression machinery from starting RNA synthesis from the wrong sites. Accurate control of these mechanisms is essential for cellular wellbeing
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18
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Dasgupta A, Mondal P, Dalui S, Das C, Roy S. Molecular characterization of substrate-induced ubiquitin transfer by UBR7-PHD finger, a newly identified histone H2BK120 ubiquitin ligase. FEBS J 2021; 289:1842-1857. [PMID: 34739193 DOI: 10.1111/febs.16262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 10/21/2021] [Accepted: 11/03/2021] [Indexed: 01/01/2023]
Abstract
Monoubiquitination of histone H2B at lysine 120 plays a vital role in active transcription and DNA damage response pathways. Ubiquitin protein ligase E3 component N-recognin 7 (UBR7) has been recently identified as an H2BK120 monoubiquitin ligase. However, the molecular details of its ubiquitin transfer mechanism are not well understood. Here, we report that the plant homeodomain (PHD) finger of UBR7 is essential for its association with E2 UbcH6 and consequent ubiquitin transfer to its substrate histone H2B. We also identified the critical region of UbcH6 involved in this function and shown that the residues stretching from 114 to 125 of histone H2B C-terminal tail are sufficient for UBR7/UbcH6-mediated ubiquitin transfer. We also employed antibody-independent mass spectrometry to confirm UBR7-mediated ubiquitination of the H2B C-terminal tail. We demonstrated that the PHD finger of UBR7 forms a dimer and this dimerization is essential for ubiquitination of histone H2B. We mapped the critical residues involved in the dimerization and mutation of these residues that abrogate E3 ligase activity and are associated with cancer. Furthermore, we compared the mode of ubiquitin discharge from UbcH6 mediated by UBR7 and RING finger protein 20 (RNF20) through a thioester hydrolysis assay. Interestingly, binding of substrate H2B to UBR7 induces a conformational change in the PHD finger, which triggers ubiquitin transfer from UbcH6. However, the RNF20 RING finger alone is sufficient to promote the release of ubiquitin from UbcH6. Overall, the mechanism of ubiquitin transfer by the newly identified E3 ubiquitin ligase UBR7 is markedly different from that of RNF20.
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Affiliation(s)
- Anirban Dasgupta
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR) - Indian Institute of Chemical Biology, Kolkata, India
| | - Payel Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.,Homi Bhaba National Institute, Mumbai, India
| | - Sambit Dalui
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR) - Indian Institute of Chemical Biology, Kolkata, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.,Homi Bhaba National Institute, Mumbai, India
| | - Siddhartha Roy
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR) - Indian Institute of Chemical Biology, Kolkata, India
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19
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Wang F, El-Saafin F, Ye T, Stierle M, Negroni L, Durik M, Fischer V, Devys D, Vincent SD, Tora L. Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA polymerase II transcription. Cell Death Differ 2021; 28:2385-2403. [PMID: 33731875 PMCID: PMC8329007 DOI: 10.1038/s41418-021-00759-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 02/18/2021] [Accepted: 02/23/2021] [Indexed: 01/31/2023] Open
Abstract
Co-activator complexes dynamically deposit post-translational modifications (PTMs) on histones, or remove them, to regulate chromatin accessibility and/or to create/erase docking surfaces for proteins that recognize histone PTMs. SAGA (Spt-Ada-Gcn5 Acetyltransferase) is an evolutionary conserved multisubunit co-activator complex with modular organization. The deubiquitylation module (DUB) of mammalian SAGA complex is composed of the ubiquitin-specific protease 22 (USP22) and three adaptor proteins, ATXN7, ATXN7L3 and ENY2, which are all needed for the full activity of the USP22 enzyme to remove monoubiquitin (ub1) from histone H2B. Two additional USP22-related ubiquitin hydrolases (called USP27X or USP51) have been described to form alternative DUBs with ATXN7L3 and ENY2, which can also deubiquitylate H2Bub1. Here we report that USP22 and ATXN7L3 are essential for normal embryonic development of mice, however their requirements are not identical during this process, as Atxn7l3-/- embryos show developmental delay already at embryonic day (E) 7.5, while Usp22-/- embryos are normal at this stage, but die at E14.5. Global histone H2Bub1 levels were only slightly affected in Usp22 null embryos, in contrast H2Bub1 levels were strongly increased in Atxn7l3 null embryos and derived cell lines. Our transcriptomic analyses carried out from wild type and Atxn7l3-/- mouse embryonic stem cells (mESCs), or primary mouse embryonic fibroblasts (MEFs) suggest that the ATXN7L3-related DUB activity regulates only a subset of genes in both cell types. However, the gene sets and the extent of their deregulation were different in mESCs and MEFs. Interestingly, the strong increase of H2Bub1 levels observed in the Atxn7l3-/- mESCs, or Atxn7l3-/- MEFs, does not correlate with the modest changes in RNA Polymerase II (Pol II) occupancy and lack of changes in Pol II elongation observed in the two Atxn7l3-/- cellular systems. These observations together indicate that deubiquitylation of histone H2Bub1 does not directly regulate global Pol II transcription elongation.
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Affiliation(s)
- Fang Wang
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France ,grid.4444.00000 0001 2112 9282Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France ,grid.7429.80000000121866389Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France ,grid.420255.40000 0004 0638 2716Université de Strasbourg, 67404 Illkirch, France
| | - Farrah El-Saafin
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France ,grid.4444.00000 0001 2112 9282Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France ,grid.7429.80000000121866389Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France ,grid.420255.40000 0004 0638 2716Université de Strasbourg, 67404 Illkirch, France ,grid.482637.cPresent Address: Olivia Newton-John Cancer Research Institute, Melbourne, VIC Australia
| | - Tao Ye
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France ,grid.4444.00000 0001 2112 9282Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France ,grid.7429.80000000121866389Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France ,grid.420255.40000 0004 0638 2716Université de Strasbourg, 67404 Illkirch, France ,Plateforme GenomEast, infrastructure France Génomique, 67404 Illkirch, France
| | - Matthieu Stierle
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France ,grid.4444.00000 0001 2112 9282Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France ,grid.7429.80000000121866389Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France ,grid.420255.40000 0004 0638 2716Université de Strasbourg, 67404 Illkirch, France
| | - Luc Negroni
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France ,grid.4444.00000 0001 2112 9282Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France ,grid.7429.80000000121866389Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France ,grid.420255.40000 0004 0638 2716Université de Strasbourg, 67404 Illkirch, France
| | - Matej Durik
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France ,grid.4444.00000 0001 2112 9282Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France ,grid.7429.80000000121866389Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France ,grid.420255.40000 0004 0638 2716Université de Strasbourg, 67404 Illkirch, France
| | - Veronique Fischer
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France ,grid.4444.00000 0001 2112 9282Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France ,grid.7429.80000000121866389Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France ,grid.420255.40000 0004 0638 2716Université de Strasbourg, 67404 Illkirch, France
| | - Didier Devys
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France ,grid.4444.00000 0001 2112 9282Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France ,grid.7429.80000000121866389Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France ,grid.420255.40000 0004 0638 2716Université de Strasbourg, 67404 Illkirch, France
| | - Stéphane D. Vincent
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France ,grid.4444.00000 0001 2112 9282Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France ,grid.7429.80000000121866389Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France ,grid.420255.40000 0004 0638 2716Université de Strasbourg, 67404 Illkirch, France
| | - László Tora
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France ,grid.4444.00000 0001 2112 9282Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France ,grid.7429.80000000121866389Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France ,grid.420255.40000 0004 0638 2716Université de Strasbourg, 67404 Illkirch, France
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20
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Pinto D, Pagé V, Fisher RP, Tanny JC. New connections between ubiquitylation and methylation in the co-transcriptional histone modification network. Curr Genet 2021; 67:695-705. [PMID: 34089069 DOI: 10.1007/s00294-021-01196-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/27/2021] [Accepted: 05/29/2021] [Indexed: 01/01/2023]
Abstract
Co-transcriptional histone modifications are a ubiquitous feature of RNA polymerase II (RNAPII) transcription, with profound but incompletely understood effects on gene expression. Unlike the covalent marks found at promoters, which are thought to be instructive for transcriptional activation, these modifications occur in gene bodies as a result of transcription, which has made elucidation of their functions challenging. Here we review recent insights into the regulation and roles of two such modifications: monoubiquitylation of histone H2B at lysine 120 (H2Bub1) and methylation of histone H3 at lysine 36 (H3K36me). Both H2Bub1 and H3K36me are enriched in the coding regions of transcribed genes, with highly overlapping distributions, but they were thought to work largely independently. We highlight our recent demonstration that, as was previously shown for H3K36me, H2Bub1 signals to the histone deacetylase (HDAC) complex Rpd3S/Clr6-CII, and that Rpd3S/Clr6-CII and H2Bub1 function in the same pathway to repress aberrant antisense transcription initiating within gene coding regions. Moreover, both of these histone modification pathways are influenced by protein phosphorylation catalyzed by the cyclin-dependent kinases (CDKs) that regulate RNAPII elongation, chiefly Cdk9. Therefore, H2Bub1 and H3K36me are more tightly linked than previously thought, sharing both upstream regulatory inputs and downstream effectors. Moreover, these newfound connections suggest extensive, bidirectional signaling between RNAPII elongation complexes and chromatin-modifying enzymes, which helps to determine transcriptional outputs and should be a focus for future investigation.
