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Zhou M, Yang T, Yuan M, Li X, Deng J, Wu S, Zhong Z, Lin Y, Zhang W, Xia B, Wu Y, Wang L, Chen T, Liu R, Pan T, Ma X, Li L, Liu B, Zhang H. ORC1 enhances repressive epigenetic modifications on HIV-1 LTR to promote HIV-1 latency. J Virol 2024; 98:e0003524. [PMID: 39082875 PMCID: PMC11334468 DOI: 10.1128/jvi.00035-24] [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: 02/21/2024] [Accepted: 06/21/2024] [Indexed: 08/21/2024] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) reservoir consists of latently infected cells which present a major obstacle to achieving a functional cure for HIV-1. The formation and maintenance of HIV-1 latency have been extensively studied, and latency-reversing agents (LRAs) that can reactivate latent HIV-1 by targeting the involved host factors are developed; however, their clinical efficacies remain unsatisfactory. Therefore, it is imperative to identify novel targets for more potential candidates or better combinations for LRAs. In this study, we utilized CRISPR affinity purification in situ of regulatory elements system to screen for host factors associated with the HIV-1 long terminal repeat region that could potentially be involved in HIV-1 latency. We successfully identified that origin recognition complex 1 (ORC1), the largest subunit of the origin recognition complex, contributes to HIV-1 latency in addition to its function in DNA replication initiation. Notably, ORC1 is enriched on the HIV-1 promoter and recruits a series of repressive epigenetic elements, including DNMT1 and HDAC1/2, and histone modifiers, such as H3K9me3 and H3K27me3, thereby facilitating the establishment and maintenance of HIV-1 latency. Moreover, the reactivation of latent HIV-1 through ORC1 depletion has been confirmed across various latency cell models and primary CD4+ T cells from people living with HIV-1. Additionally, we comprehensively validated the properties of liquid-liquid phase separation (LLPS) of ORC1 from multiple perspectives and identified the key regions that promote the formation of LLPS. This property is important for the recruitment of ORC1 to the HIV-1 promoter. Collectively, these findings highlight ORC1 as a potential novel target implicated in HIV-1 latency and position it as a promising candidate for the development of novel LRAs. IMPORTANCE Identifying host factors involved in maintaining human immunodeficiency virus type 1 (HIV-1) latency and understanding their mechanisms prepares the groundwork to discover novel targets for HIV-1 latent infection and provides further options for the selection of latency-reversing agents in the "shock" strategy. In this study, we identified a novel role of the DNA replication factor origin recognition complex 1 (ORC1) in maintaining repressive chromatin structures surrounding the HIV-1 promoter region, thereby contributing to HIV-1 latency. This discovery expands our understanding of the non-replicative functions of the ORC complex and provides a potential therapeutic strategy for HIV-1 cure.
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Affiliation(s)
- Mo Zhou
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Tao Yang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ming Yuan
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xinyu Li
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Jieyi Deng
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shiyu Wu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhihan Zhong
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yingtong Lin
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wanying Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Baijin Xia
- Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Science), Guangzhou, China
| | - Yating Wu
- Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Science), Guangzhou, China
| | - Lilin Wang
- Shenzhen Blood Center, Shenzhen, Guangdong, China
| | - Tao Chen
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, China
| | - Ruxin Liu
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Ting Pan
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Xiancai Ma
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, China
| | - Linghua Li
- Center for Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Bingfeng Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
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2
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Brunet M, Vargas C, Fanjul M, Varry D, Hanoun N, Larrieu D, Pieruccioni L, Labrousse G, Lulka H, Capilla F, Ricard A, Selves J, Couvelard A, Gigoux V, Cordelier P, Guillermet-Guibert J, Dufresne M, Torrisani J. The E3 ubiquitin ligase TRIP12 is required for pancreatic acinar cell plasticity and pancreatic carcinogenesis. J Pathol 2024; 263:466-481. [PMID: 38924548 DOI: 10.1002/path.6298] [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: 11/14/2023] [Revised: 03/15/2024] [Accepted: 04/23/2024] [Indexed: 06/28/2024]
Abstract
The E3 ubiquitin ligase thyroid hormone receptor interacting protein 12 (TRIP12) has been implicated in pancreatic adenocarcinoma (PDAC) through its role in mediating the degradation of pancreas transcription factor 1a (PTF1a). PTF1a is a transcription factor essential for the acinar differentiation state that is notably diminished during the early steps of pancreatic carcinogenesis. Despite these findings, the direct involvement of TRIP12 in the onset of pancreatic cancer has yet to be established. In this study, we demonstrated that TRIP12 protein was significantly upregulated in human pancreatic preneoplastic lesions. Furthermore, we observed that TRIP12 overexpression varied within PDAC samples and PDAC-derived cell lines. We further demonstrated that TRIP12 was required for PDAC-derived cell growth and for the expression of E2F-targeted genes. Acinar-to-ductal cell metaplasia (ADM) is a reversible process that reflects the high plasticity of acinar cells. ADM becomes irreversible in the presence of oncogenic Kras mutations and leads to the formation of preneoplastic lesions. Using two genetically modified mouse models, we showed that a loss of TRIP12 prevented acini from developing ADM in response to pancreatic injury. With two additional mouse models, we further discovered that a depletion of TRIP12 prevented the formation of KrasG12D-induced preneoplastic lesions and impaired metastasis formation in the presence of mutated KrasG12D and Trp53R172H genes. In summary our study identified an overexpression of TRIP12 from the early stages of pancreatic carcinogenesis and proposed this E3 ubiquitin ligase as a novel regulator of acinar plasticity with an important dual role in initiation and metastatic steps of PDAC. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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MESH Headings
- Animals
- Pancreatic Neoplasms/pathology
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/metabolism
- Pancreatic Neoplasms/enzymology
- Humans
- Acinar Cells/pathology
- Acinar Cells/metabolism
- Acinar Cells/enzymology
- Ubiquitin-Protein Ligases/metabolism
- Ubiquitin-Protein Ligases/genetics
- Carcinoma, Pancreatic Ductal/pathology
- Carcinoma, Pancreatic Ductal/genetics
- Carcinoma, Pancreatic Ductal/metabolism
- Carcinoma, Pancreatic Ductal/enzymology
- Metaplasia/pathology
- Metaplasia/metabolism
- Cell Plasticity
- Carcinogenesis/genetics
- Carcinogenesis/metabolism
- Mice
- Cell Line, Tumor
- Cell Proliferation
- Mice, Knockout
- Gene Expression Regulation, Neoplastic
- Precancerous Conditions/pathology
- Precancerous Conditions/genetics
- Precancerous Conditions/metabolism
- Precancerous Conditions/enzymology
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/pathology
- Cell Transformation, Neoplastic/metabolism
- Carrier Proteins
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Affiliation(s)
- Manon Brunet
- CRCT, Université de Toulouse, INSERM, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institut des Maladies Métaboliques et Cardiovasculaires, Toulouse, France
| | - Claire Vargas
- CRCT, Université de Toulouse, INSERM, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Marjorie Fanjul
- CRCT, Université de Toulouse, INSERM, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Damien Varry
- CRCT, Université de Toulouse, INSERM, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Naïma Hanoun
- CRCT, Université de Toulouse, INSERM, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Dorian Larrieu
- CRCT, Université de Toulouse, INSERM, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Laetitia Pieruccioni
- Centre de recherches RESTORE, Université de Toulouse, INSERM, CNRS, EFS, ENVT, Toulouse, France
| | - Guillaume Labrousse
- CRCT, Université de Toulouse, INSERM, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Hubert Lulka
- CRCT, Université de Toulouse, INSERM, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Florence Capilla
- Service d'Histopathologie expérimentale, INSERM US006-CREFRE, Toulouse, France
| | - Alban Ricard
- CRCT, Université de Toulouse, INSERM, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Janick Selves
- Département de Pathologie, Institut Universitaire du Cancer Toulouse Oncopole, Toulouse, France
| | - Anne Couvelard
- Département de Pathologie Beaujon-Bichat, Hôpital Bichat, APHP and Université Paris Cité, Paris, France
| | - Véronique Gigoux
- CRCT, Université de Toulouse, INSERM, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Pierre Cordelier
- CRCT, Université de Toulouse, INSERM, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Julie Guillermet-Guibert
- CRCT, Université de Toulouse, INSERM, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Marlène Dufresne
- CRCT, Université de Toulouse, INSERM, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Jérôme Torrisani
- CRCT, Université de Toulouse, INSERM, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
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3
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Kwak YT, Montalbano AP, Kelleher AM, Colon-Caraballo M, Kraus WL, Mahendroo M, Mendelson CR. Decline in corepressor CNOT1 in the pregnant myometrium near term impairs progesterone receptor function and increases contractile gene expression. J Biol Chem 2024; 300:107484. [PMID: 38897566 PMCID: PMC11301068 DOI: 10.1016/j.jbc.2024.107484] [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: 05/04/2023] [Revised: 05/18/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Progesterone (P4), acting via its nuclear receptor (PR), is critical for pregnancy maintenance by suppressing proinflammatory and contraction-associated protein (CAP)/contractile genes in the myometrium. P4/PR partially exerts these effects by tethering to NF-κB bound to their promot-ers, thereby decreasing NF-κB transcriptional activity. However, the underlying mechanisms whereby P4/PR interaction blocks proinflammatory and CAP gene expression are not fully understood. Herein, we characterized CCR-NOT transcription complex subunit 1 (CNOT1) as a corepressor that also interacts within the same chromatin complex as PR-B. In mouse myome-trium increased expression of CAP genes Oxtr and Cx43 at term coincided with a marked decline in expression and binding of CNOT1 to NF-κB-response elements within the Oxtr and Cx43 promoters. Increased CAP gene expression was accompanied by a pronounced decrease in enrichment of repressive histone marks and increase in enrichment of active histone marks to this genomic region. These changes in histone modification were associated with changes in expression of corresponding histone modifying enzymes. Myometrial tissues from P4-treated 18.5 dpc pregnant mice manifested increased Cnot1 expression at 18.5 dpc, compared to vehicle-treated controls. P4 treatment of PR-expressing hTERT-HM cells enhanced CNOT1 expression and its recruitment to PR bound NF-κB-response elements within the CX43 and OXTR promoters. Furthermore, knockdown of CNOT1 significantly increased expression of contractile genes. These novel findings suggest that decreased expression and DNA-binding of the P4/PR-regulated transcriptional corepressor CNOT1 near term and associated changes in histone modifications at the OXTR and CX43 promoters contribute to the induction of myometrial contractility leading to parturition.
