1
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Ekstrom TL, Hussain S, Bedekovics T, Ali A, Paolini L, Mahmood H, Rosok RM, Koster J, Johnsen SA, Galardy PJ. USP44 Overexpression Drives a MYC-Like Gene Expression Program in Neuroblastoma through Epigenetic Reprogramming. Mol Cancer Res 2024; 22:812-825. [PMID: 38775808 PMCID: PMC11372370 DOI: 10.1158/1541-7786.mcr-23-0454] [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: 06/05/2023] [Revised: 04/05/2024] [Accepted: 05/20/2024] [Indexed: 09/05/2024]
Abstract
Neuroblastoma is an embryonic cancer that contributes disproportionately to death in young children. Sequencing data have uncovered few recurrently mutated genes in this cancer, although epigenetic pathways have been implicated in disease pathogenesis. We used an expression-based computational screen that examined the impact of deubiquitinating enzymes on patient survival to identify potential new targets. We identified the histone H2B deubiquitinating enzyme USP44 as the enzyme with the greatest impact on survival in patients with neuroblastoma. High levels of USP44 significantly correlate with metastatic disease, unfavorable histology, advanced patient age, and MYCN amplification. The subset of patients with tumors expressing high levels of USP44 had significantly worse survival, including those with tumors lacking MYCN amplification. We showed experimentally that USP44 regulates neuroblastoma cell proliferation, migration, invasion, and neuronal development. Depletion of the histone H2B ubiquitin ligase subunit RNF20 resulted in similar findings, strongly implicating this histone mark as the target of USP44 activity in this disease. Integration of transcriptome and epigenome in analyses demonstrates a distinct set of genes that are regulated by USP44, including those in Hallmark MYC target genes in both murine embryonic fibroblasts and the SH-SY5Y neuroblastoma cell line. We conclude that USP44 is a novel epigenetic regulator that promotes aggressive features and may be a novel target in neuroblastoma. Implications: This study identifies a new genetic marker of aggressive neuroblastoma and identifies the mechanisms by which its overactivity contributes to the pathophysiology of this disease.
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Affiliation(s)
- Thomas L Ekstrom
- Mayo Clinic Graduate School of Biomedical Sciences, Rochester, Minnesota
- Robert Bosch Center for Tumor Diseases, Stuttgart, Germany
| | - Sajjad Hussain
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Family Medicine, Mayo Clinic, Rochester, Minnesota
| | - Tibor Bedekovics
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota
| | - Asma Ali
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota
| | - Lucia Paolini
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Pediatrics, University of Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Hina Mahmood
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota
| | - Raya M Rosok
- Robert Bosch Center for Tumor Diseases, Stuttgart, Germany
| | - Jan Koster
- Department of CEMM, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Paul J Galardy
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota
- Division of Pediatric Hematology-Oncology, Mayo Clinic, Rochester, Minnesota
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2
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Ghate NB, Nadkarni KS, Barik GK, Tat SS, Sahay O, Santra MK. Histone ubiquitination: Role in genome integrity and chromatin organization. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195044. [PMID: 38763317 DOI: 10.1016/j.bbagrm.2024.195044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/21/2024]
Abstract
Maintenance of genome integrity is a precise but tedious and complex job for the cell. Several post-translational modifications (PTMs) play vital roles in maintaining the genome integrity. Although ubiquitination is one of the most crucial PTMs, which regulates the localization and stability of the nonhistone proteins in various cellular and developmental processes, ubiquitination of the histones is a pivotal epigenetic event critically regulating chromatin architecture. In addition to genome integrity, importance of ubiquitination of core histones (H2A, H2A, H3, and H4) and linker histone (H1) have been reported in several cellular processes. However, the complex interplay of histone ubiquitination and other PTMs, as well as the intricate chromatin architecture and dynamics, pose a significant challenge to unravel how histone ubiquitination safeguards genome stability. Therefore, further studies are needed to elucidate the interactions between histone ubiquitination and other PTMs, and their role in preserving genome integrity. Here, we review all types of histone ubiquitinations known till date in maintaining genomic integrity during transcription, replication, cell cycle, and DNA damage response processes. In addition, we have also discussed the role of histone ubiquitination in regulating other histone PTMs emphasizing methylation and acetylation as well as their potential implications in chromatin architecture. Further, we have also discussed the involvement of deubiquitination enzymes (DUBs) in controlling histone ubiquitination in modulating cellular processes.
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Affiliation(s)
- Nikhil Baban Ghate
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India.
| | - Kaustubh Sanjay Nadkarni
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Ganesh Kumar Barik
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Sharad Shriram Tat
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Osheen Sahay
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Manas Kumar Santra
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India.
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3
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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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4
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Mensah IK, Gowher H. Epigenetic Regulation of Mammalian Cardiomyocyte Development. EPIGENOMES 2024; 8:25. [PMID: 39051183 PMCID: PMC11270418 DOI: 10.3390/epigenomes8030025] [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: 05/07/2024] [Revised: 06/07/2024] [Accepted: 06/25/2024] [Indexed: 07/27/2024] Open
Abstract
The heart is the first organ formed during mammalian development and functions to distribute nutrients and oxygen to other parts of the developing embryo. Cardiomyocytes are the major cell types of the heart and provide both structural support and contractile function to the heart. The successful differentiation of cardiomyocytes during early development is under tight regulation by physical and molecular factors. We have reviewed current studies on epigenetic factors critical for cardiomyocyte differentiation, including DNA methylation, histone modifications, chromatin remodelers, and noncoding RNAs. This review also provides comprehensive details on structural and morphological changes associated with the differentiation of fetal and postnatal cardiomyocytes and highlights their differences. A holistic understanding of all aspects of cardiomyocyte development is critical for the successful in vitro differentiation of cardiomyocytes for therapeutic purposes.
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Affiliation(s)
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
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5
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Dong B, Wang X, Song X, Wang J, Liu X, Yu Z, Zhou Y, Deng J, Wu Y. RNF20 contributes to epigenetic immunosuppression through CDK9-dependent LSD1 stabilization. Proc Natl Acad Sci U S A 2024; 121:e2307150121. [PMID: 38315842 PMCID: PMC10873621 DOI: 10.1073/pnas.2307150121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 12/28/2023] [Indexed: 02/07/2024] Open
Abstract
Cyclin-dependent kinase 9 (CDK9) plays a critical role in transcription initiation and is essential for maintaining gene silencing at heterochromatic loci. Inhibition of CDK9 increases sensitivity to immunotherapy, but the underlying mechanism remains unclear. We now report that RNF20 stabilizes LSD1 via K29-mediated ubiquitination, which is dependent on CDK9-mediated phosphorylation. This CDK9- and RNF20-dependent LSD1 stabilization is necessary for the demethylation of histone H3K4, then subsequent repression of endogenous retrovirus, and an interferon response, leading to epigenetic immunosuppression. Moreover, we found that loss of RNF20 sensitizes cancer cells to the immune checkpoint inhibitor anti-PD-1 in vivo and that this effect can be rescued by the expression of ectopic LSD1. Our findings are supported by the observation that RNF20 levels correlate with LSD1 levels in human breast cancer specimens. This study sheds light on the role of RNF20 in CDK9-dependent LSD1 stabilization, which is crucial for epigenetic silencing and immunosuppression. Our findings explore the potential importance of targeting the CDK9-RNF20-LSD1 axis in the development of new cancer therapies.
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Affiliation(s)
- Bo Dong
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY40508
- Markey Cancer Center, College of Medicine, University of Kentucky, Lexington, KY40508
| | - Xinzhao Wang
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY40508
- Markey Cancer Center, College of Medicine, University of Kentucky, Lexington, KY40508
- Department of Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong250355, People’s Republic of China
| | - Xiang Song
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY40508
- Markey Cancer Center, College of Medicine, University of Kentucky, Lexington, KY40508
- Department of Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong250355, People’s Republic of China
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong250355, People’s Republic of China
| | - Jianlin Wang
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY40508
- Markey Cancer Center, College of Medicine, University of Kentucky, Lexington, KY40508
| | - Xia Liu
- Markey Cancer Center, College of Medicine, University of Kentucky, Lexington, KY40508
| | - Zhiyong Yu
- Department of Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong250355, People’s Republic of China
| | - Yongkun Zhou
- Department of Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong250355, People’s Republic of China
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong250355, People’s Republic of China
| | - Jiong Deng
- Medical Research Institute, Binzhou Medical University Hospital, Binzhou256600, People’s Republic of China
| | - Yadi Wu
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY40508
- Markey Cancer Center, College of Medicine, University of Kentucky, Lexington, KY40508
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6
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Barish S, Berg K, Drozd J, Berglund-Brown I, Khizir L, Wasson LK, Seidman CE, Seidman JG, Chen S, Brueckner M. The H2Bub1-deposition complex is required for human and mouse cardiogenesis. Development 2023; 150:dev201899. [PMID: 38038666 PMCID: PMC10730087 DOI: 10.1242/dev.201899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 10/10/2023] [Indexed: 12/02/2023]
Abstract
De novo variants affecting monoubiquitylation of histone H2B (H2Bub1) are enriched in human congenital heart disease. H2Bub1 is required in stem cell differentiation, cilia function, post-natal cardiomyocyte maturation and transcriptional elongation. However, how H2Bub1 affects cardiogenesis is unknown. We show that the H2Bub1-deposition complex (RNF20-RNF40-UBE2B) is required for mouse cardiogenesis and for differentiation of human iPSCs into cardiomyocytes. Mice with cardiac-specific Rnf20 deletion are embryonic lethal and have abnormal myocardium. We then analyzed H2Bub1 marks during differentiation of human iPSCs into cardiomyocytes. H2Bub1 is erased from most genes at the transition from cardiac mesoderm to cardiac progenitor cells but is preserved on a subset of long cardiac-specific genes. When H2Bub1 is reduced in iPSC-derived cardiomyocytes, long cardiac-specific genes have fewer full-length transcripts. This correlates with H2Bub1 accumulation near the center of these genes. H2Bub1 accumulation near the center of tissue-specific genes was also observed in embryonic fibroblasts and fetal osteoblasts. In summary, we show that normal H2Bub1 distribution is required for cardiogenesis and cardiomyocyte differentiation, and suggest that H2Bub1 regulates tissue-specific gene expression by increasing the amount of full-length transcripts.