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Affiliation(s)
- Daniel Pinto
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Vivane Pagé
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada.
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21
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Wu Y, Li M, Yang M. Post-Translational Modifications in Oocyte Maturation and Embryo Development. Front Cell Dev Biol 2021; 9:645318. [PMID: 34150752 PMCID: PMC8206635 DOI: 10.3389/fcell.2021.645318] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/15/2021] [Indexed: 12/27/2022] Open
Abstract
Mammalian oocyte maturation and embryo development are unique biological processes regulated by various modifications. Since de novo mRNA transcription is absent during oocyte meiosis, protein-level regulation, especially post-translational modification (PTM), is crucial. It is known that PTM plays key roles in diverse cellular events such as DNA damage response, chromosome condensation, and cytoskeletal organization during oocyte maturation and embryo development. However, most previous reviews on PTM in oocytes and embryos have only focused on studies of Xenopus laevis or Caenorhabditis elegans eggs. In this review, we will discuss the latest discoveries regarding PTM in mammalian oocytes maturation and embryo development, focusing on phosphorylation, ubiquitination, SUMOylation and Poly(ADP-ribosyl)ation (PARylation). Phosphorylation functions in chromosome condensation and spindle alignment by regulating histone H3, mitogen-activated protein kinases, and some other pathways during mammalian oocyte maturation. Ubiquitination is a three-step enzymatic cascade that facilitates the degradation of proteins, and numerous E3 ubiquitin ligases are involved in modifying substrates and thus regulating oocyte maturation, oocyte-sperm binding, and early embryo development. Through the reversible addition and removal of SUMO (small ubiquitin-related modifier) on lysine residues, SUMOylation affects the cell cycle and DNA damage response in oocytes. As an emerging PTM, PARlation has been shown to not only participate in DNA damage repair, but also mediate asymmetric division of oocyte meiosis. Each of these PTMs and external environments is versatile and contributes to distinct phases during oocyte maturation and embryo development.
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Affiliation(s)
- Yu Wu
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Mo Li
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Mo Yang
- Medical Center for Human Reproduction, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
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22
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Epigenetic-Based Therapy-A Prospective Chance for Medulloblastoma Patients' Recovery. Int J Mol Sci 2021; 22:ijms22094925. [PMID: 34066495 PMCID: PMC8124462 DOI: 10.3390/ijms22094925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/21/2021] [Accepted: 04/27/2021] [Indexed: 12/25/2022] Open
Abstract
Medulloblastoma (MB) is one of the most frequent and malignant brain tumors in children. The prognosis depends on the advancement of the disease and the patient's age. Current therapies, which include surgery, chemotherapy, and irradiation, despite being quite effective, cause significant side effects that influence the central nervous system's function and cause neurocognitive deficits. Therefore, they substantially lower the quality of life, which is especially severe in a developing organism. Thus, there is a need for new therapies that are less toxic and even more effective. Recently, knowledge about the epigenetic mechanisms that are responsible for medulloblastoma development has increased. Epigenetics is a phenomenon that influences gene expression but can be easily modified by external factors. The best known epigenetic mechanisms are histone modifications, DNA methylation, or noncoding RNAs actions. Epigenetic mechanisms comprehensively explain the complex phenomena of carcinogenesis. At the same time, they seem to be a potential key to treating medulloblastoma with fewer complications than past therapies. This review presents the currently known epigenetic mechanisms that are involved in medulloblastoma pathogenesis and the potential therapies that use epigenetic traits to cure medulloblastoma while maintaining a good quality of life and ensuring a higher median overall survival rate.
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23
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Meng D, Guo K, Zhang D, Zhao C, Sun C, Zhang F. Ring finger 20/ring finger 40/WW domain-containing adaptor with coiled-coil complex interacts with p53 to regulate gene transcription in DNA damage response. Oncol Lett 2021; 21:436. [PMID: 33868474 PMCID: PMC8045150 DOI: 10.3892/ol.2021.12697] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 12/17/2020] [Indexed: 01/21/2023] Open
Abstract
p53 is one of the most important tumor suppressor genes, and its primary function is to act as a transcriptional activator to control cell cycle arrest, DNA repair and cellular metabolism by recognizing and binding to specific DNA sequences. Defects in the ring finger (RNF)20/RNF40/WW domain-containing adaptor with coiled-coil (WAC) complex, one of the histone H2B ubiquitination E3 ligases, have been reported to be a key factor in oncogenesis, cancer cell migration and invasion. Histone H2B mono-ubiquitination has been demonstrated to be essential for maintaining the functionality of the p53 tumor suppressor protein. The aim of the present study was to identify any sites in the p53 DNA-binding domain (DBD) specific to the RNF20/RNF40/WAC complex that may be involved in the gene regulation in DNA damage response. The results demonstrated that p53 and the RNF20/RNF40/WAC complex interacted with each other, and the coiled-coil regions in RNF20, RNF40 and WAC were identified to directly interact with p53. The R282 site in the p53 DBD, one of the frequent missense mutations associated with p53 mutation-dependent cancer, was demonstrated to be the key binding site for the RNF20/RNF40/WAC complex. Furthermore, knockout of RNF20/RNF40 suppressed the expression levels of p53 and its target genes in HCT116 cells compared with those in wild-type HCT116 cells. Consistent with these results, the R282W mutation in p53 inhibited the expression levels of p53 and its downstream genes by inactivating the interaction between p53 and RNF20/RNF40 compared with those in wild-type HCT116 cells. In conclusion, the results of the present study revealed the molecular mechanism of the interaction between the RNF20/RNF40/WAC complex and p53, and demonstrated that these proteins regulated gene transcription in the DNA damage response.
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Affiliation(s)
- Danni Meng
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, P.R. China
| | - Kun Guo
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, P.R. China
| | - Die Zhang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, P.R. China
| | - Cheng Zhao
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, P.R. China
| | - Chuanwen Sun
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, P.R. China
| | - Feng Zhang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, P.R. China
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24
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Mazina MY, Vorobyeva NE. Chromatin Modifiers in Transcriptional Regulation: New Findings and Prospects. Acta Naturae 2021; 13:16-30. [PMID: 33959384 PMCID: PMC8084290 DOI: 10.32607/actanaturae.11101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/17/2020] [Indexed: 02/04/2023] Open
Abstract
Histone-modifying and remodeling complexes are considered the main coregulators that affect transcription by changing the chromatin structure. Coordinated action by these complexes is essential for the transcriptional activation of any eukaryotic gene. In this review, we discuss current trends in the study of histone modifiers and chromatin remodelers, including the functional impact of transcriptional proteins/ complexes i.e., "pioneers"; remodeling and modification of non-histone proteins by transcriptional complexes; the supplementary functions of the non-catalytic subunits of remodelers, and the participation of histone modifiers in the "pause" of RNA polymerase II. The review also includes a scheme illustrating the mechanisms of recruitment of the main classes of remodelers and chromatin modifiers to various sites in the genome and their functional activities.