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Affiliation(s)
- Youn-Tae Kwak
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Alina P Montalbano
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Andrew M Kelleher
- Department of Obstetrics & Gynecology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA; Laboratory of Signaling and Gene Regulation, The University of Texas Southwestern Medical Center, Dallas, Texas, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Obstetrics, Gynecology, and Women's Health, University of Missouri, Columbia, Missouri, USA
| | - Mariano Colon-Caraballo
- Department of Obstetrics & Gynecology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, The University of Texas Southwestern Medical Center, Dallas, Texas, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Mala Mahendroo
- Department of Obstetrics & Gynecology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas, USA.
| | - Carole R Mendelson
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Obstetrics & Gynecology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas, USA; North Texas March of Dimes Birth Defects Center, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
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4
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Longhurst AD, Wang K, Suresh HG, Ketavarapu M, Ward HN, Jones IR, Narayan V, Hundley FV, Hassan AZ, Boone C, Myers CL, Shen Y, Ramani V, Andrews BJ, Toczyski DP. The PRC2.1 Subcomplex Opposes G1 Progression through Regulation of CCND1 and CCND2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585604. [PMID: 38562687 PMCID: PMC10983909 DOI: 10.1101/2024.03.18.585604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Progression through the G1 phase of the cell cycle is the most highly regulated step in cellular division. We employed a chemogenomics approach to discover novel cellular networks that regulate cell cycle progression. This approach uncovered functional clusters of genes that altered sensitivity of cells to inhibitors of the G1/S transition. Mutation of components of the Polycomb Repressor Complex 2 rescued growth inhibition caused by the CDK4/6 inhibitor palbociclib, but not to inhibitors of S phase or mitosis. In addition to its core catalytic subunits, mutation of the PRC2.1 accessory protein MTF2, but not the PRC2.2 protein JARID2, rendered cells resistant to palbociclib treatment. We found that PRC2.1 (MTF2), but not PRC2.2 (JARID2), was critical for promoting H3K27me3 deposition at CpG islands genome-wide and in promoters. This included the CpG islands in the promoter of the CDK4/6 cyclins CCND1 and CCND2, and loss of MTF2 lead to upregulation of both CCND1 and CCND2. Our results demonstrate a role for PRC2.1, but not PRC2.2, in promoting G1 progression.
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Affiliation(s)
- Adam D Longhurst
- University of California, San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kyle Wang
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Harsha Garadi Suresh
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Mythili Ketavarapu
- Gladstone Institute for Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Henry N Ward
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota - Twin Cities Minneapolis MN USA
| | - Ian R Jones
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California
| | - Vivek Narayan
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Frances V Hundley
- University of California, San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, MA 02115, USA
| | - Arshia Zernab Hassan
- Department of Computer Science and Engineering, University of Minnesota - Twin Cities Minneapolis MN USA
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Chad L Myers
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota - Twin Cities Minneapolis MN USA
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, MA 02115, USA
| | - Yin Shen
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Vijay Ramani
- Gladstone Institute for Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Brenda J Andrews
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - David P Toczyski
- University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
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5
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Xu X, Wang D, Xu W, Li H, Chen N, Li N, Yao Q, Chen W, Zhong J, Mao W. NIPBL-mediated RAD21 facilitates tumorigenicity by the PI3K pathway in non-small-cell lung cancer. Commun Biol 2024; 7:206. [PMID: 38378967 PMCID: PMC10879132 DOI: 10.1038/s42003-024-05801-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 01/10/2024] [Indexed: 02/22/2024] Open
Abstract
It is urgent to identify novel early diagnostic markers and therapeutic targets for non-small-cell lung cancer (NSCLC), which accounts for 85% of lung cancer cases and has a 5-year survival rate of 4-17%. Here, chromatin immunoprecipitation (ChIP) was used to identify DNA‒protein interactions, RNA methylation was determined by methylated RNA immunoprecipitation (MeRIP), RNA stability was tested by an RNA decay assay. We showed that RAD21, a member of the cohesin complex, is upregulated in NSCLC tissues and cell lines and found to be an independent prognostic factor for overall survival (OS) of NSCLC patients. Mechanistically, the cohesin loading factor Nipped-B-Like Protein (NIPBL) promoted RAD21 gene transcription by enhancing histone H3 lysine 27 (H3K27) demethylation via recruiting lysine demethylase 6B (KDM6B) to the RAD21 gene promoter. RAD21 enhanced phosphatidylinositol 3-kinase (PI3K) gene transcription, and NIPBL reversed the effect of enhancer of zeste 2; catalytic subunit of polycomb repressive complex 2 (EZH2) on RAD21-mediated PI3K gene transcription by disrupting the association between EZH2 and RAD21. Moreover, NIPBL level was increased by stabilization of its transcripts through mRNA methylation. These findings highlight the oncogenic role of RAD21 in NSCLC and suggest its use as a potential diagnostic marker and therapeutic target for NSCLC.
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Affiliation(s)
- Xiaoling Xu
- Department of Radiation Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, 507 Zhengmin Road, Shanghai, China
| | - Ding Wang
- Key laboratory on Diagnosis and Treatment Technology on Thoracic Cancer, Zhejiang Cancer Research Institute, 38 Guangji Road, Hangzhou, China
| | - Weizhen Xu
- Key laboratory on Diagnosis and Treatment Technology on Thoracic Cancer, Zhejiang Cancer Research Institute, 38 Guangji Road, Hangzhou, China
| | - Huihui Li
- Key laboratory on Diagnosis and Treatment Technology on Thoracic Cancer, Zhejiang Cancer Research Institute, 38 Guangji Road, Hangzhou, China
- The Second Clinical Medical College of Wenzhou Medical University, 268 West Xueyue Road, Wenzhou, China
| | - Ning Chen
- The Second Clinical Medical College of Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, China
| | - Na Li
- The Second Clinical Medical College of Wenzhou Medical University, 268 West Xueyue Road, Wenzhou, China
| | - Qifeng Yao
- The Second Clinical Medical College of Wenzhou Medical University, 268 West Xueyue Road, Wenzhou, China
| | - Wei Chen
- Key laboratory on Diagnosis and Treatment Technology on Thoracic Cancer, Zhejiang Cancer Research Institute, 38 Guangji Road, Hangzhou, China.
| | - Jianxiang Zhong
- School of Life Science and Technology, Southeast University, 2 Sipailou, Nanjing, China.
| | - Weimin Mao
- Key laboratory on Diagnosis and Treatment Technology on Thoracic Cancer, Zhejiang Cancer Research Institute, 38 Guangji Road, Hangzhou, China.
- The Second Clinical Medical College of Wenzhou Medical University, 268 West Xueyue Road, Wenzhou, China.
- Department of Thoracic Oncology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, 1 Banshan East Road, Hangzhou, China.
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6
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Kinoshita S, Kojima K, Ohnishi E, Takayama Y, Kikuchi H, Takada S, Nakabayashi K, Kawai T, Hata K. Loss of NSD2 causes dysregulation of synaptic genes and altered H3K36 dimethylation in mice. Front Genet 2024; 15:1308234. [PMID: 38419783 PMCID: PMC10899350 DOI: 10.3389/fgene.2024.1308234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
Background: Epigenetic disruptions have been implicated in neurodevelopmental disorders. NSD2 is associated with developmental delay/intellectual disability; however, its role in brain development and function remains unclear. Methods: We performed transcriptomic and epigenetic analyses using Nsd2 knockout mice to better understand the role of NSD2 in the brain. Results and discussion: Transcriptomic analysis revealed that the loss of NSD2 caused dysregulation of genes related to synaptic transmission and formation. By analyzing changes in H3 lysine 36 dimethylation (H3K36me2), NSD2-mediated H3K36me2 mainly marked quiescent state regions and the redistribution of H3K36me2 occurred at transcribed genes and enhancers. By integrating transcriptomic and epigenetic data, we observed that H3K36me2 changes in a subset of dysregulated genes related to synaptic transmission and formation. These results suggest that NSD2 is involved in the regulation of genes important for neural function through H3K36me2. Our findings provide insights into the role of NSD2 and improve our understanding of epigenetic regulation in the brain.
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Affiliation(s)
- Shiori Kinoshita
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of NCCHD Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazuaki Kojima
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Eriko Ohnishi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yuka Takayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hiroki Kikuchi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Human Molecular Genetics, Graduate School of Medicine, Gunma University, Maebashi, Gunma, Japan
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7
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Matsui S, Granitto M, Buckley M, Ludwig K, Koigi S, Shiley J, Zacharias WJ, Mayhew CN, Lim HW, Iwafuchi M. Pioneer and PRDM transcription factors coordinate bivalent epigenetic states to safeguard cell fate. Mol Cell 2024; 84:476-489.e10. [PMID: 38211589 PMCID: PMC10872272 DOI: 10.1016/j.molcel.2023.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/30/2023] [Accepted: 12/08/2023] [Indexed: 01/13/2024]
Abstract
Pioneer transcription factors (TFs) regulate cell fate by establishing transcriptionally primed and active states. However, cell fate control requires the coordination of both lineage-specific gene activation and repression of alternative-lineage programs, a process that is poorly understood. Here, we demonstrate that the pioneer TF FOXA coordinates with PRDM1 TF to recruit nucleosome remodeling and deacetylation (NuRD) complexes and Polycomb repressive complexes (PRCs), which establish highly occupied, accessible nucleosome conformation with bivalent epigenetic states, thereby preventing precocious and alternative-lineage gene expression during human endoderm differentiation. Similarly, the pioneer TF OCT4 coordinates with PRDM14 to form bivalent enhancers and repress cell differentiation programs in human pluripotent stem cells, suggesting that this may be a common and critical function of pioneer TFs. We propose that pioneer and PRDM TFs coordinate to safeguard cell fate through epigenetic repression mechanisms.
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Affiliation(s)
- Satoshi Matsui
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Marissa Granitto
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Morgan Buckley
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Katie Ludwig
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Sandra Koigi
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Joseph Shiley
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - William J Zacharias
- Division of Pulmonary Biology and Pulmonary and Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Christopher N Mayhew
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
| | - Makiko Iwafuchi
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
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8
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Bharti H, Han S, Chang HW, Reinberg D. Polycomb repressive complex 2 accessory factors: rheostats for cell fate decision? Curr Opin Genet Dev 2024; 84:102137. [PMID: 38091876 DOI: 10.1016/j.gde.2023.102137] [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: 10/04/2023] [Accepted: 11/15/2023] [Indexed: 02/12/2024]
Abstract
Epigenetic reprogramming during development is key to cell identity and the activities of the Polycomb repressive complexes are vital for this process. We focus on polycomb repressive complex 2 (PRC2), which catalyzes H3K27me1/2/3 and safeguards cellular integrity by ensuring proper gene repression. Notably, various accessory factors associate with PRC2, strongly influencing cell fate decisions, and their deregulation contributes to various illnesses. Yet, the exact role of these factors during development and carcinogenesis is not fully understood. Here, we present recent progress toward addressing these points and an analysis of the expression levels of PRC2 accessory factors in various tissues and developmental stages to highlight their abundance and roles. Last, we evaluate their contribution to cancer-specific phenotypes, providing insight into novel anticancer therapies.