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Affiliation(s)
- Syndi Barish
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Kathryn Berg
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Jeffrey Drozd
- Department of Pediatrics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Isabella Berglund-Brown
- Department of Pediatrics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Labeeqa Khizir
- Department of Pediatrics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Lauren K. Wasson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard University, Boston, MA 02115, USA
| | | | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Martina Brueckner
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
- Department of Pediatrics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
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7
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Prokakis E, Jansari S, Boshnakovska A, Wiese M, Kusch K, Kramm C, Dullin C, Rehling P, Glatzel M, Pantel K, Wikman H, Johnsen SA, Gallwas J, Wegwitz F. RNF40 epigenetically modulates glycolysis to support the aggressiveness of basal-like breast cancer. Cell Death Dis 2023; 14:641. [PMID: 37770435 PMCID: PMC10539310 DOI: 10.1038/s41419-023-06157-5] [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: 12/05/2022] [Revised: 09/06/2023] [Accepted: 09/15/2023] [Indexed: 09/30/2023]
Abstract
Triple-negative breast cancer (TNBC) is the most difficult breast cancer subtype to treat due to the lack of targeted therapies. Cancer stem cells (CSCs) are strongly enriched in TNBC lesions and are responsible for the rapid development of chemotherapy resistance and metastasis. Ubiquitin-based epigenetic circuits are heavily exploited by CSCs to regulate gene transcription and ultimately sustain their aggressive behavior. Therefore, therapeutic targeting of these ubiquitin-driven dependencies may reprogram the transcription of CSC and render them more sensitive to standard therapies. In this work, we identified the Ring Finger Protein 40 (RNF40) monoubiquitinating histone 2B at lysine 120 (H2Bub1) as an indispensable E3 ligase for sustaining the stem-cell-like features of the growing mammary gland. In addition, we found that the RNF40/H2Bub1-axis promotes the CSC properties and drug-tolerant state by supporting the glycolytic program and promoting pro-tumorigenic YAP1-signaling in TNBC. Collectively, this study unveils a novel tumor-supportive role of RNF40 and underpins its high therapeutic value to combat the malignant behavior of TNBC.
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Affiliation(s)
- Evangelos Prokakis
- Department of Gynecology and Obstetrics, University Medical Center Göttingen, Göttingen, Germany.
- Department of General, Visceral & Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany.
| | - Shaishavi Jansari
- Department of Gynecology and Obstetrics, University Medical Center Göttingen, Göttingen, Germany
| | - Angela Boshnakovska
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Maria Wiese
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Kathrin Kusch
- Institute for Auditory Neuroscience, Functional Auditory Genomics Group, University Medical Center Göttingen, Göttingen, Germany
| | - Christof Kramm
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Christian Dullin
- Institute for Diagnostic and Interventional Radiology, University Medical Center Göttingen, Göttingen, Germany
- Department of Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Pantel
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Harriet Wikman
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Steven A Johnsen
- Department of General, Visceral & Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
- The Robert Bosch Center for Tumor Diseases, Stuttgart, Germany
| | - Julia Gallwas
- Department of Gynecology and Obstetrics, University Medical Center Göttingen, Göttingen, Germany
| | - Florian Wegwitz
- Department of Gynecology and Obstetrics, University Medical Center Göttingen, Göttingen, Germany.
- Department of General, Visceral & Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany.
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8
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Xu T, Li ZY, Liu M, Zhang SB, Ding HH, Wu JY, Lin SY, Liu J, Wei JY, Zhang XQ, Xin WJ. CircFhit Modulates GABAergic Synaptic Transmission via Regulating the Parental Gene Fhit Expression in the Spinal Dorsal Horn in a Rat Model of Neuropathic Pain. Neurosci Bull 2023; 39:947-961. [PMID: 36637791 PMCID: PMC10264304 DOI: 10.1007/s12264-022-01014-5] [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: 06/26/2022] [Accepted: 09/12/2022] [Indexed: 01/14/2023] Open
Abstract
Effective treatments for neuropathic pain are lacking due to our limited understanding of the mechanisms. The circRNAs are mainly enriched in the central nervous system. However, their function in various physiological and pathological conditions have yet to be determined. Here, we identified circFhit, an exon-intron circRNA expressed in GABAergic neurons, which reduced the inhibitory synaptic transmission in the spinal dorsal horn to mediate spared nerve injury-induced neuropathic pain. Moreover, we found that circFhit decreased the expression of GAD65 and induced hyperexcitation in NK1R+ neurons by promoting the expression of its parental gene Fhit in cis. Mechanistically, circFhit was directly bound to the intronic region of Fhit, and formed a circFhit/HNRNPK complex to promote Pol II phosphorylation and H2B monoubiquitination by recruiting CDK9 and RNF40 to the Fhit intron. In summary, we revealed that the exon-intron circFhit contributes to GABAergic neuron-mediated NK1R+ neuronal hyperexcitation and neuropathic pain via regulating Fhit in cis.
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Affiliation(s)
- Ting Xu
- Neuroscience Program of Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Sun Yat-sen University, Guangzhou, 510120, China
| | - Zhen-Yu Li
- Neuroscience Program of Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Sun Yat-sen University, Guangzhou, 510120, China
| | - Meng Liu
- Department of Anesthesia and Pain Medicine, Guangzhou First People's Hospital, Guangzhou, 510000, China
| | - Su-Bo Zhang
- Neuroscience Program of Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Huan-Huan Ding
- Department of Physiology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Jia-Yan Wu
- Neuroscience Program of Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Sun Yat-sen University, Guangzhou, 510120, China
| | - Su-Yan Lin
- Department of Neurology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510000, China.
| | - Jun Liu
- Department of Neurology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510000, China
| | - Jia-You Wei
- Neuroscience Program of Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Engineering Research Center of Molecular Imaging, Guangdong Provincial Key Laboratory of Biomedical Imaging, and Department of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Xue-Qin Zhang
- The Affiliated Brain Hospital (Guangzhou Huiai Hospital) and School of Health Management, Guangzhou Medical University, Guangzhou, 510182, China.
| | - Wen-Jun Xin
- Neuroscience Program of Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China.
- Guangdong Province Key Laboratory of Brain Function and Disease, Sun Yat-sen University, Guangzhou, 510120, China.
- Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangzhou, 510000, China.
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9
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Dietlein N, Wang X, Metz J, Disson O, Shang F, Beyersdörffer C, Rodríguez Correa E, Lipka DB, Begus-Nahrmann Y, Kosinsky RL, Johnsen SA, Lecuit M, Höfer T, Rodewald HR. Usp22 is an intracellular regulator of systemic emergency hematopoiesis. Sci Immunol 2022; 7:eabq2061. [PMID: 36490327 DOI: 10.1126/sciimmunol.abq2061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Emergency hematopoiesis is a concerted response aimed toward enhanced protection from infection, involving multiple cell types and developmental stages across the immune system. Despite its importance, the underlying molecular regulation remains poorly understood. The deubiquitinase USP22 regulates the levels of monoubiquitinated histone H2B (H2Bub1), which is associated with activation of interferon responses upon viral infection. Here, we show that in the absence of infection or inflammation, mice lacking Usp22 in all hematopoietic cells display profound systemic emergency hematopoiesis, evident by increased hematopoietic stem cell proliferation, myeloid bias, and extramedullary hematopoiesis. Functionally, loss of Usp22 results in elevated phagocytosis by neutrophilic granulocytes and enhanced innate protection against Listeria monocytogenes infection. At the molecular level, we found this state of emergency hematopoiesis associated with transcriptional signatures of myeloid priming, enhanced mitochondrial respiration, and innate and adaptive immunity and inflammation. Augmented expression of many inflammatory genes was linked to elevated locus-specific H2Bub1 levels. Collectively, these results demonstrate the existence of a tunable epigenetic state that promotes systemic emergency hematopoiesis in a cell-autonomous manner to enhance innate protection, identifying potential paths toward immune enhancement.