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Affiliation(s)
- M. Yu. Mazina
- Institute of Gene Biology RAS, Group of transcriptional complexes dynamics, Moscow, 119334 Russia
| | - N. E. Vorobyeva
- Institute of Gene Biology RAS, Group of transcriptional complexes dynamics, Moscow, 119334 Russia
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25
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Beyer JN, Raniszewski NR, Burslem GM. Advances and Opportunities in Epigenetic Chemical Biology. Chembiochem 2020; 22:17-42. [PMID: 32786101 DOI: 10.1002/cbic.202000459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/10/2020] [Indexed: 12/13/2022]
Abstract
The study of epigenetics has greatly benefited from the development and application of various chemical biology approaches. In this review, we highlight the key targets for modulation and recent methods developed to enact such modulation. We discuss various chemical biology techniques to study DNA methylation and the post-translational modification of histones as well as their effect on gene expression. Additionally, we address the wealth of protein synthesis approaches to yield histones and nucleosomes bearing epigenetic modifications. Throughout, we highlight targets that present opportunities for the chemical biology community, as well as exciting new approaches that will provide additional insight into the roles of epigenetic marks.
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Affiliation(s)
- Jenna N Beyer
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - Nicole R Raniszewski
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - George M Burslem
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA.,Department of Cancer Biology and Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
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26
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Deng ZH, Ai HS, Lu CP, Li JB. The Bre1/Rad6 machinery: writing the central histone ubiquitin mark on H2B and beyond. Chromosome Res 2020; 28:247-258. [PMID: 32895784 DOI: 10.1007/s10577-020-09640-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/20/2020] [Accepted: 08/30/2020] [Indexed: 01/10/2023]
Abstract
Mono-ubiquitination on H2B (H2Bub1) is an evolutionarily conserved histone post-translational modification implicated in various important physiological processes including DNA replication, transcription activation, and DNA damage repair. The Bre1/Rad6 ubiquitination machinery is currently considered to be the sole writer of H2Bub1, but the mechanistic basis by which it operates is unclear. Recently, the RING-type E3 ligase Bre1 was proposed to associate with the E2 enzyme Rad6 through a novel interaction between Bre1 RBD (Rad6 binding domain) and Rad6; and the RING domain of Bre1 that is responsible for the nucleosomal acidic patch binding also interacts with Rad6 to stimulate its catalytic activity. Recent discoveries have yielded evidence for the phenomenon of liquid-liquid phase separation in the context of H2Bub1, and its regulation by other histone post-translational modifications. This review summarizes current knowledge about Bre1/Rad6-mediated H2B ubiquitination, including the physiological functions and the molecular basis for writing and regulation of this central histone ubiquitin mark. Possible models for the Bre1/Rad6 machinery bound to nucleosomes bearing different modifications in the writing step are also disclosed.
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Affiliation(s)
- Zhi-Heng Deng
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.,Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Hua-Song Ai
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Cheng-Piao Lu
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Jia-Bin Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.
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27
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Qian W, Li Z, Song W, Zhao T, Wang W, Peng J, Wei L, Xia Q, Cheng D. A novel transcriptional cascade is involved in Fzr-mediated endoreplication. Nucleic Acids Res 2020; 48:4214-4229. [PMID: 32182338 PMCID: PMC7192621 DOI: 10.1093/nar/gkaa158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/29/2020] [Indexed: 01/08/2023] Open
Abstract
Endoreplication, known as endocycle, is a variant of the cell cycle that differs from mitosis and occurs in specific tissues of different organisms. Endoreplicating cells generally undergo multiple rounds of genome replication without chromosome segregation. Previous studies demonstrated that Drosophila fizzy-related protein (Fzr) and its mammalian homolog Cdh1 function as key regulators of endoreplication entrance by activating the anaphase-promoting complex/cyclosome to initiate the ubiquitination and subsequent degradation of cell cycle factors such as Cyclin B (CycB). However, the molecular mechanism underlying Fzr-mediated endoreplication is not completely understood. In this study, we demonstrated that the transcription factor Myc acts downstream of Fzr during endoreplication in Drosophila salivary gland. Mechanistically, Fzr interacts with chromatin-associated histone H2B to enhance H2B ubiquitination in the Myc promoter and promotes Myc transcription. In addition to negatively regulating CycB transcription, the Fzr-ubiquitinated H2B (H2Bub)-Myc signaling cascade also positively regulates the transcription of the MCM6 gene that is involved in DNA replication by directly binding to specific motifs within their promoters. We further found that the Fzr-H2Bub-Myc signaling cascade regulating endoreplication progression is conserved between insects and mammalian cells. Altogether, our work uncovers a novel transcriptional cascade that is involved in Fzr-mediated endoreplication.
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Affiliation(s)
- Wenliang Qian
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Zheng Li
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Wei Song
- Medical Research Institute, Wuhan University, Wuhan 430071, China.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Tujing Zhao
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Weina Wang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Jian Peng
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Ling Wei
- School of Life Science, Southwest University, Chongqing 400715, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Daojun Cheng
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
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28
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Valle BL, Rodriguez-Torres S, Kuhn E, Díaz-Montes T, Parrilla-Castellar E, Lawson FP, Folawiyo O, Ili-Gangas C, Brebi-Mieville P, Eshleman JR, Herman J, Shih IM, Sidransky D, Guerrero-Preston R. HIST1H2BB and MAGI2 Methylation and Somatic Mutations as Precision Medicine Biomarkers for Diagnosis and Prognosis of High-grade Serous Ovarian Cancer. Cancer Prev Res (Phila) 2020; 13:783-794. [PMID: 32581010 DOI: 10.1158/1940-6207.capr-19-0412] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 04/15/2020] [Accepted: 06/11/2020] [Indexed: 12/23/2022]
Abstract
Molecular alterations that contribute to long-term (LT) and short-term (ST) survival in ovarian high-grade serous carcinoma (HGSC) may be used as precision medicine biomarkers. DNA promoter methylation is an early event in tumorigenesis, which can be detected in blood and urine, making it a feasible companion biomarker to somatic mutations for early detection and targeted treatment workflows. We compared the methylation profile in 12 HGSC tissue samples to 30 fallopian tube epithelium samples, using the Infinium Human Methylation 450K Array. We also used 450K methylation arrays to compare methylation among HGSCs long-term survivors (more than 5 years) and short-term survivors (less than 3 years). We verified the array results using bisulfite sequencing and methylation-specific PCR (qMSP). in another cohort of HGSC patient samples (n = 35). Immunoblot and clonogenic assays after pharmacologic unmasking show that HIST1H2BB and MAGI2 promoter methylation downregulates mRNA expression levels in ovarian cancer cells. We then used qMSP in paired tissue, ascites, plasma/serum, vaginal swabs, and urine from a third cohort of patients with HGSC cancer (n = 85) to test the clinical potential of HIST1H2BB and MAGI2 in precision medicine workflows. We also performed next-generation exome sequencing of 50 frequently mutated in human cancer genes, using the Ion AmpliSeqCancer Hotspot Panel, to show that the somatic mutation profile found in tissue and plasma can be quantified in paired urine samples from patients with HGSC. Our results suggest that HIST1H2BB and MAGI2 have growth-suppressing roles and can be used as HGSC precision medicine biomarkers.