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Affiliation(s)
- Hina Bharti
- Howard Hughes Medical Institute, University of Miami, Miller School of Medicine and Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
| | - Sungwook Han
- Howard Hughes Medical Institute, University of Miami, Miller School of Medicine and Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
| | - Han-Wen Chang
- Howard Hughes Medical Institute, University of Miami, Miller School of Medicine and Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
| | - Danny Reinberg
- Howard Hughes Medical Institute, University of Miami, Miller School of Medicine and Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA.
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9
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Ngubo M, Moradi F, Ito CY, Stanford WL. Tissue-Specific Tumour Suppressor and Oncogenic Activities of the Polycomb-like Protein MTF2. Genes (Basel) 2023; 14:1879. [PMID: 37895228 PMCID: PMC10606531 DOI: 10.3390/genes14101879] [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: 09/07/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
The Polycomb repressive complex 2 (PRC2) is a conserved chromatin-remodelling complex that catalyses the trimethylation of histone H3 lysine 27 (H3K27me3), a mark associated with gene silencing. PRC2 regulates chromatin structure and gene expression during organismal and tissue development and tissue homeostasis in the adult. PRC2 core subunits are associated with various accessory proteins that modulate its function and recruitment to target genes. The multimeric composition of accessory proteins results in two distinct variant complexes of PRC2, PRC2.1 and PRC2.2. Metal response element-binding transcription factor 2 (MTF2) is one of the Polycomb-like proteins (PCLs) that forms the PRC2.1 complex. MTF2 is highly conserved, and as an accessory subunit of PRC2, it has important roles in embryonic stem cell self-renewal and differentiation, development, and cancer progression. Here, we review the impact of MTF2 in PRC2 complex assembly, catalytic activity, and spatiotemporal function. The emerging paradoxical evidence suggesting that MTF2 has divergent roles as either a tumour suppressor or an oncogene in different tissues merits further investigations. Altogether, our review illuminates the context-dependent roles of MTF2 in Polycomb group (PcG) protein-mediated epigenetic regulation. Its impact on disease paves the way for a deeper understanding of epigenetic regulation and novel therapeutic strategies.
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Affiliation(s)
- Mzwanele Ngubo
- The Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Ottawa Institute of Systems Biology, Ottawa, ON K1H 8M5, Canada
| | - Fereshteh Moradi
- The Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Caryn Y. Ito
- The Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - William L. Stanford
- The Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Ottawa Institute of Systems Biology, Ottawa, ON K1H 8M5, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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10
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Affar M, Bottardi S, Quansah N, Lemarié M, Ramón AC, Affar EB, Milot E. IKAROS: from chromatin organization to transcriptional elongation control. Cell Death Differ 2023:10.1038/s41418-023-01212-2. [PMID: 37620540 DOI: 10.1038/s41418-023-01212-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
IKAROS is a master regulator of cell fate determination in lymphoid and other hematopoietic cells. This transcription factor orchestrates the association of epigenetic regulators with chromatin, ensuring the expression pattern of target genes in a developmental and lineage-specific manner. Disruption of IKAROS function has been associated with the development of acute lymphocytic leukemia, lymphoma, chronic myeloid leukemia and immune disorders. Paradoxically, while IKAROS has been shown to be a tumor suppressor, it has also been identified as a key therapeutic target in the treatment of various forms of hematological malignancies, including multiple myeloma. Indeed, targeted proteolysis of IKAROS is associated with decreased proliferation and increased death of malignant cells. Although the molecular mechanisms have not been elucidated, the expression levels of IKAROS are variable during hematopoiesis and could therefore be a key determinant in explaining how its absence can have seemingly opposite effects. Mechanistically, IKAROS collaborates with a variety of proteins and complexes controlling chromatin organization at gene regulatory regions, including the Nucleosome Remodeling and Deacetylase complex, and may facilitate transcriptional repression or activation of specific genes. Several transcriptional regulatory functions of IKAROS have been proposed. An emerging mechanism of action involves the ability of IKAROS to promote gene repression or activation through its interaction with the RNA polymerase II machinery, which influences pausing and productive transcription at specific genes. This control appears to be influenced by IKAROS expression levels and isoform production. In here, we summarize the current state of knowledge about the biological roles and mechanisms by which IKAROS regulates gene expression. We highlight the dynamic regulation of this factor by post-translational modifications. Finally, potential avenues to explain how IKAROS destruction may be favorable in the treatment of certain hematological malignancies are also explored.
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Affiliation(s)
- Malik Affar
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Stefania Bottardi
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Norreen Quansah
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Maud Lemarié
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Ailyn C Ramón
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - El Bachir Affar
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada.
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada.
| | - Eric Milot
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada.
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada.
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11
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Matsui Y, Djekidel MN, Lindsay K, Samir P, Connolly N, Wu G, Yang X, Fan Y, Xu B, Peng JC. SNIP1 and PRC2 coordinate cell fates of neural progenitors during brain development. Nat Commun 2023; 14:4754. [PMID: 37553330 PMCID: PMC10409800 DOI: 10.1038/s41467-023-40487-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 07/28/2023] [Indexed: 08/10/2023] Open
Abstract
Stem cell survival versus death is a developmentally programmed process essential for morphogenesis, sizing, and quality control of genome integrity and cell fates. Cell death is pervasive during development, but its programming is little known. Here, we report that Smad nuclear interacting protein 1 (SNIP1) promotes neural progenitor cell survival and neurogenesis and is, therefore, integral to brain development. The SNIP1-depleted brain exhibits dysplasia with robust induction of caspase 9-dependent apoptosis. Mechanistically, SNIP1 regulates target genes that promote cell survival and neurogenesis, and its activities are influenced by TGFβ and NFκB signaling pathways. Further, SNIP1 facilitates the genomic occupancy of Polycomb complex PRC2 and instructs H3K27me3 turnover at target genes. Depletion of PRC2 is sufficient to reduce apoptosis and brain dysplasia and to partially restore genetic programs in the SNIP1-depleted brain in vivo. These findings suggest a loci-specific regulation of PRC2 and H3K27 marks to toggle cell survival and death in the developing brain.
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Affiliation(s)
- Yurika Matsui
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Mohamed Nadhir Djekidel
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Katherine Lindsay
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Parimal Samir
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Medical Research Building, Room 7, 138E, Galveston, TX, 77550, USA
| | - Nina Connolly
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Xiaoyang Yang
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jamy C Peng
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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12
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Wang S, Fairall L, Pham TK, Ragan TJ, Vashi D, Collins M, Dominguez C, Schwabe JR. A potential histone-chaperone activity for the MIER1 histone deacetylase complex. Nucleic Acids Res 2023; 51:6006-6019. [PMID: 37099381 PMCID: PMC10325919 DOI: 10.1093/nar/gkad294] [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: 08/10/2022] [Revised: 03/10/2023] [Accepted: 04/19/2023] [Indexed: 04/27/2023] Open
Abstract
Histone deacetylases 1 and 2 (HDAC1/2) serve as the catalytic subunit of six distinct families of nuclear complexes. These complexes repress gene transcription through removing acetyl groups from lysine residues in histone tails. In addition to the deacetylase subunit, these complexes typically contain transcription factor and/or chromatin binding activities. The MIER:HDAC complex has hitherto been poorly characterized. Here, we show that MIER1 unexpectedly co-purifies with an H2A:H2B histone dimer. We show that MIER1 is also able to bind a complete histone octamer. Intriguingly, we found that a larger MIER1:HDAC1:BAHD1:C1QBP complex additionally co-purifies with an intact nucleosome on which H3K27 is either di- or tri-methylated. Together this suggests that the MIER1 complex acts downstream of PRC2 to expand regions of repressed chromatin and could potentially deposit histone octamer onto nucleosome-depleted regions of DNA.
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Affiliation(s)
- Siyu Wang
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Louise Fairall
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Trong Khoa Pham
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- biOMICS facility, Mass Spectrometry Centre, University of Sheffield, Sheffield S10 2TN, UK
| | - Timothy J Ragan
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Dipti Vashi
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Mark O Collins
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- biOMICS facility, Mass Spectrometry Centre, University of Sheffield, Sheffield S10 2TN, UK
| | - Cyril Dominguez
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - John W R Schwabe
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
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13
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Liu P, Zhang H, Della Valle F, Orlando V. Dynamic Interactome of PRC2-EZH1 Complex Using Tandem-Affinity Purification and Quantitative Mass Spectrometry. Methods Mol Biol 2023; 2655:101-116. [PMID: 37212992 DOI: 10.1007/978-1-0716-3143-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The Polycomb repressive complex 2 (PRC2) is a well-characterized chromatin regulator of transcription programs acting through H3K27me3 deposition. In mammals, there are two main versions of PRC2 complexes: PRC2-EZH2, which is prevalent in cycling cells, and PRC2-EZH1 where EZH1 replaces EZH2 in post-mitotic tissues. Stoichiometry of PRC2 complex is dynamically modulated during cellular differentiation and various stress conditions. Therefore, unraveling unique architecture of PRC2 complexes under specific biological context through comprehensive and quantitative characterization could provide insight into the underlying mechanistic molecular mechanism in regulation of transcription process. In this chapter, we describe an efficient method which combines tandem-affinity purification (TAP) with label-free quantitative proteomics strategy for studying PRC2-EZH1 complex architecture alterations and identifying novel protein regulators in post-mitotic C2C12 skeletal muscle cells.
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Affiliation(s)
- Peng Liu
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division, KAUST Environmental Epigenetics Research Program, Thuwal, Kingdom of Saudi Arabia.
| | - Huoming Zhang
- King Abdullah University of Science and Technology, Core Labs, Thuwal, Kingdom of Saudi Arabia
| | - Francesco Della Valle
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division, KAUST Environmental Epigenetics Research Program, Thuwal, Kingdom of Saudi Arabia
| | - Valerio Orlando
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division, KAUST Environmental Epigenetics Research Program, Thuwal, Kingdom of Saudi Arabia.