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Affiliation(s)
- Nikolaus Dietlein
- Division of Cellular Immunology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
| | - Xi Wang
- Division of Cellular Immunology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, China
| | - Jonas Metz
- Faculty of Biosciences, Heidelberg University, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany.,Division of Theoretical Systems Biology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Olivier Disson
- Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, 75015 Paris, France
| | - Fuwei Shang
- Division of Cellular Immunology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Faculty of Medicine, Heidelberg University, Im Neuenheimer Feld 672, 69120 Heidelberg, Germany
| | - Celine Beyersdörffer
- Division of Cellular Immunology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Esther Rodríguez Correa
- Division of Cellular Immunology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Daniel B Lipka
- Section Translational Cancer Epigenomics, Department of Translational Medical Oncology, German Cancer Research Center and National Center for Tumor Diseases, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany.,Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany
| | - Yvonne Begus-Nahrmann
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany
| | - Robyn Laura Kosinsky
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA
| | - Steven A Johnsen
- Robert Bosch Center for Tumor Diseases, Stuttgart, Germany.,Department of General, Visceral & Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Marc Lecuit
- Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, 75015 Paris, France.,Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France.,Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, APHP, Institut Imagine, 75006 Paris, France
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Hans-Reimer Rodewald
- Division of Cellular Immunology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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10
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Characterizing and exploiting the many roles of aberrant H2B monoubiquitination in cancer pathogenesis. Semin Cancer Biol 2022; 86:782-798. [PMID: 34953650 DOI: 10.1016/j.semcancer.2021.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/08/2021] [Accepted: 12/19/2021] [Indexed: 01/27/2023]
Abstract
Monoubiquitination of histone H2B on lysine 120 (H2Bub1) is implicated in the control of multiple essential processes, including transcription, DNA damage repair and mitotic chromosome segregation. Accordingly, aberrant regulation of H2Bub1 can induce transcriptional reprogramming and genome instability that may promote oncogenesis. Remarkably, alterations of the ubiquitin ligases and deubiquitinating enzymes regulating H2Bub1 are emerging as ubiquitous features in cancer, further supporting the possibility that the misregulation of H2Bub1 is an underlying mechanism contributing to cancer pathogenesis. To date, aberrant H2Bub1 dynamics have been reported in multiple cancer types and are associated with transcriptional changes that promote oncogenesis in a cancer type-specific manner. Owing to the multi-functional nature of H2Bub1, misregulation of its writers and erasers may drive disease initiation and progression through additional synergistic processes. Accordingly, understanding the molecular determinants and pathogenic impacts associated with aberrant H2Bub1 regulation may reveal novel drug targets and therapeutic vulnerabilities that can be exploited to develop innovative precision medicine strategies that better combat cancer. In this review, we present the normal functions of H2Bub1 in the control of DNA-associated processes and describe the pathogenic implications associated with its misregulation in cancer. We further discuss the challenges coupled with the development of therapeutic strategies targeting H2Bub1 misregulation and expose the potential benefits of designing treatments that synergistically exploit the multiple functionalities of H2Bub1 to improve treatment selectivity and efficacy.
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11
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Oss-Ronen L, Sarusi T, Cohen I. Histone Mono-Ubiquitination in Transcriptional Regulation and Its Mark on Life: Emerging Roles in Tissue Development and Disease. Cells 2022; 11:cells11152404. [PMID: 35954248 PMCID: PMC9368181 DOI: 10.3390/cells11152404] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/26/2022] [Accepted: 08/02/2022] [Indexed: 02/06/2023] Open
Abstract
Epigenetic regulation plays an essential role in driving precise transcriptional programs during development and homeostasis. Among epigenetic mechanisms, histone mono-ubiquitination has emerged as an important post-transcriptional modification. Two major histone mono-ubiquitination events are the mono-ubiquitination of histone H2A at lysine 119 (H2AK119ub), placed by Polycomb repressive complex 1 (PRC1), and histone H2B lysine 120 mono-ubiquitination (H2BK120ub), placed by the heteromeric RNF20/RNF40 complex. Both of these events play fundamental roles in shaping the chromatin epigenetic landscape and cellular identity. In this review we summarize the current understandings of molecular concepts behind histone mono-ubiquitination, focusing on their recently identified roles in tissue development and pathologies.
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Affiliation(s)
| | | | - Idan Cohen
- Correspondence: ; Tel.: +972-8-6477593; Fax: +972-8-6477626
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12
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El-Saafin F, Devys D, Johnsen SA, Vincent SD, Tora L. SAGA-Dependent Histone H2Bub1 Deubiquitination Is Essential for Cellular Ubiquitin Balance during Embryonic Development. Int J Mol Sci 2022; 23:ijms23137459. [PMID: 35806465 PMCID: PMC9267394 DOI: 10.3390/ijms23137459] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 12/24/2022] Open
Abstract
Ubiquitin (ub) is a small, highly conserved protein widely expressed in eukaryotic cells. Ubiquitination is a post-translational modification catalyzed by enzymes that activate, conjugate, and ligate ub to proteins. Substrates can be modified either by addition of a single ubiquitin molecule (monoubiquitination), or by conjugation of several ubs (polyubiquitination). Monoubiquitination acts as a signaling mark to control diverse biological processes. The cellular and spatial distribution of ub is determined by the opposing activities of ub ligase enzymes, and deubiquitinases (DUBs), which remove ub from proteins to generate free ub. In mammalian cells, 1–2% of total histone H2B is monoubiquitinated. The SAGA (Spt Ada Gcn5 Acetyl-transferase) is a transcriptional coactivator and its DUB module removes ub from H2Bub1. The mammalian SAGA DUB module has four subunits, ATXN7, ATXN7L3, USP22, and ENY2. Atxn7l3−/− mouse embryos, lacking DUB activity, have a five-fold increase in H2Bub1 retention, and die at mid-gestation. Interestingly, embryos lacking the ub encoding gene, Ubc, have a similar phenotype. Here we provide a current overview of data suggesting that H2Bub1 retention on the chromatin in Atxn7l3−/− embryos may lead to an imbalance in free ub distribution. Thus, we speculate that ATXN7L3-containing DUBs impact the free cellular ub pool during development.
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Affiliation(s)
- Farrah El-Saafin
- Olivia Newton-John Cancer Research Institute, Melbourne 3095, Australia;
| | - 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
- Correspondence: (S.D.V.); (L.T.); Tel.: +33-3-88653425 (S.D.V.); +33-3-88653444 (L.T.)
| | - 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
- Correspondence: (S.D.V.); (L.T.); Tel.: +33-3-88653425 (S.D.V.); +33-3-88653444 (L.T.)
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13
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Chen Y, Zhou D, Yao Y, Sun Y, Yao F, Ma L. Monoubiquitination in Homeostasis and Cancer. Int J Mol Sci 2022; 23:ijms23115925. [PMID: 35682605 PMCID: PMC9180643 DOI: 10.3390/ijms23115925] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 02/06/2023] Open
Abstract
Monoubiquitination is a post-translational modification (PTM), through which a single ubiquitin molecule is covalently conjugated to a lysine residue of the target protein. Monoubiquitination regulates the activity, subcellular localization, protein-protein interactions, or endocytosis of the substrate. In doing so, monoubiquitination is implicated in diverse cellular processes, including gene transcription, endocytosis, signal transduction, cell death, and DNA damage repair, which in turn regulate cell-cycle progression, survival, proliferation, and stress response. In this review, we summarize the functions of monoubiquitination and discuss how this PTM modulates homeostasis and cancer.
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Affiliation(s)
- Yujie Chen
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China; (Y.C.); (D.Z.); (Y.Y.)
| | - Dandan Zhou
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China; (Y.C.); (D.Z.); (Y.Y.)
| | - Yinan Yao
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China; (Y.C.); (D.Z.); (Y.Y.)
| | - Yutong Sun
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Fan Yao
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China; (Y.C.); (D.Z.); (Y.Y.)
- Hubei Clinical Research Center for Precise Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
- Correspondence: (F.Y.); (L.M.)
| | - Li Ma
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Correspondence: (F.Y.); (L.M.)
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14
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PHF13 epigenetically activates TGFβ driven epithelial to mesenchymal transition. Cell Death Dis 2022; 13:487. [PMID: 35597793 PMCID: PMC9124206 DOI: 10.1038/s41419-022-04940-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 05/04/2022] [Accepted: 05/12/2022] [Indexed: 12/14/2022]
Abstract
Epigenetic alteration is a pivotal factor in tumor metastasis. PHD finger protein 13 (PHF13) is a recently identified epigenetic reader of H3K4me2/3 that functions as a transcriptional co-regulator. In this study, we demonstrate that PHF13 is required for pancreatic-cancer-cell growth and metastasis. Integrative analysis of transcriptome and epigenetic profiles provide further mechanistic insights into the epigenetic regulation of genes associated with cell metastasis during the epithelial-to-mesenchymal transition (EMT) induced by transforming growth factor β (TGFβ). Our data suggest PHF13 depletion impairs activation of TGFβ stimulated genes and correlates with a loss of active epigenetic marks (H3K4me3 and H3K27ac) at these genomic regions. These observations argue for a dependency of TGFβ target activation on PHF13. Furthermore, PHF13-dependent chromatin regions are enriched in broad H3K4me3 domains and super-enhancers, which control genes critical to cancer-cell migration and invasion, such as SNAI1 and SOX9. Overall, our data indicate a functional and mechanistic correlation between PHF13 and EMT.