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Affiliation(s)
- Blanca L Valle
- Otolaryngology Department, Head and Neck Cancer Research Division, The Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Sebastian Rodriguez-Torres
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania
| | - Elisabetta Kuhn
- Division of Pathology, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico; Department of Biomedical, Surgical, and Dental Sciences, University of Milan, Italy.,Departments of Pathology, Gynecology and Obstetrics, The Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Teresa Díaz-Montes
- The Lya Segall Ovarian Cancer Institute, Mercy Medical Center, Baltimore, Maryland
| | | | - Fahcina P Lawson
- Otolaryngology Department, Head and Neck Cancer Research Division, The Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Oluwasina Folawiyo
- Otolaryngology Department, Head and Neck Cancer Research Division, The Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Carmen Ili-Gangas
- Laboratory Integrative Biology (LIBi), Center for Excellence in Translational Medicine-Scientific and Technological Bioresources Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Priscilla Brebi-Mieville
- Laboratory Integrative Biology (LIBi), Center for Excellence in Translational Medicine-Scientific and Technological Bioresources Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco, Chile
| | - James R Eshleman
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - James Herman
- Department of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania
| | - Ie-Ming Shih
- Division of Pathology, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico; Department of Biomedical, Surgical, and Dental Sciences, University of Milan, Italy
| | - David Sidransky
- Otolaryngology Department, Head and Neck Cancer Research Division, The Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Rafael Guerrero-Preston
- Otolaryngology Department, Head and Neck Cancer Research Division, The Johns Hopkins University, School of Medicine, Baltimore, Maryland. .,University of Puerto Rico School of Medicine, Department of Obstetrics and Gynecology, San Juan, Puerto Rico.,LifeGene Biomarks Inc., San Juan, Puerto Rico
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29
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Fiore A, Liang Y, Lin YH, Tung J, Wang H, Langlais D, Nijnik A. Deubiquitinase MYSM1 in the Hematopoietic System and beyond: A Current Review. Int J Mol Sci 2020; 21:ijms21083007. [PMID: 32344625 PMCID: PMC7216186 DOI: 10.3390/ijms21083007] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/19/2020] [Accepted: 04/20/2020] [Indexed: 01/21/2023] Open
Abstract
MYSM1 has emerged as an important regulator of hematopoietic stem cell function, blood cell production, immune response, and other aspects of mammalian physiology. It is a metalloprotease family protein with deubiquitinase catalytic activity, as well as SANT and SWIRM domains. MYSM1 normally localizes to the nucleus, where it can interact with chromatin and regulate gene expression, through deubiquitination of histone H2A and non-catalytic contacts with other transcriptional regulators. A cytosolic form of MYSM1 protein was also recently described and demonstrated to regulate signal transduction pathways of innate immunity, by promoting the deubiquitination of TRAF3, TRAF6, and RIP2. In this work we review the current knowledge on the molecular mechanisms of action of MYSM1 protein in transcriptional regulation, signal transduction, and potentially other cellular processes. The functions of MYSM1 in different cell types and aspects of mammalian physiology are also reviewed, highlighting the key checkpoints in hematopoiesis, immunity, and beyond regulated by MYSM1. Importantly, mutations in MYSM1 in human were recently linked to a rare hereditary disorder characterized by leukopenia, anemia, and other hematopoietic and developmental abnormalities. Our growing knowledge of MYSM1 functions and mechanisms of actions sheds important insights into its role in mammalian physiology and the etiology of the MYSM1-deficiency disorder in human.
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Affiliation(s)
- Amanda Fiore
- Department of Physiology, McGill University, Montreal, QC 3655, Canada; (A.F.); (Y.L.); (Y.H.L.); (J.T.); (H.W.)
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
| | - Yue Liang
- Department of Physiology, McGill University, Montreal, QC 3655, Canada; (A.F.); (Y.L.); (Y.H.L.); (J.T.); (H.W.)
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
| | - Yun Hsiao Lin
- Department of Physiology, McGill University, Montreal, QC 3655, Canada; (A.F.); (Y.L.); (Y.H.L.); (J.T.); (H.W.)
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
| | - Jacky Tung
- Department of Physiology, McGill University, Montreal, QC 3655, Canada; (A.F.); (Y.L.); (Y.H.L.); (J.T.); (H.W.)
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
| | - HanChen Wang
- Department of Physiology, McGill University, Montreal, QC 3655, Canada; (A.F.); (Y.L.); (Y.H.L.); (J.T.); (H.W.)
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
- Department of Human Genetics, McGill University, Montreal, QC 3640, Canada
| | - David Langlais
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
- Department of Human Genetics, McGill University, Montreal, QC 3640, Canada
- McGill University Genome Centre, Montreal, QC 740, Canada
| | - Anastasia Nijnik
- Department of Physiology, McGill University, Montreal, QC 3655, Canada; (A.F.); (Y.L.); (Y.H.L.); (J.T.); (H.W.)
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
- Correspondence: ; Tel.: +1-514-398-5567
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Nardi IK, Stark JM, Larsen A, Salgia R, Raz DJ. USP22 Interacts with PALB2 and Promotes Chemotherapy Resistance via Homologous Recombination of DNA Double-Strand Breaks. Mol Cancer Res 2019; 18:424-435. [PMID: 31685642 PMCID: PMC9285637 DOI: 10.1158/1541-7786.mcr-19-0053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/15/2019] [Accepted: 10/29/2019] [Indexed: 11/16/2022]
Abstract
Homologous recombination (HR) is a highly conserved pathway that can facilitate the repair of DNA double-strand breaks (DSB). Several Deubiquitinases (DUB) have been implicated as key players in DNA damage repair (DDR) through HR. Here, we report USP22, a DUB that is highly overexpressed in multiple cancer types, is necessary for HR through a direct interaction with PALB2 through its C-terminal WD40 domain. This interaction stimulates USP22 catalytic activity in vitro. Furthermore, we show USP22 is necessary for BRCA2, PALB2, and Rad51 recruitment to DSBs and this is, in part, through USP22 stabilizing BRCA2 and PALB2 levels. Taken together, our results describe a role for USP22 in DNA repair. IMPLICATIONS: This research provides new and exciting mechanistic insights into how USP22 overexpression promotes chemoresistance in lung cancer. We believe this study, and others, will help aid in developing targeted drugs toward USP22 and known binding partners for lung cancer treatment.
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Affiliation(s)
- Isaac K Nardi
- Division of Thoracic Surgery, Baum Family Thoracic Oncology Laboratory, City of Hope National Medical Center, Duarte, California.
- Beckman Research Institute, City of Hope National Medical Center, Duarte, California
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center, Duarte, California
| | - Adrien Larsen
- Department of Computational Therapeutics, City of Hope National Medical Center, Duarte, California
| | - Ravi Salgia
- Department of Medical Oncology, City of Hope National Medical Center, Duarte, California
| | - Dan J Raz
- Division of Thoracic Surgery, Baum Family Thoracic Oncology Laboratory, City of Hope National Medical Center, Duarte, California
- Beckman Research Institute, City of Hope National Medical Center, Duarte, California
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Oya E, Nakagawa R, Yoshimura Y, Tanaka M, Nishibuchi G, Machida S, Shirai A, Ekwall K, Kurumizaka H, Tagami H, Nakayama J. H3K14 ubiquitylation promotes H3K9 methylation for heterochromatin assembly. EMBO Rep 2019; 20:e48111. [PMID: 31468675 PMCID: PMC6776926 DOI: 10.15252/embr.201948111] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 08/07/2019] [Accepted: 08/09/2019] [Indexed: 12/28/2022] Open
Abstract
The methylation of histone H3 at lysine 9 (H3K9me), performed by the methyltransferase Clr4/SUV39H, is a key event in heterochromatin assembly. In fission yeast, Clr4, together with the ubiquitin E3 ligase Cul4, forms the Clr4 methyltransferase complex (CLRC), whose physiological targets and biological role are currently unclear. Here, we show that CLRC-dependent H3 ubiquitylation regulates Clr4's methyltransferase activity. Affinity-purified CLRC ubiquitylates histone H3, and mass spectrometric and mutation analyses reveal that H3 lysine 14 (H3K14) is the preferred target of the complex. Chromatin immunoprecipitation analysis shows that H3K14 ubiquitylation (H3K14ub) is closely associated with H3K9me-enriched chromatin. Notably, the CLRC-mediated H3 ubiquitylation promotes H3K9me by Clr4, suggesting that H3 ubiquitylation is intimately linked to the establishment and/or maintenance of H3K9me. These findings demonstrate a cross-talk mechanism between histone ubiquitylation and methylation that is involved in heterochromatin assembly.