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14
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Davis JL, Kennedy C, Clerkin S, Treacy NJ, Dodd T, Moss C, Murphy A, Brazil DP, Cagney G, Brougham DF, Murad R, Finlay D, Vuori K, Crean J. Single-cell multiomics reveals the complexity of TGFβ signalling to chromatin in iPSC-derived kidney organoids. Commun Biol 2022; 5:1301. [PMID: 36435939 PMCID: PMC9701233 DOI: 10.1038/s42003-022-04264-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 11/11/2022] [Indexed: 11/28/2022] Open
Abstract
TGFβ1 plays a regulatory role in the determination of renal cell fate and the progression of renal fibrosis. Here we show an association between SMAD3 and the histone methyltransferase, EZH2, during cell differentiation; ChIP-seq revealed that SMAD3 and EZH2 co-occupy the genome in iPSCs and in iPSC-derived nephron progenitors. Through integration of single cell gene expression and epigenome profiling, we identified de novo ACTA2+ve/POSTN+ve myofibroblasts in kidney organoids treated with TGFβ1, characterised by increased SMAD3-dependent cis chromatin accessibility and gene expression associated with fibroblast activation. We have identified fibrosis-associated regulons characterised by enrichment of SMAD3, AP1, the ETS family of transcription factors, and NUAK1, CREB3L1, and RARG, corresponding to enriched motifs at accessible loci identified by scATACseq. Treatment with the EZH2 specific inhibitor GSK343, blocked SMAD3-dependent cis co-accessibility and inhibited myofibroblast activation. This mechanism, through which TGFβ signals directly to chromatin, represents a critical determinant of fibrotic, differentiated states.
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Affiliation(s)
- Jessica L. Davis
- grid.7886.10000 0001 0768 2743UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Ciaran Kennedy
- grid.7886.10000 0001 0768 2743UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Shane Clerkin
- grid.7886.10000 0001 0768 2743UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Niall J. Treacy
- grid.7886.10000 0001 0768 2743UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Thomas Dodd
- grid.7886.10000 0001 0768 2743UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Catherine Moss
- grid.7886.10000 0001 0768 2743UCD Genomics Core Facility, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Alison Murphy
- grid.7886.10000 0001 0768 2743UCD Genomics Core Facility, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Derek P. Brazil
- grid.4777.30000 0004 0374 7521Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, BT9 7BL Northern Ireland, UK
| | - Gerard Cagney
- grid.7886.10000 0001 0768 2743UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Dermot F. Brougham
- grid.7886.10000 0001 0768 2743UCD School of Chemistry, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Rabi Murad
- grid.479509.60000 0001 0163 8573Sanford Burnham Prebys Institute for Medical Discovery, La Jolla, CA 92037 USA
| | - Darren Finlay
- grid.479509.60000 0001 0163 8573Sanford Burnham Prebys Institute for Medical Discovery, La Jolla, CA 92037 USA
| | - Kristiina Vuori
- grid.479509.60000 0001 0163 8573Sanford Burnham Prebys Institute for Medical Discovery, La Jolla, CA 92037 USA
| | - John Crean
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4, Ireland.
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15
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Kim JJ, Kingston RE. Context-specific Polycomb mechanisms in development. Nat Rev Genet 2022; 23:680-695. [PMID: 35681061 PMCID: PMC9933872 DOI: 10.1038/s41576-022-00499-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2022] [Indexed: 12/11/2022]
Abstract
Polycomb group (PcG) proteins are crucial chromatin regulators that maintain repression of lineage-inappropriate genes and are therefore required for stable cell fate. Recent advances show that PcG proteins form distinct multi-protein complexes in various cellular environments, such as in early development, adult tissue maintenance and cancer. This surprising compositional diversity provides the basis for mechanistic diversity. Understanding this complexity deepens and refines the principles of PcG complex recruitment, target-gene repression and inheritance of memory. We review how the core molecular mechanism of Polycomb complexes operates in diverse developmental settings and propose that context-dependent changes in composition and mechanism are essential for proper epigenetic regulation in development.
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Affiliation(s)
- Jongmin J. Kim
- Department of Molecular Biology and MGH Research Institute, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Robert E. Kingston
- Department of Molecular Biology and MGH Research Institute, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,
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16
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Laudadio I, Bastianelli A, Fulci V, Carissimi C, Colantoni E, Palone F, Vitali R, Lorefice E, Cucchiara S, Negroni A, Stronati L. ZNF281 Promotes Colon Fibroblast Activation in TGFβ1-Induced Gut Fibrosis. Int J Mol Sci 2022; 23:ijms231810261. [PMID: 36142169 PMCID: PMC9499662 DOI: 10.3390/ijms231810261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/29/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
Crohn’s disease (CD) and ulcerative colitis (UC) are chronic inflammatory disorders of the gastrointestinal tract. Chronic inflammation is the main factor leading to intestinal fibrosis, resulting in recurrent stenosis, especially in CD patients. Currently, the underlying molecular mechanisms of fibrosis are still unclear. ZNF281 is a zinc-finger transcriptional regulator that has been characterized as an epithelial-to-mesenchymal transition (EMT)-inducing transcription factor, suggesting its involvement in the regulation of pluripotency, stemness, and cancer. The aim of this study is to investigate in vivo and in vitro the role of ZNF281 in intestinal fibrogenesis. Intestinal fibrosis was studied in vivo in C57BL/6J mice with chronic colitis induced by two or three cycles of administration of dextran sulfate sodium (DSS). The contribution of ZNF281 to gut fibrosis was studied in vitro in the human colon fibroblast cell line CCD-18Co, activated by the pro-fibrotic cytokine TGFβ1. ZNF281 was downregulated by siRNA transfection, and RNA-sequencing was performed to identify genes regulated by TGFβ1 in activated colon fibroblasts via ZNF281. Results showed a marked increase of ZNF281 in in vivo murine fibrotic colon as well as in in vitro human colon fibroblasts activated by TGFβ1. Moreover, abrogation of ZNF281 in TGFβ1-treated fibroblasts affected the expression of genes belonging to specific pathways linked to fibroblast activation and differentiation into myofibroblasts. We demonstrated that ZNF281 is a key regulator of colon fibroblast activation and myofibroblast differentiation upon fibrotic stimuli by transcriptionally controlling extracellular matrix (ECM) composition, remodeling, and cell contraction, highlighting a new role in the onset and progression of gut fibrosis.
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Affiliation(s)
- Ilaria Laudadio
- Department of Molecular Medicine, Sapienza University, 00161 Rome, Italy
- Correspondence:
| | - Alex Bastianelli
- Department of Molecular Medicine, Sapienza University, 00161 Rome, Italy
| | - Valerio Fulci
- Department of Molecular Medicine, Sapienza University, 00161 Rome, Italy
| | - Claudia Carissimi
- Department of Molecular Medicine, Sapienza University, 00161 Rome, Italy
| | | | - Francesca Palone
- Division of Health Protection Technologies, ENEA, 00123 Rome, Italy
| | - Roberta Vitali
- Division of Health Protection Technologies, ENEA, 00123 Rome, Italy
| | - Elisa Lorefice
- Department of Molecular Medicine, Sapienza University, 00161 Rome, Italy
| | - Salvatore Cucchiara
- Department of Maternal Infantile and Urological Sciences, Sapienza University, 00161 Rome, Italy
| | - Anna Negroni
- Division of Health Protection Technologies, ENEA, 00123 Rome, Italy
| | - Laura Stronati
- Department of Molecular Medicine, Sapienza University, 00161 Rome, Italy
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17
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Critical Roles of Polycomb Repressive Complexes in Transcription and Cancer. Int J Mol Sci 2022; 23:ijms23179574. [PMID: 36076977 PMCID: PMC9455514 DOI: 10.3390/ijms23179574] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Polycomp group (PcG) proteins are members of highly conserved multiprotein complexes, recognized as gene transcriptional repressors during development and shown to play a role in various physiological and pathological processes. PcG proteins consist of two Polycomb repressive complexes (PRCs) with different enzymatic activities: Polycomb repressive complexes 1 (PRC1), a ubiquitin ligase, and Polycomb repressive complexes 2 (PRC2), a histone methyltransferase. Traditionally, PRCs have been described to be associated with transcriptional repression of homeotic genes, as well as gene transcription activating effects. Particularly in cancer, PRCs have been found to misregulate gene expression, not only depending on the function of the whole PRCs, but also through their separate subunits. In this review, we focused especially on the recent findings in the transcriptional regulation of PRCs, the oncogenic and tumor-suppressive roles of PcG proteins, and the research progress of inhibitors targeting PRCs.
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18
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De Novo Polycomb Recruitment and Repressive Domain Formation. EPIGENOMES 2022; 6:epigenomes6030025. [PMID: 35997371 PMCID: PMC9397058 DOI: 10.3390/epigenomes6030025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 11/29/2022] Open
Abstract
Every cell of an organism shares the same genome; even so, each cellular lineage owns a different transcriptome and proteome. The Polycomb group proteins (PcG) are essential regulators of gene repression patterning during development and homeostasis. However, it is unknown how the repressive complexes, PRC1 and PRC2, identify their targets and elicit new Polycomb domains during cell differentiation. Classical recruitment models consider the pre-existence of repressive histone marks; still, de novo target binding overcomes the absence of both H3K27me3 and H2AK119ub. The CpG islands (CGIs), non-core proteins, and RNA molecules are involved in Polycomb recruitment. Nonetheless, it is unclear how de novo targets are identified depending on the physiological context and developmental stage and which are the leading players stabilizing Polycomb complexes at domain nucleation sites. Here, we examine the features of de novo sites and the accessory elements bridging its recruitment and discuss the first steps of Polycomb domain formation and transcriptional regulation, comprehended by the experimental reconstruction of the repressive domains through time-resolved genomic analyses in mammals.
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The Role of Polycomb Proteins in Cell Lineage Commitment and Embryonic Development. EPIGENOMES 2022; 6:epigenomes6030023. [PMID: 35997369 PMCID: PMC9397020 DOI: 10.3390/epigenomes6030023] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
Embryonic development is a highly intricate and complex process. Different regulatory mechanisms cooperatively dictate the fate of cells as they progress from pluripotent stem cells to terminally differentiated cell types in tissues. A crucial regulator of these processes is the Polycomb Repressive Complex 2 (PRC2). By catalyzing the mono-, di-, and tri-methylation of lysine residues on histone H3 tails (H3K27me3), PRC2 compacts chromatin by cooperating with Polycomb Repressive Complex 1 (PRC1) and represses transcription of target genes. Proteomic and biochemical studies have revealed two variant complexes of PRC2, namely PRC2.1 which consists of the core proteins (EZH2, SUZ12, EED, and RBBP4/7) interacting with one of the Polycomb-like proteins (MTF2, PHF1, PHF19), and EPOP or PALI1/2, and PRC2.2 which contains JARID2 and AEBP2 proteins. MTF2 and JARID2 have been discovered to have crucial roles in directing and recruiting PRC2 to target genes for repression in embryonic stem cells (ESCs). Following these findings, recent work in the field has begun to explore the roles of different PRC2 variant complexes during different stages of embryonic development, by examining molecular phenotypes of PRC2 mutants in both in vitro (2D and 3D differentiation) and in vivo (knock-out mice) assays, analyzed with modern single-cell omics and biochemical assays. In this review, we discuss the latest findings that uncovered the roles of different PRC2 proteins during cell-fate and lineage specification and extrapolate these findings to define a developmental roadmap for different flavors of PRC2 regulation during mammalian embryonic development.