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15
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Kosinsky RL, Zerche M, Kutschat AP, Nair A, Ye Z, Saul D, von Heesen M, Friton JJ, Schwarzer AC, Paglilla N, Sheikh SZ, Wegwitz F, Sun Z, Ghadimi M, Newberry RD, Sartor RB, Faubion WA, Johnsen SA. RNF20 and RNF40 regulate vitamin D receptor-dependent signaling in inflammatory bowel disease. Cell Death Differ 2021; 28:3161-3175. [PMID: 34088983 PMCID: PMC8563960 DOI: 10.1038/s41418-021-00808-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 05/07/2021] [Accepted: 05/12/2021] [Indexed: 02/04/2023] Open
Abstract
Despite the identification of several genetic factors linked to increased susceptibility to inflammatory bowel disease (IBD), underlying molecular mechanisms remain to be elucidated in detail. The ubiquitin ligases RNF20 and RNF40 mediate the monoubiquitination of histone H2B at lysine 120 (H2Bub1) and were shown to play context-dependent roles in the development of inflammation. Here, we aimed to examine the function of the RNF20/RNF40/H2Bub1 axis in intestinal inflammation in IBD patients and mouse models. For this purpose, intestinal sections from IBD patients were immunohistochemically stained for H2Bub1. Rnf20 or Rnf40 were conditionally deleted in the mouse intestine and mice were monitored for inflammation-associated symptoms. Using mRNA-seq and chromatin immunoprecipitation (ChIP)-seq, we analyzed underlying molecular pathways in primary intestinal epithelial cells (IECs) isolated from these animals and confirmed these findings in IBD resection specimens using ChIP-seq.The majority (80%) of IBD patients displayed a loss of H2Bub1 levels in inflamed areas and the intestine-specific deletion of Rnf20 or Rnf40 resulted in spontaneous colorectal inflammation in mice. Consistently, deletion of Rnf20 or Rnf40 promoted IBD-associated gene expression programs, including deregulation of various IBD risk genes in these animals. Further analysis of murine IECs revealed that H3K4me3 occupancy and transcription of the Vitamin D Receptor (Vdr) gene and VDR target genes is RNF20/40-dependent. Finally, these effects were confirmed in a subgroup of Crohn's disease patients which displayed epigenetic and expression changes in RNF20/40-dependent gene signatures. Our findings reveal that loss of H2B monoubiquitination promotes intestinal inflammation via decreased VDR activity thereby identifying RNF20 and RNF40 as critical regulators of IBD.
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Affiliation(s)
- Robyn Laura Kosinsky
- grid.66875.3a0000 0004 0459 167XDivision of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN USA
| | - Maria Zerche
- grid.411984.10000 0001 0482 5331Department of General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Ana Patricia Kutschat
- grid.411984.10000 0001 0482 5331Department of General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Asha Nair
- grid.66875.3a0000 0004 0459 167XDivision of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN USA
| | - Zhenqing Ye
- grid.66875.3a0000 0004 0459 167XDivision of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN USA
| | - Dominik Saul
- grid.66875.3a0000 0004 0459 167XKogod Center on Aging and Division of Endocrinology, Mayo Clinic, Rochester, MN USA
| | - Maximilian von Heesen
- grid.411984.10000 0001 0482 5331Department of General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Jessica J. Friton
- grid.66875.3a0000 0004 0459 167XDivision of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN USA
| | - Ana Carolina Schwarzer
- grid.411984.10000 0001 0482 5331Department of General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Nadia Paglilla
- grid.411984.10000 0001 0482 5331Department of General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Shehzad Z. Sheikh
- grid.10698.360000000122483208Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Florian Wegwitz
- grid.411984.10000 0001 0482 5331Department of General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Zhifu Sun
- grid.66875.3a0000 0004 0459 167XDivision of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN USA
| | - Michael Ghadimi
- grid.411984.10000 0001 0482 5331Department of General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Rodney D. Newberry
- grid.4367.60000 0001 2355 7002Division of Gastroenterology, Washington University School of Medicine, St. Louis, MO USA
| | - R. Balfour Sartor
- grid.10698.360000000122483208Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - William A. Faubion
- grid.66875.3a0000 0004 0459 167XDivision of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN USA
| | - Steven A. Johnsen
- grid.411984.10000 0001 0482 5331Department of General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Goettingen, Germany ,grid.66875.3a0000 0004 0459 167XGene Regulatory Mechanisms and Molecular Epigenetics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN USA
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16
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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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17
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Massively parallel in vivo CRISPR screening identifies RNF20/40 as epigenetic regulators of cardiomyocyte maturation. Nat Commun 2021; 12:4442. [PMID: 34290256 PMCID: PMC8295283 DOI: 10.1038/s41467-021-24743-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/02/2021] [Indexed: 02/06/2023] Open
Abstract
The forward genetic screen is a powerful, unbiased method to gain insights into biological processes, yet this approach has infrequently been used in vivo in mammals because of high resource demands. Here, we use in vivo somatic Cas9 mutagenesis to perform an in vivo forward genetic screen in mice to identify regulators of cardiomyocyte (CM) maturation, the coordinated changes in phenotype and gene expression that occur in neonatal CMs. We discover and validate a number of transcriptional regulators of this process. Among these are RNF20 and RNF40, which form a complex that monoubiquitinates H2B on lysine 120. Mechanistic studies indicate that this epigenetic mark controls dynamic changes in gene expression required for CM maturation. These insights into CM maturation will inform efforts in cardiac regenerative medicine. More broadly, our approach will enable unbiased forward genetics across mammalian organ systems.
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18
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Wang L, Xu Z, Wang L, Liu C, Wei H, Zhang R, Chen Y, Wang L, Liu W, Xiao S, Li W, Li W. Histone H2B ubiquitination mediated chromatin relaxation is essential for the induction of somatic cell reprogramming. Cell Prolif 2021; 54:e13080. [PMID: 34155716 PMCID: PMC8349662 DOI: 10.1111/cpr.13080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES Cell reprogramming has significant impacts on their potential application in regenerative medicine. Chromatin remodelling plays a very important role in cell reprogramming, but its underlying mechanism remains poorly understood. MATERIALS AND METHODS RNA-seq, quantitative RT-PCR and western blot analysis were applied to study the role of RNF20 and H2B ubiquitination during mouse somatic cell reprogramming. Chromatin structure and the recruitment of transcription factors were analysed by ChIP-seq, micrococcal nuclease sensitivity assays and immunofluorescence staining. RESULTS We show that RNF20 is highly expressed at the early stage of reprogramming along with the accumulation of H2B ubiquitination at the same stage, and Rnf20 knockout results in the failure of reprogramming at the initial stage but not the maturation and stabilization stages. RNA-seq showed that Rnf20 knockout mainly affects the early stage of cell reprogramming by impairing the transcription of MET-related genes and early pluripotency genes. Importantly, Rnf20 knockout results in a more compacted chromosomes structure in reprogrammable cells, suppressing the recruitment of reprogramming transcription factors to their proper locations on the chromosomes, and finally resulting in the failure of pluripotent gene network establishment. CONCLUSIONS Histone H2B ubiquitination mediated chromatin relaxation is essential for the induction of somatic cell reprogramming.
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Affiliation(s)
- Liying Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Zhiliang Xu
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Libin Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Huafang Wei
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Ruidan Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Yinghong Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Lina Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Wenwen Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Sai Xiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
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19
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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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20
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Su D, Wang W, Hou Y, Wang L, Yi X, Cao C, Wang Y, Gao H, Wang Y, Yang C, Liu B, Chen X, Wu X, Wu J, Yan D, Wei S, Han L, Liu S, Wang Q, Shi L, Shan L. Bimodal regulation of the PRC2 complex by USP7 underlies tumorigenesis. Nucleic Acids Res 2021; 49:4421-4440. [PMID: 33849069 PMCID: PMC8096222 DOI: 10.1093/nar/gkab209] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/01/2021] [Indexed: 12/27/2022] Open
Abstract
Although overexpression of EZH2, a catalytic subunit of the polycomb repressive complex 2 (PRC2), is an eminent feature of various cancers, the regulation of its abundance and function remains insufficiently understood. We report here that the PRC2 complex is physically associated with ubiquitin-specific protease USP7 in cancer cells where USP7 acts to deubiquitinate and stabilize EZH2. Interestingly, we found that USP7-catalyzed H2BK120ub1 deubiquitination is a prerequisite for chromatin loading of PRC2 thus H3K27 trimethylation, and this process is not affected by H2AK119 ubiquitination catalyzed by PRC1. Genome-wide analysis of the transcriptional targets of the USP7/PRC2 complex identified a cohort of genes including FOXO1 that are involved in cell growth and proliferation. We demonstrated that the USP7/PRC2 complex drives cancer cell proliferation and tumorigenesis in vitro and in vivo. We showed that the expression of both USP7 and EZH2 elevates during tumor progression, corresponding to a diminished FOXO1 expression, and the level of the expression of USP7 and EZH2 strongly correlates with histological grades and prognosis of tumor patients. These results reveal a dual role for USP7 in the regulation of the abundance and function of EZH2, supporting the pursuit of USP7 as a therapeutic target for cancer intervention.