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Affiliation(s)
- Eriko Oya
- Graduate School of Natural SciencesNagoya City UniversityNagoyaJapan
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
- Present address:
Faculty of Science and EngineeringChuo UniversityBunkyo‐ku, TokyoJapan
| | - Reiko Nakagawa
- Laboratory for PhyloinformaticsRIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Yuriko Yoshimura
- Division of Chromatin RegulationNational Institute for Basic BiologyOkazakiJapan
| | - Mayo Tanaka
- Division of Chromatin RegulationNational Institute for Basic BiologyOkazakiJapan
| | - Gohei Nishibuchi
- Graduate School of Natural SciencesNagoya City UniversityNagoyaJapan
- Present address:
Graduate School of ScienceOsaka UniversityToyonakaJapan
| | - Shinichi Machida
- Laboratory of Structural BiologyGraduate School of Advanced Science and EngineeringWaseda UniversityShinjuku‐ku, TokyoJapan
- Present address:
Institute of Human GeneticsCNRS UMR 9002MontpellierFrance
| | | | - Karl Ekwall
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
| | - Hitoshi Kurumizaka
- Laboratory of Structural BiologyGraduate School of Advanced Science and EngineeringWaseda UniversityShinjuku‐ku, TokyoJapan
- Laboratory of Chromatin Structure and FunctionInstitute for Quantitative BiosciencesThe University of TokyoBunkyo‐ku, TokyoJapan
| | - Hideaki Tagami
- Graduate School of Natural SciencesNagoya City UniversityNagoyaJapan
| | - Jun‐ichi Nakayama
- Graduate School of Natural SciencesNagoya City UniversityNagoyaJapan
- Division of Chromatin RegulationNational Institute for Basic BiologyOkazakiJapan
- Department of Basic BiologySchool of Life ScienceThe Graduate University for Advanced Studies (SOKENDAI)OkazakiJapan
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Huang M, Zhou B, Gong J, Xing L, Ma X, Wang F, Wu W, Shen H, Sun C, Zhu X, Yang Y, Sun Y, Liu Y, Tang TS, Guo C. RNA-splicing factor SART3 regulates translesion DNA synthesis. Nucleic Acids Res 2019; 46:4560-4574. [PMID: 29590477 PMCID: PMC5961147 DOI: 10.1093/nar/gky220] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/15/2018] [Indexed: 12/15/2022] Open
Abstract
Translesion DNA synthesis (TLS) is one mode of DNA damage tolerance that uses specialized DNA polymerases to replicate damaged DNA. DNA polymerase η (Polη) is well known to facilitate TLS across ultraviolet (UV) irradiation and mutations in POLH are implicated in skin carcinogenesis. However, the basis for recruitment of Polη to stalled replication forks is not completely understood. In this study, we used an affinity purification approach to isolate a Polη-containing complex and have identified SART3, a pre-mRNA splicing factor, as a critical regulator to modulate the recruitment of Polη and its partner RAD18 after UV exposure. We show that SART3 interacts with Polη and RAD18 via its C-terminus. Moreover, SART3 can form homodimers to promote the Polη/RAD18 interaction and PCNA monoubiquitination, a key event in TLS. Depletion of SART3 also impairs UV-induced single-stranded DNA (ssDNA) generation and RPA focus formation, resulting in an impaired Polη recruitment and a higher mutation frequency and hypersensitivity after UV treatment. Notably, we found that several SART3 missense mutations in cancer samples lessen its stimulatory effect on PCNA monoubiquitination. Collectively, our findings establish SART3 as a novel Polη/RAD18 association regulator that protects cells from UV-induced DNA damage, which functions in a RNA binding-independent fashion.
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Affiliation(s)
- Min Huang
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Bo Zhou
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Juanjuan Gong
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Lingyu Xing
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaolu Ma
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Fengli Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Wu
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongyan Shen
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Chenyi Sun
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuefei Zhu
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Yeran Yang
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Yazhou Sun
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Yang Liu
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Tie-Shan Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Caixia Guo
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
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33
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van Welsem T, Korthout T, Ekkebus R, Morais D, Molenaar TM, van Harten K, Poramba-Liyanage DW, Sun SM, Lenstra TL, Srivas R, Ideker T, Holstege FCP, van Attikum H, El Oualid F, Ovaa H, Stulemeijer IJE, Vlaming H, van Leeuwen F. Dot1 promotes H2B ubiquitination by a methyltransferase-independent mechanism. Nucleic Acids Res 2019; 46:11251-11261. [PMID: 30203048 PMCID: PMC6265471 DOI: 10.1093/nar/gky801] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/27/2018] [Indexed: 12/16/2022] Open
Abstract
The histone methyltransferase Dot1 is conserved from yeast to human and methylates lysine 79 of histone H3 (H3K79) on the core of the nucleosome. H3K79 methylation by Dot1 affects gene expression and the response to DNA damage, and is enhanced by monoubiquitination of the C-terminus of histone H2B (H2Bub1). To gain more insight into the functions of Dot1, we generated genetic interaction maps of increased-dosage alleles of DOT1. We identified a functional relationship between increased Dot1 dosage and loss of the DUB module of the SAGA co-activator complex, which deubiquitinates H2Bub1 and thereby negatively regulates H3K79 methylation. Increased Dot1 dosage was found to promote H2Bub1 in a dose-dependent manner and this was exacerbated by the loss of SAGA-DUB activity, which also caused a negative genetic interaction. The stimulatory effect on H2B ubiquitination was mediated by the N-terminus of Dot1, independent of methyltransferase activity. Our findings show that Dot1 and H2Bub1 are subject to bi-directional crosstalk and that Dot1 possesses chromatin regulatory functions that are independent of its methyltransferase activity.
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Affiliation(s)
- Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Tessy Korthout
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Reggy Ekkebus
- Division of Cell Biology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Dominique Morais
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Thom M Molenaar
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Kirsten van Harten
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | | | - Su Ming Sun
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Tineke L Lenstra
- Molecular Cancer Research, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands
| | - Rohith Srivas
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Trey Ideker
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Frank C P Holstege
- Molecular Cancer Research, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | | | - Huib Ovaa
- Division of Cell Biology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Iris J E Stulemeijer
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Hanneke Vlaming
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
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Keren I, Lapidot M, Citovsky V. Coordinate activation of a target gene by KDM1C histone demethylase and OTLD1 histone deubiquitinase in Arabidopsis. Epigenetics 2019; 14:602-610. [PMID: 30964380 DOI: 10.1080/15592294.2019.1603982] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Potential functional coordination between histone deubiquitinases and histone lysine demethylases represents one of the least studied aspects of epigenetic control of transcriptional outcomes. Here, this question was addressed using Arabidopsis histone modification erasers deubiquitinase OTLD1 and demethylase KDM1C known to interact with each other in plant cells. Characterization of gain- and loss-of-function mutants of OTLD1 and KDM1C showed that both enzymes associate with the promoter chromatin of their target gene AN3 and function as coactivators of its expression. This transcriptional outcome was underlain by demethylation of the H3K9 repression mark, presumably by the KDM1C histone demethylase activity. Association of KDM1C and OTLD1 with the target chromatin was interdependent such that OTLD1 was not detected at the AN3 in the absence of KDM1C and KDM1C displayed a different and non-functional pattern of association in the absence of OTLD1. Thus, OTLD1 and KDM1C may crosstalk with each other to assemble a functional coactivator complex at the AN3 promoter chromatin and set the KDM1C specificity for the methylated H3K9 to determine the correct transcriptional outcome.
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Affiliation(s)
- Ido Keren
- a Department of Biochemistry and Cell Biology , State University of New York , Stony Brook , NY , USA
| | - Moshe Lapidot
- b Department of Vegetable Research , Institute of Plant Sciences, ARO, Volcani Center , Bet Dagan , Israel
| | - Vitaly Citovsky
- a Department of Biochemistry and Cell Biology , State University of New York , Stony Brook , NY , USA
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35
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Zhao W, Neyt P, Van Lijsebettens M, Shen WH, Berr A. Interactive and noninteractive roles of histone H2B monoubiquitination and H3K36 methylation in the regulation of active gene transcription and control of plant growth and development. THE NEW PHYTOLOGIST 2019; 221:1101-1116. [PMID: 30156703 DOI: 10.1111/nph.15418] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/27/2018] [Indexed: 05/23/2023]
Abstract
Covalent modifications of histones are essential to control a wide range of processes during development and adaptation to environmental changes. With the establishment of reference epigenomes, patterns of histone modifications were correlated with transcriptionally active or silenced genes. These patterns imply the need for the precise and dynamic coordination of different histone-modifying enzymes to control transcription at a given gene. Classically, the influence of these enzymes on gene expression is examined separately and their interplays rarely established. In Arabidopsis, HISTONE MONOUBIQUITINATION2 (HUB2) mediates H2B monoubiquitination (H2Bub1), whereas SET DOMAIN GROUP8 (SDG8) catalyzes H3 lysine 36 trimethylation (H3K36me3). In this work, we crossed hub2 with sdg8 mutants to elucidate their functional relationships. Despite similar phenotypic defects, sdg8 and hub2 mutations broadly affect genome transcription and plant growth and development synergistically. Also, whereas H3K4 methylation appears largely dependent on H2Bub1, H3K36me3 and H2Bub1 modifications mutually reinforce each other at some flowering time genes. In addition, SDG8 and HUB2 jointly antagonize the increase of the H3K27me3 repressive mark. Collectively, our data provide an important insight into the interplay between histone marks and highlight their interactive complexity in regulating chromatin landscape which might be necessary to fine-tune transcription and ensure plant developmental plasticity.