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20
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Drosos Y, Myers JA, Xu B, Mathias KM, Beane EC, Radko-Juettner S, Mobley RJ, Larsen ME, Piccioni F, Ma X, Low J, Hansen BS, Peters ST, Bhanu NV, Dhanda SK, Chen T, Upadhyaya SA, Pruett-Miller SM, Root DE, Garcia BA, Partridge JF, Roberts CW. NSD1 mediates antagonism between SWI/SNF and polycomb complexes and is required for transcriptional activation upon EZH2 inhibition. Mol Cell 2022; 82:2472-2489.e8. [DOI: 10.1016/j.molcel.2022.04.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/03/2022] [Accepted: 04/11/2022] [Indexed: 12/13/2022]
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21
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Oliviero G, Kovalchuk S, Rogowska-Wrzesinska A, Schwämmle V, Jensen ON. Distinct and diverse chromatin-proteomes of ageing mouse organs reveal protein signatures that correlate with physiological functions. eLife 2022; 11:73524. [PMID: 35259090 PMCID: PMC8933006 DOI: 10.7554/elife.73524] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
Temporal molecular changes in ageing mammalian organs are of relevance to disease aetiology because many age-related diseases are linked to changes in the transcriptional and epigenetic machinery that regulate gene expression. We performed quantitative proteome analysis of chromatin-enriched protein extracts to investigate the dynamics of the chromatin proteomes of the mouse brain, heart, lung, kidney, liver, and spleen at 3, 5, 10, and 15 months of age. Each organ exhibited a distinct chromatin proteome and sets of unique proteins. The brain and spleen chromatin proteomes were the most extensive, diverse, and heterogenous among the six organs. The spleen chromatin proteome appeared static during the lifespan, presenting a young phenotype that reflects the permanent alertness state and important role of this organ in physiological defence and immunity. We identified a total of 5928 proteins, including 2472 nuclear or chromatin-associated proteins across the six mouse organs. Up to 3125 proteins were quantified in each organ, demonstrating distinct and organ-specific temporal protein expression timelines and regulation at the post-translational level. Bioinformatics meta-analysis of these chromatin proteomes revealed distinct physiological and ageing-related features for each organ. Our results demonstrate the efficiency of organelle-specific proteomics for in vivo studies of a model organism and consolidate the hypothesis that chromatin-associated proteins are involved in distinct and specific physiological functions in ageing organs.
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Affiliation(s)
- Giorgio Oliviero
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Sergey Kovalchuk
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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22
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Chan N, Huang J, Ma G, Zeng H, Donahue K, Wang Y, Li L, Xu W. The transcriptional elongation factor CTR9 demarcates PRC2-mediated H3K27me3 domains by altering PRC2 subtype equilibrium. Nucleic Acids Res 2022; 50:1969-1992. [PMID: 35137163 PMCID: PMC8887485 DOI: 10.1093/nar/gkac047] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 01/07/2022] [Accepted: 01/14/2022] [Indexed: 01/27/2023] Open
Abstract
CTR9 is the scaffold subunit in polymerase-associated factor complex (PAFc), a multifunctional complex employed in multiple steps of RNA Polymerase II (RNAPII)-mediated transcription. CTR9/PAFc is well known as an evolutionarily conserved elongation factor that regulates gene activation via coupling with histone modifications enzymes. However, little is known about its function to restrain repressive histone markers. Using inducible and stable CTR9 knockdown breast cancer cell lines, we discovered that the H3K27me3 levels are strictly controlled by CTR9. Quantitative profiling of histone modifications revealed a striking increase of H3K27me3 levels upon loss of CTR9. Moreover, loss of CTR9 leads to genome-wide expansion of H3K27me3, as well as increased recruitment of PRC2 on chromatin, which can be reversed by CTR9 restoration. Further, CTR9 depletion triggers a PRC2 subtype switch from the less active PRC2.2, to the more active PRC2.1 with higher methyltransferase activity. As a consequence, CTR9 depletion generates vulnerability that renders breast cancer cells hypersensitive to PRC2 inhibitors. Our findings that CTR9 demarcates PRC2-mediated H3K27me3 levels and genomic distribution provide a unique mechanism that explains the transition from transcriptionally active chromatin states to repressive chromatin states and sheds light on the biological functions of CTR9 in development and cancer.
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Affiliation(s)
- Ngai Ting Chan
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Gui Ma
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hao Zeng
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kristine Donahue
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yidan Wang
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA,Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wei Xu
- To whom correspondence should be addressed. Tel: +1 608 265 5540; Fax: +1 608 262 2824; Email :
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23
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Osokine I, Siewiera J, Rideaux D, Ma S, Tsukui T, Erlebacher A. Gene silencing by EZH2 suppresses TGF-β activity within the decidua to avert pregnancy-adverse wound healing at the maternal-fetal interface. Cell Rep 2022; 38:110329. [PMID: 35108527 PMCID: PMC8833843 DOI: 10.1016/j.celrep.2022.110329] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 10/23/2021] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
A little-appreciated feature of early pregnancy is that embryo implantation and placental outgrowth do not evoke wound-healing responses in the decidua, the specialized endometrial tissue that surrounds the conceptus. Here, we provide evidence that this phenomenon is partly due to an active program of gene silencing mediated by EZH2, a histone methyltransferase that generates repressive histone 3 lysine 27 trimethyl (H3K27me3) histone marks. We find that pregnancies in mice with EZH2-deficient decidual stromal cells frequently fail by mid-gestation, with the decidua showing ectopic myofibroblast formation, peri-embryonic collagen deposition, and gene expression profiles associated with transforming growth factor β (TGF-β)-driven fibroblast activation and fibrogenic extracellular matrix (ECM) remodeling. Analogous responses are observed when the mutant decidua is surgically wounded, while blockade of TGF-β receptor signaling inhibits the defects and improves reproductive outcomes. Together, these results highlight a critical feature of reproductive success and have implications for the context-specific control of TGF-β-mediated wound-healing responses elsewhere in the body.
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Affiliation(s)
- Ivan Osokine
- Department of Laboratory Medicine, University of California San Francisco, 513 Parnassus Avenue Medical Sciences, S-1057B, San Francisco, CA 94143-0451, USA
| | - Johan Siewiera
- Department of Laboratory Medicine, University of California San Francisco, 513 Parnassus Avenue Medical Sciences, S-1057B, San Francisco, CA 94143-0451, USA
| | - Damon Rideaux
- Department of Laboratory Medicine, University of California San Francisco, 513 Parnassus Avenue Medical Sciences, S-1057B, San Francisco, CA 94143-0451, USA
| | - Stephany Ma
- Department of Laboratory Medicine, University of California San Francisco, 513 Parnassus Avenue Medical Sciences, S-1057B, San Francisco, CA 94143-0451, USA
| | - Tatsuya Tsukui
- Lung Biology Center, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Adrian Erlebacher
- Department of Laboratory Medicine, University of California San Francisco, 513 Parnassus Avenue Medical Sciences, S-1057B, San Francisco, CA 94143-0451, USA; Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Program, University of California San Francisco, San Francisco, CA 94143, USA; Bakar ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA.
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24
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Gardner ML, Freitas MA. Multiple Imputation Approaches Applied to the Missing Value Problem in Bottom-Up Proteomics. Int J Mol Sci 2021; 22:ijms22179650. [PMID: 34502557 PMCID: PMC8431783 DOI: 10.3390/ijms22179650] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/28/2021] [Accepted: 08/31/2021] [Indexed: 01/15/2023] Open
Abstract
Analysis of differential abundance in proteomics data sets requires careful application of missing value imputation. Missing abundance values widely vary when performing comparisons across different sample treatments. For example, one would expect a consistent rate of “missing at random” (MAR) across batches of samples and varying rates of “missing not at random” (MNAR) depending on the inherent difference in sample treatments within the study. The missing value imputation strategy must thus be selected that best accounts for both MAR and MNAR simultaneously. Several important issues must be considered when deciding the appropriate missing value imputation strategy: (1) when it is appropriate to impute data; (2) how to choose a method that reflects the combinatorial manner of MAR and MNAR that occurs in an experiment. This paper provides an evaluation of missing value imputation strategies used in proteomics and presents a case for the use of hybrid left-censored missing value imputation approaches that can handle the MNAR problem common to proteomics data.
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Affiliation(s)
- Miranda L. Gardner
- Ohio State Biochemistry Program, Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA;
- Cancer Biology and Genetics, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA
| | - Michael A. Freitas
- Ohio State Biochemistry Program, Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA;
- Cancer Biology and Genetics, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA
- Correspondence: or
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25
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PALI1 facilitates DNA and nucleosome binding by PRC2 and triggers an allosteric activation of catalysis. Nat Commun 2021; 12:4592. [PMID: 34321472 PMCID: PMC8319299 DOI: 10.1038/s41467-021-24866-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/07/2021] [Indexed: 01/07/2023] Open
Abstract
The polycomb repressive complex 2 (PRC2) is a histone methyltransferase that maintains cell identities. JARID2 is the only accessory subunit of PRC2 that known to trigger an allosteric activation of methyltransferase. Yet, this mechanism cannot be generalised to all PRC2 variants as, in vertebrates, JARID2 is mutually exclusive with most of the accessory subunits of PRC2. Here we provide functional and structural evidence that the vertebrate-specific PRC2 accessory subunit PALI1 emerged through a convergent evolution to mimic JARID2 at the molecular level. Mechanistically, PRC2 methylates PALI1 K1241, which then binds to the PRC2-regulatory subunit EED to allosterically activate PRC2. PALI1 K1241 is methylated in mouse and human cell lines and is essential for PALI1-induced allosteric activation of PRC2. High-resolution crystal structures revealed that PALI1 mimics the regulatory interactions formed between JARID2 and EED. Independently, PALI1 also facilitates DNA and nucleosome binding by PRC2. In acute myelogenous leukemia cells, overexpression of PALI1 leads to cell differentiation, with the phenotype altered by a separation-of-function PALI1 mutation, defective in allosteric activation and active in DNA binding. Collectively, we show that PALI1 facilitates catalysis and substrate binding by PRC2 and provide evidence that subunit-induced allosteric activation is a general property of holo-PRC2 complexes. The polycomb repressive complex 2 (PRC2) is a histone methyltransferase regulating cell differentiation and identity. Here, the authors show that the vertebrate-specific PRC2 accessory subunit PALI1 facilitates substrate binding by the complex and elucidate the allosteric mechanism of PALI1- mediated PRC2 activation.