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Affiliation(s)
- Dongxue Su
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China.,State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Wenjuan Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Yongqiang Hou
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Liyong Wang
- Core Facilities for Molecular Biology, Capital Medical University, Beijing 100069, China
| | - Xianfu Yi
- School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China
| | - Cheng Cao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yuejiao Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Huan Gao
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Yue Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Chao Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Beibei Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xing Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xiaodi Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Jiajing Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Dong Yan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Shuqi Wei
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Lulu Han
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Shumeng Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Qian Wang
- Tianjin Medical University Cancer Institute and Hospital, Tianjin Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin 300060, China
| | - Lei Shi
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Lin Shan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
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21
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Cole AJ, Dickson KA, Liddle C, Stirzaker C, Shah JS, Clifton-Bligh R, Marsh DJ. Ubiquitin chromatin remodelling after DNA damage is associated with the expression of key cancer genes and pathways. Cell Mol Life Sci 2021; 78:1011-1027. [PMID: 32458023 PMCID: PMC11072370 DOI: 10.1007/s00018-020-03552-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 04/17/2020] [Accepted: 05/13/2020] [Indexed: 12/12/2022]
Abstract
Modification of the cancer-associated chromatin landscape in response to therapeutic DNA damage influences gene expression and contributes to cell fate. The central histone mark H2Bub1 results from addition of a single ubiquitin on lysine 120 of histone H2B and is an important regulator of gene expression. Following treatment with a platinum-based chemotherapeutic, there is a reduction in global levels of H2Bub1 accompanied by an increase in levels of the tumor suppressor p53. Although total H2Bub1 decreases following DNA damage, H2Bub1 is enriched downstream of transcription start sites of specific genes. Gene-specific H2Bub1 enrichment was observed at a defined group of genes that clustered into cancer-related pathways and correlated with increased gene expression. H2Bub1-enriched genes encompassed fifteen p53 target genes including PPM1D, BTG2, PLK2, MDM2, CDKN1A and BBC3, genes related to ERK/MAPK signalling, those participating in nucleotide excision repair including XPC, and genes involved in the immune response and platinum drug resistance including POLH. Enrichment of H2Bub1 at key cancer-related genes may function to regulate gene expression and influence the cellular response to therapeutic DNA damage.
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Affiliation(s)
- Alexander J Cole
- Hormones and Cancer Group, Kolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, Sydney, NSW, Australia
- Department of Medicine, Magee Women's Cancer Research Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kristie-Ann Dickson
- Hormones and Cancer Group, Kolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, Sydney, NSW, Australia
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Christopher Liddle
- Storr Liver Centre, Westmead Institute for Medical Research and Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Clare Stirzaker
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, UNSW, Sydney, NSW, Australia
- St. Vincent's Clinical School, UNSW Medicine, UNSW, Sydney, NSW, Australia
| | - Jaynish S Shah
- Hormones and Cancer Group, Kolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, Sydney, NSW, Australia
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Roderick Clifton-Bligh
- Hormones and Cancer Group, Kolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, Sydney, NSW, Australia
| | - Deborah J Marsh
- Hormones and Cancer Group, Kolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, Sydney, NSW, Australia.
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
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22
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Marsh DJ, Ma Y, Dickson KA. Histone Monoubiquitination in Chromatin Remodelling: Focus on the Histone H2B Interactome and Cancer. Cancers (Basel) 2020; 12:E3462. [PMID: 33233707 PMCID: PMC7699835 DOI: 10.3390/cancers12113462] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 12/21/2022] Open
Abstract
Chromatin remodelling is a major mechanism by which cells control fundamental processes including gene expression, the DNA damage response (DDR) and ensuring the genomic plasticity required by stem cells to enable differentiation. The post-translational modification of histone H2B resulting in addition of a single ubiquitin, in humans at lysine 120 (K120; H2Bub1) and in yeast at K123, has key roles in transcriptional elongation associated with the RNA polymerase II-associated factor 1 complex (PAF1C) and in the DDR. H2Bub1 itself has been described as having tumour suppressive roles and a number of cancer-related proteins and/or complexes are recognised as part of the H2Bub1 interactome. These include the RING finger E3 ubiquitin ligases RNF20, RNF40 and BRCA1, the guardian of the genome p53, the PAF1C member CDC73, subunits of the switch/sucrose non-fermenting (SWI/SNF) chromatin remodelling complex and histone methyltransferase complexes DOT1L and COMPASS, as well as multiple deubiquitinases including USP22 and USP44. While globally depleted in many primary human malignancies, including breast, lung and colorectal cancer, H2Bub1 is selectively enriched at the coding region of certain highly expressed genes, including at p53 target genes in response to DNA damage, functioning to exercise transcriptional control of these loci. This review draws together extensive literature to cement a significant role for H2Bub1 in a range of human malignancies and discusses the interplay between key cancer-related proteins and H2Bub1-associated chromatin remodelling.
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Affiliation(s)
- Deborah J. Marsh
- Translational Oncology Group, Faculty of Science, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (Y.M.); (K.-A.D.)
- Kolling Institute, Faculty of Medicine and Health, Northern Clinical School, University of Sydney, Camperdown, NSW 2006, Australia
| | - Yue Ma
- Translational Oncology Group, Faculty of Science, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (Y.M.); (K.-A.D.)
| | - Kristie-Ann Dickson
- Translational Oncology Group, Faculty of Science, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (Y.M.); (K.-A.D.)
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23
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Epigenetic modification and a role for the E3 ligase RNF40 in cancer development and metastasis. Oncogene 2020; 40:465-474. [PMID: 33199825 PMCID: PMC7819849 DOI: 10.1038/s41388-020-01556-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 10/15/2020] [Accepted: 11/02/2020] [Indexed: 12/19/2022]
Abstract
RNF40 (OMIM: 607700) is a really interesting new gene (RING) finger E3 ubiquitin ligase containing multiple coiled-coil domains and a C-terminal RING finger motif, which engage in protein–DNA and protein–protein interactions. RNF40 encodes a polypeptide of 1001 amino acids with a predicted molecular mass of 113,678 Da. RNF40 and its paralog RNF20 form a stable heterodimer complex that can monoubiquitylate histone H2B at lysine 120 as well as other nonhistone proteins. Cancer is a major public health problem and the second leading cause of death. Through its protein ubiquitylation activity, RNF40 acts as a tumor suppressor or oncogene to play major epigenetic roles in cancer development, progression, and metastasis, highlighting the essential function of RNF40 and the importance of studying it. In this review, we summarize current knowledge about RNF40 gene structure and the role of RNF40 in histone H2B monoubiquitylation, DNA damage repair, apoptosis, cancer development, and metastasis. We also underscore challenges in applying this information to cancer prognosis and prevention and highlight the urgent need for additional investigations of RNF40 as a potential target for cancer therapeutics.
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24
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Wüst HM, Wegener A, Fröb F, Hartwig AC, Wegwitz F, Kari V, Schimmel M, Tamm ER, Johnsen SA, Wegner M, Sock E. Egr2-guided histone H2B monoubiquitination is required for peripheral nervous system myelination. Nucleic Acids Res 2020; 48:8959-8976. [PMID: 32672815 PMCID: PMC7498331 DOI: 10.1093/nar/gkaa606] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 12/30/2022] Open
Abstract
Schwann cells are the nerve ensheathing cells of the peripheral nervous system. Absence, loss and malfunction of Schwann cells or their myelin sheaths lead to peripheral neuropathies such as Charcot-Marie-Tooth disease in humans. During Schwann cell development and myelination chromatin is dramatically modified. However, impact and functional relevance of these modifications are poorly understood. Here, we analyzed histone H2B monoubiquitination as one such chromatin modification by conditionally deleting the Rnf40 subunit of the responsible E3 ligase in mice. Rnf40-deficient Schwann cells were arrested immediately before myelination or generated abnormally thin, unstable myelin, resulting in a peripheral neuropathy characterized by hypomyelination and progressive axonal degeneration. By combining sequencing techniques with functional studies we show that H2B monoubiquitination does not influence global gene expression patterns, but instead ensures selective high expression of myelin and lipid biosynthesis genes and proper repression of immaturity genes. This requires the specific recruitment of the Rnf40-containing E3 ligase by Egr2, the central transcriptional regulator of peripheral myelination, to its target genes. Our study identifies histone ubiquitination as essential for Schwann cell myelination and unravels new disease-relevant links between chromatin modifications and transcription factors in the underlying regulatory network.