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Affiliation(s)
- Wei Zhao
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France
| | - Pia Neyt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Mieke Van Lijsebettens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France
| | - Alexandre Berr
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France
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36
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Pisanu S, Cubeddu T, Cacciotto C, Pilicchi Y, Pagnozzi D, Uzzau S, Rocca S, Addis MF. Characterization of paucibacillary ileal lesions in sheep with subclinical active infection by Mycobacterium avium subsp. paratuberculosis. Vet Res 2018; 49:117. [PMID: 30514405 PMCID: PMC6278003 DOI: 10.1186/s13567-018-0612-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/13/2018] [Indexed: 01/10/2023] Open
Abstract
Paratuberculosis (PTB) or Johne's disease is a contagious enteritis of ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP). Ovine PTB is less understood than bovine PTB, especially concerning paucibacillary infection and its evolution into clinical disease. We combined shotgun proteomics, histopathology and immunohistochemistry for the characterization of ileal tissues collected from seven asymptomatic sheep negative to serum ELISA, positive to feces and tissue MAP IS900 and F57 PCR, histologically classified as paucibacillary, actively infected, together with 3 MAP-free controls (K). Following shotgun proteomics with label-free quantitation and differential analysis, 96 proteins were significantly changed in PTB vs K, and were mostly involved in immune defense processes and in the macrophage-MAP interaction. Principal component analysis (PCA) of protein abundances highlighted two PTB sample clusters, PTB1 and PTB2, indicating a dichotomy in their proteomic profiles. This was in line with the PCA of histopathology data and was related to features of type 2 (PTB1) and type 3a (PTB2) lesions, respectively. PTB2 proteomes differed more than PTB1 proteomes from K: 43 proteins changed significantly only in PTB2 and 11 only in PTB1. The differential proteins cathelicidin, haptoglobin, S100A8 and S100A9 were evaluated by immunohistochemistry. K tissues were negative to cathelicidin and haptoglobin and sparsely positive to S100A8 and S100A9. PTB tissues were positive to all four proteins, with significantly more cells in PTB2 than in PTB1. In conclusion, we described several pathways altered in paucibacillary PTB, highlighted some proteomic differences among paucibacillary PTB cases, and identified potential markers for disease understanding, staging, and detection.
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Affiliation(s)
- Salvatore Pisanu
- Porto Conte Ricerche, SP 55 Porto Conte/Capo Caccia, Km 8.400, Loc. Tramariglio, 07041, Alghero, Italy
| | - Tiziana Cubeddu
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Carla Cacciotto
- Porto Conte Ricerche, SP 55 Porto Conte/Capo Caccia, Km 8.400, Loc. Tramariglio, 07041, Alghero, Italy
| | - Ylenia Pilicchi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Daniela Pagnozzi
- Porto Conte Ricerche, SP 55 Porto Conte/Capo Caccia, Km 8.400, Loc. Tramariglio, 07041, Alghero, Italy
| | - Sergio Uzzau
- Porto Conte Ricerche, SP 55 Porto Conte/Capo Caccia, Km 8.400, Loc. Tramariglio, 07041, Alghero, Italy.,Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Viale S. Pietro 43/B, 07100, Sassari, Italy
| | - Stefano Rocca
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Maria Filippa Addis
- Porto Conte Ricerche, SP 55 Porto Conte/Capo Caccia, Km 8.400, Loc. Tramariglio, 07041, Alghero, Italy. .,Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Via Celoria 10, 20133, Milan, Italy.
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Rad6-Bre1 mediated histone H2Bub1 protects uncapped telomeres from exonuclease Exo1 in Saccharomyces cerevisiae. DNA Repair (Amst) 2018; 72:64-76. [PMID: 30254011 DOI: 10.1016/j.dnarep.2018.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/22/2018] [Accepted: 09/14/2018] [Indexed: 12/11/2022]
Abstract
Histone H2B lysine 123 mono-ubiquitination (H2Bub1), catalyzed by Rad6 and Bre1 in Saccharomyces cerevisiae, modulates chromatin structure and affects diverse cellular functions. H2Bub1 plays roles in telomeric silencing and telomere replication. Here, we have explored a novel role of H2Bub1 in telomere protection at uncapped telomeres in yku70Δ and cdc13-1 cells. Deletion of RAD6 or BRE1, or mutation of H2BK123R enhances the temperature sensitivity of both yku70Δ and cdc13-1 telomere capping mutants. Consistently, BRE1 deletion increases accumulation of telomeric single-stranded DNA (ssDNA) in yku70Δ and cdc13-1 cells, and EXO1 deletion improves the growth of yku70Δ bre1Δ and cdc13-1 bre1Δ cells and decreases ssDNA accumulation. Additionally, deletion of BRE1 exacerbates the rate of entry into senescence of yku70Δ mre11Δ cells with telomere defects, and increases the recombination of subtelomeric Y' element that is required for telomere maintenance and survivor generation. Furthermore, Exo1 contributes to the abrupt senescence of yku70Δ mre11Δ bre1Δ cells, and Rad51 is essential for Y' recombination to generate survivors. Finally, deletion of BRE1 or mutation of H2BK123R results in nucleosome instability at subtelomeric regions. Collectively, this study provides a mechanistic link between H2Bub1-mediated chromatin structure and telomere protection after telomere uncapping.
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38
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Jarome TJ, Devulapalli RK. The Ubiquitin-Proteasome System and Memory: Moving Beyond Protein Degradation. Neuroscientist 2018. [DOI: 10.1177/1073858418762317] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cellular models of memory formation have focused on the need for protein synthesis. Recently, evidence has emerged that protein degradation mediated by the ubiquitin-proteasome system (UPS) is also important for this process. This has led to revised cellular models of memory formation that focus on a balance between protein degradation and synthesis. However, protein degradation is only one function of the UPS. Studies using single-celled organisms have shown that non-proteolytic ubiquitin-proteasome signaling is involved in histone modifications and DNA methylation, suggesting that ubiquitin and the proteasome can regulate chromatin remodeling independent of protein degradation. Despite this evidence, the idea that the UPS is more than a protein degradation pathway has not been examined in the context of memory formation. In this article, we summarize recent findings implicating protein degradation in memory formation and discuss various ways in which both ubiquitin signaling and the proteasome could act independently to regulate epigenetic-mediated transcriptional processes necessary for learning-dependent synaptic plasticity. We conclude by proposing comprehensive models of how non-proteolytic functions of the UPS could work in concert to control epigenetic regulation of the cellular memory consolidation process, which will serve as a framework for future studies examining the role of the UPS in memory formation.
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Affiliation(s)
- Timothy J. Jarome
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Rishi K. Devulapalli
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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39
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Somasagara RR, Spencer SM, Tripathi K, Clark DW, Mani C, da Silva LM, Scalici J, Kothayer H, Westwell AD, Rocconi RP, Palle K. RAD6 promotes DNA repair and stem cell signaling in ovarian cancer and is a promising therapeutic target to prevent and treat acquired chemoresistance. Oncogene 2017; 36:6680-6690. [PMID: 28806395 PMCID: PMC5709226 DOI: 10.1038/onc.2017.279] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/14/2017] [Accepted: 07/07/2017] [Indexed: 12/28/2022]
Abstract
Ovarian cancer (OC) is the most deadly gynecological cancer and unlike most other neoplasms, survival rates for OC have not significantly improved in recent decades. We show that RAD6, an ubiquitin-conjugating enzyme, is significantly overexpressed in ovarian tumors and its expression increases in response to carboplatin chemotherapy. RAD6 expression correlated strongly with acquired chemoresistance and malignant behavior of OC cells, expression of stem cell genes and poor prognosis of OC patients, suggesting an important role for RAD6 in ovarian tumor progression. Upregulated RAD6 enhances DNA damage tolerance and repair efficiency of OC cells and promotes their survival. Increased RAD6 levels cause histone 2B ubiquitination-mediated epigenetic changes that stimulate transcription of stem cell genes, including ALDH1A1 and SOX2, leading to a cancer stem cell phenotype, which is implicated in disease recurrence and metastasis. Downregulation of RAD6 or its inhibition using a small molecule inhibitor attenuated DNA repair signaling and expression of cancer stem cells markers and sensitized chemoresistant OC cells to carboplatin. Together, these results suggest that RAD6 could be a therapeutic target to prevent and treat acquired chemoresistance and disease recurrence in OC and enhance the efficacy of standard chemotherapy.