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26
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Petracovici A, Bonasio R. Distinct PRC2 subunits regulate maintenance and establishment of Polycomb repression during differentiation. Mol Cell 2021; 81:2625-2639.e5. [PMID: 33887196 PMCID: PMC8217195 DOI: 10.1016/j.molcel.2021.03.038] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 02/10/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023]
Abstract
The Polycomb repressive complex 2 (PRC2) is an essential epigenetic regulator that deposits repressive H3K27me3. PRC2 subunits form two holocomplexes-PRC2.1 and PRC2.2-but the roles of these two PRC2 assemblies during differentiation are unclear. We employed auxin-inducible degradation to deplete PRC2.1 subunit MTF2 or PRC2.2 subunit JARID2 during differentiation of embryonic stem cells (ESCs) to neural progenitors (NPCs). Depletion of either MTF2 or JARID2 resulted in incomplete differentiation due to defects in gene regulation. Distinct sets of Polycomb target genes were derepressed in the absence of MTF2 or JARID2. MTF2-sensitive genes were marked by H3K27me3 in ESCs and remained silent during differentiation, whereas JARID2-sensitive genes were preferentially active in ESCs and became newly repressed in NPCs. Thus, MTF2 and JARID2 contribute non-redundantly to Polycomb silencing, suggesting that PRC2.1 and PRC2.2 have distinct functions in maintaining and establishing, respectively, Polycomb repression during differentiation.
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Affiliation(s)
- Ana Petracovici
- Graduate Group in Cell and Molecular Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Roberto Bonasio
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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27
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Liu X. A Structural Perspective on Gene Repression by Polycomb Repressive Complex 2. Subcell Biochem 2020; 96:519-562. [PMID: 33252743 DOI: 10.1007/978-3-030-58971-4_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Polycomb Repressive Complex 2 (PRC2) is a major repressive chromatin complex formed by the Polycomb Group (PcG) proteins. PRC2 mediates trimethylation of histone H3 lysine 27 (H3K27me3), a hallmark of gene silencing. PRC2 is a key regulator of development, impacting many fundamental biological processes, like stem cell differentiation in mammals and vernalization in plants. Misregulation of PRC2 function is linked to a variety of human cancers and developmental disorders. In correlation with its diverse roles in development, PRC2 displays a high degree of compositional complexity and plasticity. Structural biology research over the past decade has shed light on the molecular mechanisms of the assembly, catalysis, allosteric activation, autoinhibition, chemical inhibition, dimerization and chromatin targeting of various developmentally regulated PRC2 complexes. In addition to these aspects, structure-function analysis is also discussed in connection with disease data in this chapter.
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Affiliation(s)
- Xin Liu
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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28
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Brunet M, Vargas C, Larrieu D, Torrisani J, Dufresne M. E3 Ubiquitin Ligase TRIP12: Regulation, Structure, and Physiopathological Functions. Int J Mol Sci 2020; 21:ijms21228515. [PMID: 33198194 PMCID: PMC7697007 DOI: 10.3390/ijms21228515] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023] Open
Abstract
The Thyroid hormone Receptor Interacting Protein 12 (TRIP12) protein belongs to the 28-member Homologous to the E6-AP C-Terminus (HECT) E3 ubiquitin ligase family. First described as an interactor of the thyroid hormone receptor, TRIP12’s biological importance was revealed by the embryonic lethality of a murine model bearing an inactivating mutation in the TRIP12 gene. Further studies showed the participation of TRIP12 in the regulation of major biological processes such as cell cycle progression, DNA damage repair, chromatin remodeling, and cell differentiation by an ubiquitination-mediated degradation of key protein substrates. Moreover, alterations of TRIP12 expression have been reported in cancers that can serve as predictive markers of therapeutic response. The TRIP12 gene is also referenced as a causative gene associated to intellectual disorders such as Clark–Baraitser syndrome and is clearly implicated in Autism Spectrum Disorder. The aim of the review is to provide an exhaustive and integrated overview of the different aspects of TRIP12 ranging from its regulation, molecular functions and physio-pathological implications.
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Affiliation(s)
- Manon Brunet
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
| | - Claire Vargas
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
| | - Dorian Larrieu
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
| | - Jérôme Torrisani
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
- Correspondence: (J.T.); (M.D.); Tel.: +33-582-741-644 (J.T.); +33-582-741-643 (M.D.)
| | - Marlène Dufresne
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
- Correspondence: (J.T.); (M.D.); Tel.: +33-582-741-644 (J.T.); +33-582-741-643 (M.D.)
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29
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Bradfield A, Button L, Drury J, Green DC, Hill CJ, Hapangama DK. Investigating the Role of Telomere and Telomerase Associated Genes and Proteins in Endometrial Cancer. Methods Protoc 2020; 3:E63. [PMID: 32899298 PMCID: PMC7565490 DOI: 10.3390/mps3030063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/24/2020] [Accepted: 08/30/2020] [Indexed: 12/16/2022] Open
Abstract
Endometrial cancer (EC) is the commonest gynaecological malignancy. Current prognostic markers are inadequate to accurately predict patient survival, necessitating novel prognostic markers, to improve treatment strategies. Telomerase has a unique role within the endometrium, whilst aberrant telomerase activity is a hallmark of many cancers. The aim of the current in silico study is to investigate the role of telomere and telomerase associated genes and proteins (TTAGPs) in EC to identify potential prognostic markers and therapeutic targets. Analysis of RNA-seq data from The Cancer Genome Atlas identified differentially expressed genes (DEGs) in EC (568 TTAGPs out of 3467) and ascertained DEGs associated with histological subtypes, higher grade endometrioid tumours and late stage EC. Functional analysis demonstrated that DEGs were predominantly involved in cell cycle regulation, while the survival analysis identified 69 DEGs associated with prognosis. The protein-protein interaction network constructed facilitated the identification of hub genes, enriched transcription factor binding sites and drugs that may target the network. Thus, our in silico methods distinguished many critical genes associated with telomere maintenance that were previously unknown to contribute to EC carcinogenesis and prognosis, including NOP56, WFS1, ANAPC4 and TUBB4A. Probing the prognostic and therapeutic utility of these novel TTAGP markers will form an exciting basis for future research.
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Affiliation(s)
- Alice Bradfield
- Department of Women’s and Children’s Health, University of Liverpool, Crown St, Liverpool L69 7ZX, UK; (A.B.); (J.D.); (C.J.H.)
| | - Lucy Button
- Faculty of Health and Life Sciences, University of Liverpool, Brownlow Hill, Liverpool L69 7ZX, UK;
| | - Josephine Drury
- Department of Women’s and Children’s Health, University of Liverpool, Crown St, Liverpool L69 7ZX, UK; (A.B.); (J.D.); (C.J.H.)
| | - Daniel C. Green
- Institute of Life Course and Medical Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L7 8TX, UK;
| | - Christopher J. Hill
- Department of Women’s and Children’s Health, University of Liverpool, Crown St, Liverpool L69 7ZX, UK; (A.B.); (J.D.); (C.J.H.)
| | - Dharani K. Hapangama
- Department of Women’s and Children’s Health, University of Liverpool, Crown St, Liverpool L69 7ZX, UK; (A.B.); (J.D.); (C.J.H.)
- Liverpool Women’s NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool L8 7SS, UK
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30
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Ybx1 fine-tunes PRC2 activities to control embryonic brain development. Nat Commun 2020; 11:4060. [PMID: 32792512 PMCID: PMC7426271 DOI: 10.1038/s41467-020-17878-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 07/22/2020] [Indexed: 01/28/2023] Open
Abstract
Chromatin modifiers affect spatiotemporal gene expression programs that underlie organismal development. The Polycomb repressive complex 2 (PRC2) is a crucial chromatin modifier in executing neurodevelopmental programs. Here, we find that PRC2 interacts with the nucleic acid-binding protein Ybx1. In the mouse embryo in vivo, Ybx1 is required for forebrain specification and restricting mid-hindbrain growth. In neural progenitor cells (NPCs), Ybx1 controls self-renewal and neuronal differentiation. Mechanistically, Ybx1 highly overlaps PRC2 binding genome-wide, controls PRC2 distribution, and inhibits H3K27me3 levels. These functions are consistent with Ybx1-mediated promotion of genes involved in forebrain specification, cell proliferation, or neuronal differentiation. In Ybx1-knockout NPCs, H3K27me3 reduction by PRC2 enzymatic inhibitor or genetic depletion partially rescues gene expression and NPC functions. Our findings suggest that Ybx1 fine-tunes PRC2 activities to regulate spatiotemporal gene expression in embryonic neural development and uncover a crucial epigenetic mechanism balancing forebrain-hindbrain lineages and self-renewal-differentiation choices in NPCs.
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31
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Richart L, Margueron R. Drugging histone methyltransferases in cancer. Curr Opin Chem Biol 2020; 56:51-62. [DOI: 10.1016/j.cbpa.2019.11.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 02/06/2023]
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Larrieu D, Brunet M, Vargas C, Hanoun N, Ligat L, Dagnon L, Lulka H, Pommier RM, Selves J, Jády BE, Bartholin L, Cordelier P, Dufresne M, Torrisani J. The E3 ubiquitin ligase TRIP12 participates in cell cycle progression and chromosome stability. Sci Rep 2020; 10:789. [PMID: 31964993 PMCID: PMC6972862 DOI: 10.1038/s41598-020-57762-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/03/2020] [Indexed: 12/29/2022] Open
Abstract
Several studies have linked the E3 ubiquitin ligase TRIP12 (Thyroid hormone Receptor Interacting Protein 12) to the cell cycle. However, the regulation and the implication of this protein during the cell cycle are largely unknown. In this study, we show that TRIP12 expression is regulated during the cell cycle, which correlates with its nuclear localization. We identify an euchromatin-binding function of TRIP12 mediated by a N-terminal intrinsically disordered region. We demonstrate the functional implication of TRIP12 in the mitotic entry by controlling the duration of DNA replication that is independent from its catalytic activity. We also show the requirement of TRIP12 in the mitotic progression and chromosome stability. Altogether, our findings show that TRIP12 is as a new chromatin-associated protein with several implications in the cell cycle progression and in the maintenance of genome integrity.
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Affiliation(s)
- D Larrieu
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - M Brunet
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - C Vargas
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - N Hanoun
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - L Ligat
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - L Dagnon
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - H Lulka
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - R M Pommier
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon, 69008, France
| | - J Selves
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - B E Jády
- Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, Centre de Biologie Intégrative, Université Toulouse III-Paul Sabatier, Toulouse, Cedex 9, France
| | - L Bartholin
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon, 69008, France
| | - P Cordelier
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - M Dufresne
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - J Torrisani
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France.