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Affiliation(s)
- Hannah M Wüst
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstrasse 17, D-91054 Erlangen, Germany
| | - Amélie Wegener
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstrasse 17, D-91054 Erlangen, Germany
| | - Franziska Fröb
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstrasse 17, D-91054 Erlangen, Germany
| | - Anna C Hartwig
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstrasse 17, D-91054 Erlangen, Germany
| | - Florian Wegwitz
- Department of General, Visceral, and Pediatric Surgery, University Medical Center Göttingen, D-37075 Göttingen, Germany
| | - Vijayalakshmi Kari
- Department of General, Visceral, and Pediatric Surgery, University Medical Center Göttingen, D-37075 Göttingen, Germany
| | - Margit Schimmel
- Institut für Humananatomie und Embryologie, Universität Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
| | - Ernst R Tamm
- Institut für Humananatomie und Embryologie, Universität Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
| | - Steven A Johnsen
- Department of General, Visceral, and Pediatric Surgery, University Medical Center Göttingen, D-37075 Göttingen, Germany.,Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN, USA
| | - Michael Wegner
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstrasse 17, D-91054 Erlangen, Germany
| | - Elisabeth Sock
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstrasse 17, D-91054 Erlangen, Germany
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25
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Wegwitz F, Prokakis E, Pejkovska A, Kosinsky RL, Glatzel M, Pantel K, Wikman H, Johnsen SA. The histone H2B ubiquitin ligase RNF40 is required for HER2-driven mammary tumorigenesis. Cell Death Dis 2020; 11:873. [PMID: 33070155 PMCID: PMC7568723 DOI: 10.1038/s41419-020-03081-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/31/2022]
Abstract
The HER2-positive breast cancer subtype (HER2+-BC) displays a particularly aggressive behavior. Anti-HER2 therapies have significantly improved the survival of patients with HER2+-BC. However, a large number of patients become refractory to current targeted therapies, necessitating the development of new treatment strategies. Epigenetic regulators are commonly misregulated in cancer and represent attractive molecular therapeutic targets. Monoubiquitination of histone 2B (H2Bub1) by the heterodimeric ubiquitin ligase complex RNF20/RNF40 has been described to have tumor suppressor functions and loss of H2Bub1 has been associated with cancer progression. In this study, we utilized human tumor samples, cell culture models, and a mammary carcinoma mouse model with tissue-specific Rnf40 deletion and identified an unexpected tumor-supportive role of RNF40 in HER2+-BC. We demonstrate that RNF40-driven H2B monoubiquitination is essential for transcriptional activation of RHO/ROCK/LIMK pathway components and proper actin-cytoskeleton dynamics through a trans-histone crosstalk with histone 3 lysine 4 trimethylation (H3K4me3). Collectively, this work demonstrates a previously unknown essential role of RNF40 in HER2+-BC, revealing the H2B monoubiquitination axis as a possible tumor context-dependent therapeutic target in breast cancer.
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Affiliation(s)
- Florian Wegwitz
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany.,Department of Gynecology and Obstetrics, University Medical Center Göttingen, Göttingen, Germany
| | - Evangelos Prokakis
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Anastasija Pejkovska
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Robyn Laura Kosinsky
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Markus Glatzel
- Institute for Neuropathology, University of Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Pantel
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Harriet Wikman
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Steven A Johnsen
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany. .,Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. .,Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA.
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Genome-wide chromatin accessibility is restricted by ANP32E. Nat Commun 2020; 11:5063. [PMID: 33033242 PMCID: PMC7546623 DOI: 10.1038/s41467-020-18821-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/16/2020] [Indexed: 12/11/2022] Open
Abstract
Genome-wide chromatin state underlies gene expression potential and cellular function. Epigenetic features and nucleosome positioning contribute to the accessibility of DNA, but widespread regulators of chromatin state are largely unknown. Our study investigates how coordination of ANP32E and H2A.Z contributes to genome-wide chromatin state in mouse fibroblasts. We define H2A.Z as a universal chromatin accessibility factor, and demonstrate that ANP32E antagonizes H2A.Z accumulation to restrict chromatin accessibility genome-wide. In the absence of ANP32E, H2A.Z accumulates at promoters in a hierarchical manner. H2A.Z initially localizes downstream of the transcription start site, and if H2A.Z is already present downstream, additional H2A.Z accumulates upstream. This hierarchical H2A.Z accumulation coincides with improved nucleosome positioning, heightened transcription factor binding, and increased expression of neighboring genes. Thus, ANP32E dramatically influences genome-wide chromatin accessibility through subtle refinement of H2A.Z patterns, providing a means to reprogram chromatin state and to hone gene expression levels. Chromatin state underlies cellular function, and transcription factor binding patterns along with epigenetic marks define chromatin state. Here the authors show that the histone chaperone ANP32E functions through regulation of H2A.Z to restrict genome-wide chromatin accessibility and to inhibit gene transcriptional activation.
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RNF40 exerts stage-dependent functions in differentiating osteoblasts and is essential for bone cell crosstalk. Cell Death Differ 2020; 28:700-714. [PMID: 32901120 DOI: 10.1038/s41418-020-00614-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 08/18/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023] Open
Abstract
The role of histone ubiquitination in directing cell lineage specification is only poorly understood. Our previous work indicated a role of the histone 2B ubiquitin ligase RNF40 in controlling osteoblast differentiation in vitro. Here, we demonstrate that RNF40 has a stage-dependent function in controlling osteoblast differentiation in vivo. RNF40 expression is essential for early stages of lineage specification, but is dispensable in mature osteoblasts. Paradoxically, while osteoblast-specific RNF40 deletion led to impaired bone formation, it also resulted in increased bone mass due to impaired bone cell crosstalk. Loss of RNF40 resulted in decreased osteoclast number and function through modulation of RANKL expression in OBs. Mechanistically, we demonstrate that Tnfsf11 (encoding RANKL) is an important target gene of H2B monoubiquitination. These data reveal an important role of RNF40-mediated H2B monoubiquitination in bone formation and remodeling and provide a basis for exploring this pathway for the treatment of conditions such as osteoporosis or cancer-associated osteolysis.
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Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194567. [PMID: 32360393 PMCID: PMC7294231 DOI: 10.1016/j.bbagrm.2020.194567] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/24/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
The precise regulation of gene transcription is required to establish and maintain cell type-specific gene expression programs during multicellular development. In addition to transcription factors, chromatin, and its chemical modification, play a central role in regulating gene expression. In vertebrates, DNA is pervasively methylated at CG dinucleotides, a modification that is repressive to transcription. However, approximately 70% of vertebrate gene promoters are associated with DNA elements called CpG islands (CGIs) that are refractory to DNA methylation. CGIs integrate the activity of a range of chromatin-regulating factors that can post-translationally modify histones and modulate gene expression. This is exemplified by the trimethylation of histone H3 at lysine 4 (H3K4me3), which is enriched at CGI-associated gene promoters and correlates with transcriptional activity. Through studying H3K4me3 at CGIs it has become clear that CGIs shape the distribution of H3K4me3 and, in turn, H3K4me3 influences the chromatin landscape at CGIs. Here we will discuss our understanding of the emerging relationship between CGIs, H3K4me3, and gene expression.
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The H2B ubiquitin-protein ligase RNF40 is required for somatic cell reprogramming. Cell Death Dis 2020; 11:287. [PMID: 32341358 PMCID: PMC7184622 DOI: 10.1038/s41419-020-2482-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 12/11/2022]
Abstract
Direct reprogramming of somatic cells to induced pluripotent stem cells (iPSCs) requires a resetting of the epigenome in order to facilitate a cell fate transition. Previous studies have shown that epigenetic modifying enzymes play a central role in controlling induced pluripotency and the generation of iPSC. Here we show that RNF40, a histone H2B lysine 120 E3 ubiquitin-protein ligase, is specifically required for early reprogramming during induced pluripotency. Loss of RNF40-mediated H2B monoubiquitination (H2Bub1) impaired early gene activation in reprogramming. We further show that RNF40 contributes to tissue-specific gene suppression via indirect effects by controlling the expression of the polycomb repressive complex-2 histone methyltransferase component EZH2, as well as through more direct effects by promoting the resolution of H3K4me3/H3K27me3 bivalency on H2Bub1-occupied pluripotency genes. Thus, we identify RNF40 as a central epigenetic mediator of cell state transition with distinct functions in resetting somatic cell state to pluripotency.
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Sun M, Zhang J. Allele-specific single-cell RNA sequencing reveals different architectures of intrinsic and extrinsic gene expression noises. Nucleic Acids Res 2020; 48:533-547. [PMID: 31799601 PMCID: PMC6954418 DOI: 10.1093/nar/gkz1134] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/19/2019] [Accepted: 11/20/2019] [Indexed: 01/13/2023] Open
Abstract
Gene expression noise refers to the variation of the expression level of a gene among isogenic cells in the same environment, and has two sources: extrinsic noise arising from the disparity of the cell state and intrinsic noise arising from the stochastic process of gene expression in the same cell state. Due to the low throughput of the existing method for measuring the two noise components, the architectures of intrinsic and extrinsic expression noises remain elusive. Using allele-specific single-cell RNA sequencing, we here estimate the two noise components of 3975 genes in mouse fibroblast cells. Our analyses verify predicted influences of several factors such as the TATA-box and microRNA targeting on intrinsic or extrinsic noises and reveal gene function-associated noise trends implicating the action of natural selection. These findings unravel differential regulations, optimizations, and biological consequences of intrinsic and extrinsic noises and can aid the construction of desired synthetic circuits.