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Affiliation(s)
- Ranganatha R. Somasagara
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, Alabama 36604, USA
| | - Sebastian M. Spencer
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, Alabama 36604, USA
| | - Kaushlendra Tripathi
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, Alabama 36604, USA
| | - David W. Clark
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, Alabama 36604, USA
| | - Chinnadurai Mani
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, Alabama 36604, USA
| | - Luciana Madeira da Silva
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, Alabama 36604, USA
| | - Jennifer Scalici
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, Alabama 36604, USA
| | - Hend Kothayer
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Egypt
| | - Andrew D. Westwell
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff CF10 3NB, Wales, UK
| | - Rodney P. Rocconi
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, Alabama 36604, USA
| | - Komaraiah Palle
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, Alabama 36604, USA
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40
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The evolutionarily conserved factor Sus1/ENY2 plays a role in telomere length maintenance. Curr Genet 2017; 64:635-644. [DOI: 10.1007/s00294-017-0778-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 11/26/2022]
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41
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Wu Z, Liu J, Zhang QD, Lv DK, Wu NF, Zhou JQ. Rad6-Bre1-mediated H2B ubiquitination regulates telomere replication by promoting telomere-end resection. Nucleic Acids Res 2017; 45:3308-3322. [PMID: 28180293 PMCID: PMC5389628 DOI: 10.1093/nar/gkx101] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 02/08/2017] [Indexed: 12/20/2022] Open
Abstract
Rad6 and Bre1, ubiquitin-conjugating E2 and E3 enzymes respectively, are responsible for histone H2B lysine 123 mono-ubiquitination (H2Bub1) in Saccharomyces cerevisiae. Previous studies have shown that Rad6 and Bre1 regulate telomere length and recombination. However, the underlying molecular mechanism remains largely unknown. Here we report that H2BK123 mutation results in telomere shortening, while inactivation of Ubp8 and/or Ubp10, deubiquitinases of H2Bub1, leads to telomere lengthening in Rad6–Bre1-dependent manner. In telomerase-deficient cells, inactivation of Rad6–Bre1 pathway retards telomere shortening rate and the onset of senescence, while deletion of UBP8 and/or UBP10 accelerates senescence. Thus, Rad6–Bre1 pathway regulates both telomere length and recombination through its role in H2Bub1. Additionally, inactivation of both Rad6–Bre1–H2Bub1 and Mre11–Rad50–Xrs2 (MRX) pathways causes synthetic growth defects and telomere shortening in telomerase-proficient cells, and significantly accelerates senescence and eliminates type II telomere recombination in telomerase-deficient cells. Furthermore, RAD6 or BRE1 deletion, or H2BK123R mutation decreases the accumulation of ssDNA at telomere ends. These results support the model that Rad6–Bre1–H2Bub1 cooperates with MRX to promote telomere-end resection and thus positively regulates both telomerase- and recombination-dependent telomere replication. This study provides a mechanistic link between histone H2B ubiquitination and telomere replication.
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Affiliation(s)
- Zhenfang Wu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Jun Liu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Qiong-Di Zhang
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - De-Kang Lv
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Nian-Feng Wu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Jin-Qiu Zhou
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.,School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, China
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Hyun K, Jeon J, Park K, Kim J. Writing, erasing and reading histone lysine methylations. Exp Mol Med 2017; 49:e324. [PMID: 28450737 PMCID: PMC6130214 DOI: 10.1038/emm.2017.11] [Citation(s) in RCA: 700] [Impact Index Per Article: 100.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 02/08/2023] Open
Abstract
Histone modifications are key epigenetic regulatory features that have important roles in many cellular events. Lysine methylations mark various sites on the tail and globular domains of histones and their levels are precisely balanced by the action of methyltransferases ('writers') and demethylases ('erasers'). In addition, distinct effector proteins ('readers') recognize specific methyl-lysines in a manner that depends on the neighboring amino-acid sequence and methylation state. Misregulation of histone lysine methylation has been implicated in several cancers and developmental defects. Therefore, histone lysine methylation has been considered a potential therapeutic target, and clinical trials of several inhibitors of this process have shown promising results. A more detailed understanding of histone lysine methylation is necessary for elucidating complex biological processes and, ultimately, for developing and improving disease treatments. This review summarizes enzymes responsible for histone lysine methylation and demethylation and how histone lysine methylation contributes to various biological processes.
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Affiliation(s)
- Kwangbeom Hyun
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jongcheol Jeon
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Kihyun Park
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jaehoon Kim
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
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Chen S, Jing Y, Kang X, Yang L, Wang DL, Zhang W, Zhang L, Chen P, Chang JF, Yang XM, Sun FL. Histone H2B monoubiquitination is a critical epigenetic switch for the regulation of autophagy. Nucleic Acids Res 2017; 45:1144-1158. [PMID: 28180298 PMCID: PMC5388390 DOI: 10.1093/nar/gkw1025] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 10/08/2016] [Accepted: 10/19/2016] [Indexed: 12/16/2022] Open
Abstract
Autophagy is an evolutionarily conserved cellular process that primarily participates in lysosome-mediated protein degradation. Although autophagy is a cytoplasmic event, how epigenetic pathways are involved in the regulation of autophagy remains incompletely understood. Here, we found that H2B monoubiquitination (H2Bub1) is down-regulated in cells under starvation conditions and that the decrease in H2Bub1 results in the activation of autophagy. We also identified that the deubiquitinase USP44 is responsible for the starvation-induced decrease in H2Bub1. Furthermore, the changes in H2Bub1 affect the transcription of genes involved in the regulation of autophagy. Therefore, this study reveals a novel epigenetic pathway for the regulation of autophagy through H2Bub1.
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Affiliation(s)
- Su Chen
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
- School of Forensic Sciences, Xi'an Jiao Tong University Health Science Center, Xi'an, Shaanxi 710061, PR China
- Department of Science and Education, People's Hospital of Zunhua, Tangshan, Hebei 064200, PR China
| | - Yuanya Jing
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Xuan Kang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Lu Yang
- Research Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiao Tong University, Shaanxi 710061, PR China
| | - Da-Liang Wang
- School of Medicine, Tsinghua University, Beijing 100084, PR China
| | - Wei Zhang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Lei Zhang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Ping Chen
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Jian-Feng Chang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Xiao-Mei Yang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Fang-Lin Sun
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
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44
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Circulating Nucleosomes and Nucleosome Modifications as Biomarkers in Cancer. Cancers (Basel) 2017; 9:cancers9010005. [PMID: 28075351 PMCID: PMC5295776 DOI: 10.3390/cancers9010005] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 12/31/2016] [Accepted: 01/01/2017] [Indexed: 12/17/2022] Open
Abstract
Traditionally the stratification of many cancers involves combining tumour and clinicopathological features (e.g., patient age; tumour size, grade, receptor status and location) to inform treatment options and predict recurrence risk and survival. However, current biomarkers often require invasive excision of the tumour for profiling, do not allow monitoring of the response to treatment and stratify patients into broad heterogeneous groups leading to inconsistent treatment responses. Here we explore and describe the benefits of using circulating biomarkers (nucleosomes and/or modifications to nucleosomes) as a non-invasive method for detecting cancer and monitoring response to treatment. Nucleosomes (DNA wound around eight core histone proteins) are responsible for compacting our genome and their composition and post-translational modifications are responsible for regulating gene expression. Here, we focus on breast and colorectal cancer as examples where utilizing circulating nucleosomes as biomarkers hold real potential as liquid biopsies. Utilizing circulating nucleosomes as biomarkers is an exciting new area of research that promises to allow both the early detection of cancer and monitoring of treatment response. Nucleosome-based biomarkers combine with current biomarkers, increasing both specificity and sensitivity of current tests and have the potential to provide individualised precision-medicine based treatments for patients.