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C10ORF12 modulates PRC2 histone methyltransferase activity and H3K27me3 levels. Acta Pharmacol Sin 2019; 40:1457-1465. [PMID: 31186533 DOI: 10.1038/s41401-019-0247-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/05/2019] [Indexed: 01/03/2023] Open
Abstract
The polycomb repressive complex 2 (PRC2) catalyzes the methylation of histone H3 on lysine 27 (H3K27) to generate trimethyl-H3K27 (H3K27me3) marks, thereby leading to a repressive chromatin state that inhibits gene expression. C10ORF12 was recently identified as a novel PRC2 interactor. Here, we show that C10ORF12 specifically interacts with PRC2 through its middle region (positions 619-718). C10ORF12 significantly enhances the histone methyltransferase activity of PRC2 in vitro and dramatically increases the total H3K27me3 levels in HeLa cells. C10ORF12 also antagonizes Jarid2, which is an auxiliary factor of the PRC2.2 subcomplex, to promote increased H3K27me3 levels in HeLa cells. Moreover, C10ORF12 alters the substrate preference of PRC2. These results indicate that C10ORF12 functions as a positive regulator of PRC2 and facilitates PRC2-mediated H3K27me3 modification of chromatin. These findings provide new insight into the roles of C10ORF12 in regulating the activity of the PRC2 complex.
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Abstract
Polycomb repressive complex 2 (PRC2) is a conserved chromatin regulator that is responsible for the methylation of histone H3 lysine 27 (H3K27). PRC2 is essential for normal development and its loss of function thus results in a range of developmental phenotypes. Here, we review the latest advances in our understanding of mammalian PRC2 activity and present an updated summary of the phenotypes associated with its loss of function in mice. We then discuss recent studies that have highlighted regulatory interplay between the modifications laid down by PRC2 and other chromatin modifiers, including NSD1 and DNMT3A. Finally, we propose a model in which the dysregulation of these modifications at intergenic regions is a shared molecular feature of genetically distinct but highly phenotypically similar overgrowth syndromes in humans.
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Affiliation(s)
- Orla Deevy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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Healy E, Mucha M, Glancy E, Fitzpatrick DJ, Conway E, Neikes HK, Monger C, Van Mierlo G, Baltissen MP, Koseki Y, Vermeulen M, Koseki H, Bracken AP. PRC2.1 and PRC2.2 Synergize to Coordinate H3K27 Trimethylation. Mol Cell 2019; 76:437-452.e6. [PMID: 31521505 DOI: 10.1016/j.molcel.2019.08.012] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/28/2019] [Accepted: 08/12/2019] [Indexed: 12/12/2022]
Abstract
Polycomb repressive complex 2 (PRC2) is composed of EED, SUZ12, and EZH1/2 and mediates mono-, di-, and trimethylation of histone H3 at lysine 27. At least two independent subcomplexes exist, defined by their specific accessory proteins: PRC2.1 (PCL1-3, EPOP, and PALI1/2) and PRC2.2 (AEBP2 and JARID2). We show that PRC2.1 and PRC2.2 share the majority of target genes in mouse embryonic stem cells. The loss of PCL1-3 is sufficient to evict PRC2.1 from Polycomb target genes but only leads to a partial reduction of PRC2.2 and H3K27me3. Conversely, disruption of PRC2.2 function through the loss of either JARID2 or RING1A/B is insufficient to completely disrupt targeting of SUZ12 by PCLs. Instead, the combined loss of both PRC2.1 and PRC2.2 is required, leading to the global mislocalization of SUZ12. This supports a model in which the specific accessory proteins within PRC2.1 and PRC2.2 cooperate to direct H3K27me3 via both synergistic and independent mechanisms.
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Affiliation(s)
- Evan Healy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Marlena Mucha
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eleanor Glancy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Eric Conway
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Hannah K Neikes
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Craig Monger
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Guido Van Mierlo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Marijke P Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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van Mierlo G, Wester RA, Marks H. A Mass Spectrometry Survey of Chromatin-Associated Proteins in Pluripotency and Early Lineage Commitment. Proteomics 2019; 19:e1900047. [PMID: 31219242 DOI: 10.1002/pmic.201900047] [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: 04/28/2019] [Revised: 06/07/2019] [Indexed: 12/12/2022]
Abstract
Pluripotency can be captured in vitro in the form of Embryonic Stem Cells (ESCs). These ESCs can be either maintained in the unrestricted "naïve" state of pluripotency, adapted to developmentally more constrained "primed" pluripotency or differentiated towards each of the three germ layers. Epigenetic protein complexes and transcription factors have been shown to specify and instruct transitions from ESCs to distinct cell states. In this study, proteomic profiling of the chromatin landscape by chromatin enrichment for proteomics (ChEP) is used in mouse naive pluripotent ESCs, primed pluripotent Epiblast stem cells (EpiSCs), and cells in early stages of differentiation. A comprehensive overview of epigenetic protein complexes associated with the chromatin is provided and proteins associated with the maintenance and loss of pluripotency are identified. The data reveal major compositional alterations of epigenetic complexes during priming and differentiation of naïve pluripotent ESCs. These results contribute to the understanding of ESC differentiation and provide a framework for future studies of lineage commitment of ESCs.
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Affiliation(s)
- Guido van Mierlo
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, 6525GA, The Netherlands.,Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University, Nijmegen, 6525GA, The Netherlands
| | - Roelof Alexander Wester
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, 6525GA, The Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, 6525GA, The Netherlands
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37
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van Mierlo G, Veenstra GJC, Vermeulen M, Marks H. The Complexity of PRC2 Subcomplexes. Trends Cell Biol 2019; 29:660-671. [PMID: 31178244 DOI: 10.1016/j.tcb.2019.05.004] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/26/2019] [Accepted: 05/03/2019] [Indexed: 12/12/2022]
Abstract
Polycomb repressive complex 2 (PRC2) is a multisubunit protein complex essential for the development of multicellular organisms. Recruitment of PRC2 to target genes, followed by deposition and propagation of its catalytic product histone H3 lysine 27 trimethylation (H3K27me3), are key to the spatiotemporal control of developmental gene expression. Recent breakthrough studies have uncovered unexpected roles for substoichiometric PRC2 subunits in these processes. Here, we elaborate on how the facultative PRC2 subunits regulate catalytic activity, locus-specific PRC2 binding, and propagation of H3K27me3, and how this affects chromatin structure, gene expression, and cell fate.
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Affiliation(s)
- Guido van Mierlo
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen 6525GA, The Netherlands; Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University, Nijmegen 6525GA, The Netherlands
| | - Gert Jan C Veenstra
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen 6500HB, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen 6525GA, The Netherlands; Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University, Nijmegen 6525GA, The Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen 6525GA, The Netherlands.
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38
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Lei A, Chen L, Zhang M, Yang X, Xu L, Cao N, Zhang Z, Cao Y. EZH2 Regulates Protein Stability via Recruiting USP7 to Mediate Neuronal Gene Expression in Cancer Cells. Front Genet 2019; 10:422. [PMID: 31130994 PMCID: PMC6510286 DOI: 10.3389/fgene.2019.00422] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/17/2019] [Indexed: 01/01/2023] Open
Abstract
Misexpression of chromatin modification factors and changed epigenetic modifications play crucial roles for tumorigenesis. Our previous studies demonstrated that inhibition of epigenetic modification enzymes EZH2, LSD1, DNMTs, and HDACs caused post-mitotic neuron-like differentiation in different cancer cells. However, how they regulate neuronal differentiation in cancer cells was unknown. Here, we show that EZH2, LSD1, DNMT1, and HDAC1 form interactions themselves, meanwhile, they also interact with SMAD proteins and β-CATENIN in cancer cells. Chemical inhibition of these enzymes leads to reduced level of proteins except HDAC1. The change in protein level and/or enzymatic activities further result in changed chromatin modifications on neuronal gene promoters, and activation of neuronal genes. Inhibition of these enzymes in neural progenitor cells (NPCs) also caused neuronal differentiation, similar to cancer cells. Particularly, EZH2 interacts with and required for the stability of LSD1, HDAC1, DNMT1, β-CATENIN, or SMAD2/4, via recruitment of deubiquitinase USP7. Reduced EZH2 leads to enhanced ubiquitination and degradation of these proteins, and decreased binding of LSD1, HDAC1, and DNMT1 to neuronal gene promoters, and lessened Wnt and TGFβ target gene activation. Hence, EZH2 sustains a series of proteins that promote tumorigenesis, in addition to its original function of histone methylation. Considering together with other studies, we conclude that these chromatin modification factors function in the same way in cancer cells as in neural progenitor/stem cells. The similarity between cancer cells and neural progenitor/stem cells provides an insight into the essence and unified framework for cancer initiation and progression, and are suggestive for novel strategies of cancer therapy.
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Affiliation(s)
- Anhua Lei
- China's Ministry of Education, Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
| | - Lu Chen
- China's Ministry of Education, Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
| | - Min Zhang
- China's Ministry of Education, Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
| | - Xiaoli Yang
- China's Ministry of Education, Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
| | - Liyang Xu
- China's Ministry of Education, Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
| | - Ning Cao
- China's Ministry of Education, Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
| | - Zan Zhang
- China's Ministry of Education, Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
| | - Ying Cao
- China's Ministry of Education, Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
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Andrews D, Oliviero G, De Chiara L, Watson A, Rochford E, Wynne K, Kennedy C, Clerkin S, Doyle B, Godson C, Connell P, O'Brien C, Cagney G, Crean J. Unravelling the transcriptional responses of TGF‐β: Smad3 and EZH2 constitute a regulatory switch that controls neuroretinal epithelial cell fate specification. FASEB J 2019; 33:6667-6681. [DOI: 10.1096/fj.201800566rr] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Darrell Andrews
- Diabetes Complications Research CentreUniversity College Dublin Dublin Ireland
- UCD School of Medicine and Medical ScienceUniversity College Dublin Dublin Ireland
| | - Giorgio Oliviero
- National Institute for Bioprocessing Research and TrainingUniversity College Dublin Dublin Ireland
| | - Letizia De Chiara
- Department of Biomedical, Experimental, and Clinical SciencesCentro di Eccellenza DeNotheUniversity of Florence Florence Italy
| | - Ariane Watson
- Systems Biology IrelandUniversity College Dublin Dublin Ireland
| | - Emily Rochford
- University College Dublin (UCD) School of Biomolecular and Biomedical ScienceConway Institute of Biomolecular and Biomedical ScienceUniversity College Dublin Dublin Ireland
| | - Kieran Wynne
- University College Dublin (UCD) School of Biomolecular and Biomedical ScienceConway Institute of Biomolecular and Biomedical ScienceUniversity College Dublin Dublin Ireland
| | - Ciaran Kennedy
- Diabetes Complications Research CentreUniversity College Dublin Dublin Ireland
- University College Dublin (UCD) School of Biomolecular and Biomedical ScienceConway Institute of Biomolecular and Biomedical ScienceUniversity College Dublin Dublin Ireland
| | - Shane Clerkin
- Diabetes Complications Research CentreUniversity College Dublin Dublin Ireland
- University College Dublin (UCD) School of Biomolecular and Biomedical ScienceConway Institute of Biomolecular and Biomedical ScienceUniversity College Dublin Dublin Ireland
| | - Benjamin Doyle
- University College Dublin (UCD) School of Biomolecular and Biomedical ScienceConway Institute of Biomolecular and Biomedical ScienceUniversity College Dublin Dublin Ireland
| | - Catherine Godson
- Diabetes Complications Research CentreUniversity College Dublin Dublin Ireland
- UCD School of Medicine and Medical ScienceUniversity College Dublin Dublin Ireland
| | - Paul Connell
- UCD School of Medicine and Medical ScienceUniversity College Dublin Dublin Ireland
- Department of OphthalmologyMater Misericordiae University Hospital Dublin Ireland
| | - Colm O'Brien
- UCD School of Medicine and Medical ScienceUniversity College Dublin Dublin Ireland
- Department of OphthalmologyMater Misericordiae University Hospital Dublin Ireland
| | - Gerard Cagney
- University College Dublin (UCD) School of Biomolecular and Biomedical ScienceConway Institute of Biomolecular and Biomedical ScienceUniversity College Dublin Dublin Ireland
| | - John Crean
- Diabetes Complications Research CentreUniversity College Dublin Dublin Ireland
- University College Dublin (UCD) School of Biomolecular and Biomedical ScienceConway Institute of Biomolecular and Biomedical ScienceUniversity College Dublin Dublin Ireland
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40
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Föcking M, Doyle B, Munawar N, Dillon ET, Cotter D, Cagney G. Epigenetic Factors in Schizophrenia: Mechanisms and Experimental Approaches. MOLECULAR NEUROPSYCHIATRY 2019; 5:6-12. [PMID: 31019914 DOI: 10.1159/000495063] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/30/2018] [Indexed: 12/12/2022]
Abstract
Schizophrenia is a chronic mental disorder that is still poorly understood despite decades of study. Many factors have been found to contribute to the pathogenesis, including neurodevelopmental disturbance, genetic risk, and environmental insult, but no single root cause has emerged. While evidence from twin studies suggests a strong heritable component, few individual loci have been identified in genomewide screens, suggesting a role for epigenetic effects. Rather, large numbers of weakly acting loci may cumulatively increase disease risk, including several mapping to epigenetic pathways. In this review, we discuss mechanisms of epigenetic regulation and evidence for an epigenetic contribution to disease phenotype. We further describe the range of experimental tools currently available to study epigenetic effects associated with the disease.