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Affiliation(s)
- Mengyi Sun
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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Chen FX, Smith ER, Shilatifard A. Born to run: control of transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol 2019; 19:464-478. [PMID: 29740129 DOI: 10.1038/s41580-018-0010-5] [Citation(s) in RCA: 261] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The dynamic regulation of transcription elongation by RNA polymerase II (Pol II) is an integral part of the implementation of gene expression programmes during development. In most metazoans, the majority of transcribed genes exhibit transient pausing of Pol II at promoter-proximal regions, and the release of Pol II into gene bodies is controlled by many regulatory factors that respond to environmental and developmental cues. Misregulation of the elongation stage of transcription is implicated in cancer and other human diseases, suggesting that mechanistic understanding of transcription elongation control is therapeutically relevant. In this Review, we discuss the features, establishment and maintenance of Pol II pausing, the transition into productive elongation, the control of transcription elongation by enhancers and by factors of other cellular processes, such as topoisomerases and poly(ADP-ribose) polymerases (PARPs), and the potential of therapeutic targeting of the elongation stage of transcription by Pol II.
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Affiliation(s)
- Fei Xavier Chen
- Simpson Querrey Center for Epigenetics and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Edwin R Smith
- Simpson Querrey Center for Epigenetics and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ali Shilatifard
- Simpson Querrey Center for Epigenetics and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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32
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Schneider D, Chua RL, Molitor N, Hamdan FH, Rettenmeier EM, Prokakis E, Mishra VK, Kari V, Wegwitz F, Johnsen SA, Kosinsky RL. The E3 ubiquitin ligase RNF40 suppresses apoptosis in colorectal cancer cells. Clin Epigenetics 2019; 11:98. [PMID: 31266541 PMCID: PMC6604314 DOI: 10.1186/s13148-019-0698-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/20/2019] [Indexed: 01/08/2023] Open
Abstract
Background Colorectal cancer (CRC) is the fourth leading cause of cancer-related deaths worldwide, and deciphering underlying molecular mechanism is essential. The loss of monoubiquitinated histone H2B (H2Bub1) was correlated with poor prognosis of CRC patients and, accordingly, H2Bub1 was suggested as a tumor-suppressive mark. Surprisingly, our previous work revealed that the H2B ubiquitin ligase RING finger protein 40 (RNF40) might exert tumor-promoting functions. Here, we investigated the effect of RNF40 loss on tumorigenic features of CRC cells and their survival in vitro. Methods We evaluated the effects of RNF40 depletion in several human CRC cell lines in vitro. To evaluate cell cycle progression, cells were stained with propidium iodide and analyzed by flow cytometry. In addition, to assess apoptosis rates, caspase 3/7 activity was assessed in a Celigo® S-based measurement and, additionally, an Annexin V assay was performed. Genomic occupancy of H2Bub1, H3K79me3, and H3K27ac was determined by chromatin immunoprecipitation. Transcriptome-wide effects of RNF40 loss were evaluated based on mRNA-seq results, qRT-PCR, and Western blot. To rescue apoptosis-related effects, cells were treated with Z-VAD-FMK. Results Human CRC cell lines displayed decreased cell numbers in vitro after RNF40 depletion. While the differences in confluence were not mediated by changes in cell cycle progression, we discovered highly increased apoptosis rates after RNF40 knockdown due to elevated caspase 3/7 activity. This effect can be explained by reduced mRNA levels of anti-apoptotic and upregulation of pro-apoptotic BCL2 family members. Moreover, the direct occupancy of the RNF40-mediated H2B monoubiquitination was observed in the transcribed region of anti-apoptotic genes. Caspase inhibition by Z-VAD-FMK treatment rescued apoptosis in RNF40-depleted cells. However, knockdown cells still displayed decreased tumorigenic features despite the absence of apoptosis. Conclusions Our findings reveal that RNF40 is essential for maintaining tumorigenic features of CRC cells in vitro by controlling the expression of genes encoding central apoptotic regulators. Electronic supplementary material The online version of this article (10.1186/s13148-019-0698-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Deborah Schneider
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Robert Lorenz Chua
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Nicole Molitor
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Feda H Hamdan
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.,Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN, USA
| | - Eva Maria Rettenmeier
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Evangelos Prokakis
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Vivek Kumar Mishra
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.,Department of Dermatology and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Vijayalakshmi Kari
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Florian Wegwitz
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Steven A Johnsen
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany. .,Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN, USA.
| | - Robyn Laura Kosinsky
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.
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Wade AK, Liu Y, Bethea MM, Toren E, Tse HM, Hunter CS. LIM-domain transcription complexes interact with ring-finger ubiquitin ligases and thereby impact islet β-cell function. J Biol Chem 2019; 294:11728-11740. [PMID: 31186351 DOI: 10.1074/jbc.ra118.006985] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 06/02/2019] [Indexed: 12/27/2022] Open
Abstract
Diabetes is characterized by a loss of β-cell mass, and a greater understanding of the transcriptional mechanisms governing β-cell function is required for future therapies. Previously, we reported that a complex of the Islet-1 (Isl1) transcription factor and the co-regulator single-stranded DNA-binding protein 3 (SSBP3) regulates the genes necessary for β-cell function, but few proteins are known to interact with this complex in β-cells. To identify additional components, here we performed SSBP3 reverse-cross-linked immunoprecipitation (ReCLIP)- and MS-based experiments with mouse β-cell extracts and compared the results with those from our previous Isl1 ReCLIP study. Our analysis identified the E3 ubiquitin ligases ring finger protein 20 (RNF20) and RNF40, factors that in nonpancreatic cells regulate transcription through imparting monoubiquitin marks on histone H2B (H2Bub1), a precursor to histone H3 lysine 4 trimethylation (H3K4me3). We hypothesized that RNF20 and RNF40 regulate similar genes as those regulated by Isl1 and SSBP3 and are important for β-cell function. We observed that Rnf20 and Rnf40 depletion reduces β-cell H2Bub1 marks and uncovered several target genes, including glucose transporter 2 (Glut2), MAF BZIP transcription factor A (MafA), and uncoupling protein 2 (Ucp2). Strikingly, we also observed that Isl1 and SSBP3 depletion reduces H2Bub1 and H3K4me3 marks, suggesting that they have epigenetic roles. We noted that the RNF complex is required for glucose-stimulated insulin secretion and normal mitochondrial reactive oxygen species levels. These findings indicate that RNF20 and RNF40 regulate β-cell gene expression and insulin secretion and establish a link between Isl1 complexes and global cellular epigenetics.
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Affiliation(s)
- Alexa K Wade
- Department of Medicine, Division of Endocrinology Diabetes and Metabolism, University of Alabama at Birmingham, Birmingham, Alabama 35294.,Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Yanping Liu
- Department of Medicine, Division of Endocrinology Diabetes and Metabolism, University of Alabama at Birmingham, Birmingham, Alabama 35294.,Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Maigen M Bethea
- Department of Medicine, Division of Endocrinology Diabetes and Metabolism, University of Alabama at Birmingham, Birmingham, Alabama 35294.,Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Eliana Toren
- Department of Medicine, Division of Endocrinology Diabetes and Metabolism, University of Alabama at Birmingham, Birmingham, Alabama 35294.,Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Hubert M Tse
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, Alabama 35294.,Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Chad S Hunter
- Department of Medicine, Division of Endocrinology Diabetes and Metabolism, University of Alabama at Birmingham, Birmingham, Alabama 35294 .,Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, Alabama 35294
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Kosinsky RL, Chua RL, Qui M, Saul D, Mehlich D, Ströbel P, Schildhaus HU, Wegwitz F, Faubion WA, Johnsen SA. Loss of RNF40 Decreases NF-κB Activity in Colorectal Cancer Cells and Reduces Colitis Burden in Mice. J Crohns Colitis 2019; 13:362-373. [PMID: 30321325 PMCID: PMC6599279 DOI: 10.1093/ecco-jcc/jjy165] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Inflammatory bowel diseases are linked to an increased risk of developing colorectal cancer [CRC]. Previous studies suggested that the H2B ubiquitin ligase RING finger protein-20 [RNF20] inhibited inflammatory signaling mediated by the nuclear factor kappa-light-chain-enhancer of activated B cells [NF-κB]. However, the role of RNF40, the obligate heterodimeric partner of RNF20, in the context of inflammation and CRC has not been addressed. Here, we examined the effect of RNF40 loss on CRC cells in vitro and on inflammation and inflammatory signaling in vitro and in vivo. METHODS We evaluated H2Bub1 levels in human and murine colorectal tumors by immunohistochemistry. Moreover, we correlated H2Bub1 and RNF40 levels in vivo and assessed the consequences of RNF40 depletion on cellular phenotype and gene expression in CRC cells in vitro. Finally, we examined the effect of a colon-specific loss of Rnf40 in a murine model of colitis, and assessed both local and systemic inflammation-associated consequences. RESULTS In vitro studies revealed that the tumorigenic phenotype of CRC cells decreased after RNF40 depletion and displayed gene expression changes related to chromosome segregation and DNA replication, as well as decreased induction of several NF-κB-associated cytokines. This effect was associated with decreased nuclear localization of NF-κB following tumor necrosis factor alpha treatment. Consistently, the colon-specific loss of Rnf40 exerted a protective local, as well as systemic, effect following acute colitis. CONCLUSIONS Our findings suggest that RNF40 plays a central role in the maintenance of tumorigenic features and inflammatory signaling by promoting nuclear NF-κB activity.