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45
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CRL4(Wdr70) regulates H2B monoubiquitination and facilitates Exo1-dependent resection. Nat Commun 2016; 7:11364. [PMID: 27098497 PMCID: PMC4844679 DOI: 10.1038/ncomms11364] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 03/18/2016] [Indexed: 01/16/2023] Open
Abstract
Double-strand breaks repaired by homologous recombination (HR) are first resected to form single-stranded DNA, which binds replication protein A (RPA). RPA attracts mediators that load the Rad51 filament to promote strand invasion, the defining feature of HR. How the resection machinery navigates nucleosome-packaged DNA is poorly understood. Here we report that in Schizosaccharomyces pombe a conserved DDB1-CUL4-associated factor (DCAF), Wdr70, is recruited to DSBs as part of the Cullin4-DDB1 ubiquitin ligase (CRL4(Wdr70)) and stimulates distal H2B lysine 119 mono-ubiquitination (uH2B). Wdr70 deletion, or uH2B loss, results in increased loading of the checkpoint adaptor and resection inhibitor Crb2(53BP1), decreased Exo1 association and delayed resection. Wdr70 is dispensable for resection upon Crb2(53BP1) loss, or when the Set9 methyltransferase that creates docking sites for Crb2 is deleted. Finally, we establish that this histone regulatory cascade similarly controls DSB resection in human cells.
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46
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Krasnov AN, Mazina MY, Nikolenko JV, Vorobyeva NE. On the way of revealing coactivator complexes cross-talk during transcriptional activation. Cell Biosci 2016; 6:15. [PMID: 26913181 PMCID: PMC4765067 DOI: 10.1186/s13578-016-0081-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 02/09/2016] [Indexed: 08/07/2023] Open
Abstract
Transcriptional activation is a complex, multistage process implemented by hundreds of proteins. Many transcriptional proteins are organized into coactivator complexes, which participate in transcription regulation at numerous genes and are a driver of this process. The molecular action mechanisms of coactivator complexes remain largely understudied. Relevant publications usually deal with the involvement of these complexes in the entire process of transcription, and only a few studies are aimed to elucidate their functions at its particular stages. This review summarizes available information on the participation of key coactivator complexes in transcriptional activation. The timing of coactivator complex binding/removal has been used for restructuring previously described information about the transcriptional process. Several major stages of transcriptional activation have been distinguished based on the presence of covalent histone modifications and general transcriptional factors, and the recruitment and/or removal phases have been determined for each coactivator included in analysis. Recruitment of Mediator, SWItch/Sucrose Non-Fermentable and NUcleosome Remodeling Factor complexes during transcription activation has been investigated thoroughly; CHD and INOsitol auxotrophy 80 families are less well studied. In most cases, the molecular mechanisms responsible for the removal of certain coactivator complexes after the termination of their functions at the promoters are still not understood. On the basis of the summarized information, we propose a scheme that illustrates the involvement of coactivator complexes in different stages of the transcription activation process. This scheme may help to gain a deeper insight into the molecular mechanism of functioning of coactivator complexes, find novel participants of the process, and reveal novel structural or functional connections between different coactivators.
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Affiliation(s)
- Aleksey N Krasnov
- Department of Transcription Regulation and Chromatin Dynamic, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - Marina Yu Mazina
- Department of Transcription Regulation and Chromatin Dynamic, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - Julia V Nikolenko
- Department of Transcription Regulation and Chromatin Dynamic, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - Nadezhda E Vorobyeva
- Department of Transcription Regulation and Chromatin Dynamic, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
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Fahrenkrog B. Histone modifications as regulators of life and death in Saccharomyces cerevisiae. MICROBIAL CELL 2015; 3:1-13. [PMID: 28357312 PMCID: PMC5354586 DOI: 10.15698/mic2016.01.472] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Apoptosis or programmed cell death is an integrated, genetically controlled
suicide program that not only regulates tissue homeostasis of multicellular
organisms, but also the fate of damaged and aged cells of lower eukaryotes, such
as the yeast Saccharomyces cerevisiae. Recent years have
revealed key apoptosis regulatory proteins in yeast that play similar roles in
mammalian cells. Apoptosis is a process largely defined by characteristic
structural rearrangements in the dying cell that include chromatin condensation
and DNA fragmentation. The mechanism by which chromosomes restructure during
apoptosis is still poorly understood, but it is becoming increasingly clear that
altered epigenetic histone modifications are fundamental parameters that
influence the chromatin state and the nuclear rearrangements within apoptotic
cells. The present review will highlight recent work on the epigenetic
regulation of programmed cell death in budding yeast.
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Affiliation(s)
- Birthe Fahrenkrog
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, Rue Profs. Jeener et Brachet 12; 6041 Charleroi, Belgium
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48
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Boriack-Sjodin PA, Swinger KK. Protein Methyltransferases: A Distinct, Diverse, and Dynamic Family of Enzymes. Biochemistry 2015; 55:1557-69. [PMID: 26652298 DOI: 10.1021/acs.biochem.5b01129] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methyltransferase proteins make up a superfamily of enzymes that add one or more methyl groups to substrates that include protein, DNA, RNA, and small molecules. The subset of proteins that act upon arginine and lysine side chains are characterized as epigenetic targets because of their activity on histone molecules and their ability to affect transcriptional regulation. However, it is now clear that these enzymes target other protein substrates, as well, greatly expanding their potential impact on normal and disease biology. Protein methyltransferases are well-characterized structurally. In addition to revealing the overall architecture of the subfamilies of enzymes, structures of complexes with substrates and ligands have permitted detailed analysis of biochemical mechanism, substrate recognition, and design of potent and selective inhibitors. This review focuses on how knowledge gained from structural studies has impacted the understanding of this large class of epigenetic enzymes.
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Affiliation(s)
- P Ann Boriack-Sjodin
- Epizyme, Inc. , 400 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Kerren K Swinger
- Epizyme, Inc. , 400 Technology Square, Cambridge, Massachusetts 02139, United States
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49
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Abstract
DNA in human cells is constantly assaulted by endogenous and exogenous DNA damaging agents. It is vital for the cell to respond rapidly and precisely to DNA damage to maintain genome integrity and reduce the risk of mutagenesis. Sophisticated reactions occur in chromatin surrounding the damaged site leading to the activation of DNA damage response (DDR), including transcription reprogramming, cell cycle checkpoint, and DNA repair. Histone proteins around the DNA damage play essential roles in DDR, through extensive post-translational modifications (PTMs) by a variety of modifying enzymes. One PTM on histones, mono-ubiquitylation, has emerged as a key player in cellular response to DNA damage. In this review, we will (1) briefly summarize the history of histone H2A and H2B ubiquitylation (H2Aub and H2Bub, respectively), (2) discuss their roles in transcription, and (3) their functions in DDR.
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50
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Murray SC, Haenni S, Howe FS, Fischl H, Chocian K, Nair A, Mellor J. Sense and antisense transcription are associated with distinct chromatin architectures across genes. Nucleic Acids Res 2015; 43:7823-37. [PMID: 26130720 PMCID: PMC4652749 DOI: 10.1093/nar/gkv666] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 06/18/2015] [Indexed: 11/15/2022] Open
Abstract
Genes from yeast to mammals are frequently subject to non-coding transcription of their antisense strand; however the genome-wide role for antisense transcription remains elusive. As transcription influences chromatin structure, we took a genome-wide approach to assess which chromatin features are associated with nascent antisense transcription, and contrast these with features associated with nascent sense transcription. We describe a distinct chromatin architecture at the promoter and gene body specifically associated with antisense transcription, marked by reduced H2B ubiquitination, H3K36 and H3K79 trimethylation and increased levels of H3 acetylation, chromatin remodelling enzymes, histone chaperones and histone turnover. The difference in sense transcription between genes with high or low levels of antisense transcription is slight; thus the antisense transcription-associated chromatin state is not simply analogous to a repressed state. Using mutants in which the level of antisense transcription is reduced at GAL1, or altered genome-wide, we show that non-coding transcription is associated with high H3 acetylation and H3 levels across the gene, while reducing H3K36me3. Set1 is required for these antisense transcription-associated chromatin changes in the gene body. We propose that nascent antisense and sense transcription have fundamentally distinct relationships with chromatin, and that both should be considered canonical features of eukaryotic genes.
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Affiliation(s)
- Struan C Murray
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Simon Haenni
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Françoise S Howe
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Harry Fischl
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Karolina Chocian
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Anitha Nair
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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