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Affiliation(s)
- Robyn Laura Kosinsky
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Göttingen, Germany
| | - Robert Lorenz Chua
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Göttingen, Germany
| | - Martin Qui
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Göttingen, Germany
| | - Dominik Saul
- Department of Trauma, Orthopedics and Reconstructive Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Dawid Mehlich
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Göttingen, Germany
| | - Philipp Ströbel
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Florian Wegwitz
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Göttingen, Germany
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Steven A Johnsen
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Göttingen, Germany,Corresponding author: Prof. Steven A. Johnsen, PhD, University Medical Center Göttingen, Göttingen Center for Molecular Biosciences, Clinic for General, Visceral and Pediatric Surgery, Section of Tumor Epigenetics, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Tel.: +49 551 39-13711; fax: +49 551 39-13713; email
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DeltaNp63-dependent super enhancers define molecular identity in pancreatic cancer by an interconnected transcription factor network. Proc Natl Acad Sci U S A 2018; 115:E12343-E12352. [PMID: 30541891 DOI: 10.1073/pnas.1812915116] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Molecular subtyping of cancer offers tremendous promise for the optimization of a precision oncology approach to anticancer therapy. Recent advances in pancreatic cancer research uncovered various molecular subtypes with tumors expressing a squamous/basal-like gene expression signature displaying a worse prognosis. Through unbiased epigenome mapping, we identified deltaNp63 as a major driver of a gene signature in pancreatic cancer cell lines, which we report to faithfully represent the highly aggressive pancreatic squamous subtype observed in vivo, and display the specific epigenetic marking of genes associated with decreased survival. Importantly, depletion of deltaNp63 in these systems significantly decreased cell proliferation and gene expression patterns associated with a squamous subtype and transcriptionally mimicked a subtype switch. Using genomic localization data of deltaNp63 in pancreatic cancer cell lines coupled with epigenome mapping data from patient-derived xenografts, we uncovered that deltaNp63 mainly exerts its effects by activating subtype-specific super enhancers. Furthermore, we identified a group of 45 subtype-specific super enhancers that are associated with poorer prognosis and are highly dependent on deltaNp63. Genes associated with these enhancers included a network of transcription factors, including HIF1A, BHLHE40, and RXRA, which form a highly intertwined transcriptional regulatory network with deltaNp63 to further activate downstream genes associated with poor survival.
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High-fidelity CRISPR/Cas9- based gene-specific hydroxymethylation rescues gene expression and attenuates renal fibrosis. Nat Commun 2018; 9:3509. [PMID: 30158531 PMCID: PMC6115451 DOI: 10.1038/s41467-018-05766-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 04/27/2018] [Indexed: 12/26/2022] Open
Abstract
While suppression of specific genes through aberrant promoter methylation contributes to different diseases including organ fibrosis, gene-specific reactivation technology is not yet available for therapy. TET enzymes catalyze hydroxymethylation of methylated DNA, reactivating gene expression. We here report generation of a high-fidelity CRISPR/Cas9-based gene-specific dioxygenase by fusing an endonuclease deactivated high-fidelity Cas9 (dHFCas9) to TET3 catalytic domain (TET3CD), targeted to specific genes by guiding RNAs (sgRNA). We demonstrate use of this technology in four different anti-fibrotic genes in different cell types in vitro, among them RASAL1 and Klotho, both hypermethylated in kidney fibrosis. Furthermore, in vivo lentiviral delivery of the Rasal1-targeted fusion protein to interstitial cells and of the Klotho-targeted fusion protein to tubular epithelial cells each results in specific gene reactivation and attenuation of fibrosis, providing gene-specific demethylating technology in a disease model. Suppression of gene expression due to aberrant promoter methylation contributes to organ fibrosis. Here, the authors couple a deactivated Cas9 to the TET3 catalytic domain to induce expression of four antifibrotic genes, and show that lentiviral-mediated delivery is effective in reducing kidney fibrosis in mouse models.
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Shah VJ, Maddika S. CRL7 SMU1 E3 ligase complex-driven H2B ubiquitylation functions in sister chromatid cohesion by regulating SMC1 expression. J Cell Sci 2018; 131:jcs.213868. [PMID: 29507117 DOI: 10.1242/jcs.213868] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/26/2018] [Indexed: 12/26/2022] Open
Abstract
Cullin-RING-type E3 ligases (CRLs) control a broad range of biological processes by ubiquitylating numerous cellular substrates. However, the role of CRL E3 ligases in chromatid cohesion is unknown. In this study, we identified a new CRL-type E3 ligase (designated as CRL7SMU1 complex) that has an essential role in the maintenance of chromatid cohesion. We demonstrate that SMU1, DDB1, CUL7 and RNF40 are integral components of this complex. SMU1, by acting as a substrate recognition module, binds to H2B and mediates monoubiquitylation at the lysine (K) residue K120 through CRL7SMU1 E3 ligase complex. Depletion of CRL7SMU1 leads to loss of H2B ubiquitylation at the SMC1a locus and, thus, subsequently compromised SMC1a expression in cells. Knockdown of CRL7SMU1 components or loss of H2B ubiquitylation leads to defective sister chromatid cohesion, which is rescued by restoration of SMC1a expression. Together, our results unveil an important role of CRL7SMU1 E3 ligase in promoting H2B ubiquitylation for maintenance of sister chromatid cohesion during mitosis.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Varun Jayeshkumar Shah
- Laboratory of Cell Death & Cell Survival, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India-500 039.,Graduate studies, Manipal Academy of Higher Education, Manipal, India-576 104
| | - Subbareddy Maddika
- Laboratory of Cell Death & Cell Survival, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India-500 039
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Functional crosstalk between histone H2B ubiquitylation and H2A modifications and variants. Nat Commun 2018; 9:1394. [PMID: 29643390 PMCID: PMC5895630 DOI: 10.1038/s41467-018-03895-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/20/2018] [Indexed: 01/30/2023] Open
Abstract
Ubiquitylation of histone H2B at lysine residue 120 (H2BK120ub) is a prominent histone posttranslational modification (PTM) associated with the actively transcribed genome. Although H2BK120ub triggers several critical downstream histone modification pathways and changes in chromatin structure, less is known about the regulation of the ubiquitylation reaction itself, in particular with respect to the modification status of the chromatin substrate. Here we employ an unbiased library screening approach to profile the impact of pre-existing chromatin modifications on de novo ubiquitylation of H2BK120 by the cognate human E2:E3 ligase pair, UBE2A:RNF20/40. Deposition of H2BK120ub is found to be highly sensitive to PTMs on the N-terminal tail of histone H2A, a crosstalk that extends to the common histone variant H2A.Z. Based on a series of biochemical and cell-based studies, we propose that this crosstalk contributes to the spatial organization of H2BK120ub on gene bodies, and is thus important for transcriptional regulation. Ubiquitylation of H2B is associated with transcription and regulation of chromatin structure. Here, the authors perform an unbiased screen to identify the role of chromatin modifications on ubiquitylation of H2BK120 and characterize the crosstalk between H2BK120ub and H2A modifications and variants.
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40
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Wang L, Cao C, Wang F, Zhao J, Li W. H2B ubiquitination: Conserved molecular mechanism, diverse physiologic functions of the E3 ligase during meiosis. Nucleus 2017. [PMID: 28628358 DOI: 10.1080/19491034.2017.1330237] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
RNF20/Bre1 mediated H2B ubiquitination (H2Bub) has various physiologic functions. Recently, we found that H2Bub participates in meiotic recombination by promoting chromatin relaxation during meiosis. We then analyzed the phylogenetic relationships among the E3 ligase for H2Bub, its E2 Rad6 and their partner WW domain-containing adaptor with a coiled-coil (WAC) or Lge1, and found that the molecular mechanism underlying H2Bub is evolutionarily conserved from yeast to mammals. However, RNF20 has diverse physiologic functions in different organisms, which might be caused by the evolutionary divergency of their domain/motif architectures. In the current extra view, we not only elucidate the evolutionarily conserved molecular mechanism underlying H2Bub, but also discuss the diverse physiologic functions of RNF20 during meiosis.
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Affiliation(s)
- Liying Wang
- a State Key Laboratory of Stem Cell and Reproductive Biology , Institute of Zoology, Chinese Academy of Sciences , Beijing , P.R. China.,b University of Chinese Academy of Sciences , Beijing , P.R. China
| | - Chunwei Cao
- a State Key Laboratory of Stem Cell and Reproductive Biology , Institute of Zoology, Chinese Academy of Sciences , Beijing , P.R. China.,b University of Chinese Academy of Sciences , Beijing , P.R. China
| | - Fang Wang
- a State Key Laboratory of Stem Cell and Reproductive Biology , Institute of Zoology, Chinese Academy of Sciences , Beijing , P.R. China.,b University of Chinese Academy of Sciences , Beijing , P.R. China
| | - Jianguo Zhao
- a State Key Laboratory of Stem Cell and Reproductive Biology , Institute of Zoology, Chinese Academy of Sciences , Beijing , P.R. China
| | - Wei Li
- a State Key Laboratory of Stem Cell and Reproductive Biology , Institute of Zoology, Chinese Academy of Sciences , Beijing , P.R. China
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