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Affiliation(s)
- Melanie Föcking
- Department of Psychiatry, Royal College of Surgeons in Ireland (RCSI), Beaumont Hospital, Dublin, Ireland
| | - Benjamin Doyle
- Department of Psychiatry, Royal College of Surgeons in Ireland (RCSI), Beaumont Hospital, Dublin, Ireland
| | - Nayla Munawar
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - Eugene T Dillon
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - David Cotter
- Department of Psychiatry, Royal College of Surgeons in Ireland (RCSI), Beaumont Hospital, Dublin, Ireland
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
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41
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Föcking M, Doyle B, Munawar N, Dillon E, Cotter D, Cagney G. Epigenetic Factors in Schizophrenia: Mechanisms and Experimental Approaches. MOLECULAR NEUROPSYCHIATRY 2019. [DOI: https://doi.org/10.1159/000495063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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42
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Faughn JD, Dean WL, Schaner Tooley CE. The N-terminal methyltransferase homologs NRMT1 and NRMT2 exhibit novel regulation of activity through heterotrimer formation. Protein Sci 2018; 27:1585-1599. [PMID: 30151928 DOI: 10.1002/pro.3456] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/07/2018] [Accepted: 06/08/2018] [Indexed: 12/13/2022]
Abstract
Protein, DNA, and RNA methyltransferases have an ever-expanding list of novel substrates and catalytic activities. Even within families and between homologs, it is becoming clear the intricacies of methyltransferase specificity and regulation are far more diverse than originally thought. In addition to specific substrates and distinct methylation levels, methyltransferase activity can be altered by complex formation with close homologs. We work with the N-terminal methyltransferase homologs NRMT1 and NRMT2. NRMT1 is a ubiquitously expressed distributive trimethylase. NRMT2 is a monomethylase expressed at low levels in a tissue-specific manner. They are both nuclear methyltransferases with overlapping consensus sequences but have distinct enzymatic activities and tissue expression patterns. Co-expression with NRMT2 increases the trimethylation rate of NRMT1, and here we aim to understand how this occurs. We use analytical ultracentrifugation to show that while NRMT1 primarily exists as a dimer and NRMT2 as a monomer, when co-expressed they form a heterotrimer. We use co-immunoprecipitation and molecular modeling to demonstrate in vivo binding and map areas of interaction. While overexpression of NRMT2 increases the half-life of NRMT1, the converse is not true, indicating that NRMT2 may be increasing NRMT1 activity by stabilizing the enzyme. Accordingly, the catalytic activity of NRMT2 is not needed to increase NRMT1 activity or increase its affinity for less preferred substrates. Monomethylation can also not rescue phenotypes seen with loss of trimethylation. Taken together, these data support a model where NRMT2 expression activates NRMT1 activity, not through priming, but by increasing its stability and substrate affinity.
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Affiliation(s)
- Jon D Faughn
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, 40202
| | - William L Dean
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, 40202
| | - Christine E Schaner Tooley
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, 14203
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43
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Nakagawa T, Yoneda M, Higashi M, Ohkuma Y, Ito T. Enhancer function regulated by combinations of transcription factors and cofactors. Genes Cells 2018; 23:808-821. [PMID: 30092612 DOI: 10.1111/gtc.12634] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 12/11/2022]
Abstract
Regulation of the expression of diverse genes is essential for making possible the complexity of higher organisms, and the temporal and spatial regulation of gene expression allows for the alteration of cell types and growth patterns. A critical component of this regulation is the DNA sequence-specific binding of transcription factors (TFs). However, most TFs do not independently participate in gene transcriptional regulation, because they lack an effector function. Instead, TFs are thought to work by recruiting cofactors, including Mediator complex (Mediator), chromatin-remodeling complexes (CRCs), and histone-modifying complexes (HMCs). Mediator associates with the majority of transcribed genes and acts as an integrator of multiple signals. On the other hand, CRCs and HMCs are selectively recruited by TFs. Although all the pairings between TFs and CRCs or HMCs are not fully known, there are a growing number of established TF-CRC and TF-HMC combinations. In this review, we focused on the most important of these pairings and discuss how they control gene expression.
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Affiliation(s)
- Takeya Nakagawa
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Mitsuhiro Yoneda
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Miki Higashi
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Yoshiaki Ohkuma
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Takashi Ito
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, Japan
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Guarnieri V, Muscarella LA, Verdelli C, Corbetta S. Alterations of DNA methylation in parathyroid tumors. Mol Cell Endocrinol 2018; 469:60-69. [PMID: 28501573 DOI: 10.1016/j.mce.2017.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 05/01/2017] [Accepted: 05/07/2017] [Indexed: 12/11/2022]
Abstract
Parathyroid tumors are common endocrine neoplasias associated with primary hyperparathyroidism, a metabolic disorder characterized by parathormone hypersecretion. Parathyroid neoplasia are frequently benign adenomas or multiple glands hyperplasia, while malignancies are rare. The epigenetic scenario in parathyroid tumors has just begun to be decoded: DNA methylation, histones and chromatin modifiers expression have been investigated so far. The main findings suggest that DNA methylation and chromatin remodeling are active and deregulated in parathyroid tumors, cooperating with genetic alterations to drive the tumor phenotype: the tumor suppressors menin and parafibromin, involved in parathyroid tumorigenesis, interact with chromatin modifiers, defining distinct epigenetic derangements. Many epigenetic alterations identified in parathyroid tumors are common to those in human cancers; moreover, some aspects of the epigenetic profile resemble epigenetic features of embryonic stem cells. Epigenetic profile may contribute to define the heterogeneity of parathyroid tumors and to provide targets for new therapeutic approaches.
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Affiliation(s)
- Vito Guarnieri
- Genetic Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Lucia Anna Muscarella
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Chiara Verdelli
- Laboratory of Experimental Endocrinology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Sabrina Corbetta
- Endocrinology Service, Department of Biomedical Sciences for Health, University of Milan, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy.
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45
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Zhang H, Peng J, Li X, Liu S, Hu Z, Xu G, Wu R. A nano-bio interfacial protein corona on silica nanoparticle. Colloids Surf B Biointerfaces 2018; 167:220-228. [DOI: 10.1016/j.colsurfb.2018.04.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 01/01/2023]
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46
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Youmans DT, Schmidt JC, Cech TR. Live-cell imaging reveals the dynamics of PRC2 and recruitment to chromatin by SUZ12-associated subunits. Genes Dev 2018; 32:794-805. [PMID: 29891558 PMCID: PMC6049511 DOI: 10.1101/gad.311936.118] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/30/2018] [Indexed: 12/21/2022]
Abstract
Polycomb-repressive complex 2 (PRC2) is a histone methyltransferase that promotes epigenetic gene silencing, but the dynamics of its interactions with chromatin are largely unknown. Here we quantitatively measured the binding of PRC2 to chromatin in human cancer cells. Genome editing of a HaloTag into the endogenous EZH2 and SUZ12 loci and single-particle tracking revealed that ∼80% of PRC2 rapidly diffuses through the nucleus, while ∼20% is chromatin-bound. Short-term treatment with a small molecule inhibitor of the EED-H3K27me3 interaction had no immediate effect on the chromatin residence time of PRC2. In contrast, separation-of-function mutants of SUZ12, which still form the core PRC2 complex but cannot bind accessory proteins, revealed a major contribution of AEBP2 and PCL homolog proteins to chromatin binding. We therefore quantified the dynamics of this chromatin-modifying complex in living cells and separated the contributions of H3K27me3 histone marks and various PRC2 subunits to recruitment of PRC2 to chromatin.
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Affiliation(s)
- Daniel T Youmans
- BioFrontiers Institute, University of Colorado at Boulder, Boulder, Colorado 80303, USA.,Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80303, USA.,Anschutz Medical Campus, University of Colorado at Denver, Aurora, Colorado 80045, USA.,Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, Colorado 80303, USA
| | - Jens C Schmidt
- BioFrontiers Institute, University of Colorado at Boulder, Boulder, Colorado 80303, USA.,Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80303, USA
| | - Thomas R Cech
- BioFrontiers Institute, University of Colorado at Boulder, Boulder, Colorado 80303, USA.,Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80303, USA.,Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, Colorado 80303, USA
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47
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Genetic interaction between Gli3 and Ezh2 during limb pattern formation. Mech Dev 2018; 151:30-36. [PMID: 29729398 DOI: 10.1016/j.mod.2018.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/18/2018] [Accepted: 05/01/2018] [Indexed: 12/13/2022]
Abstract
Anteroposterior polarity of the early limb bud is essential for proper skeletal pattern formation. In order to establish anterior identity, hedgehog signalling needs to be repressed by GLI3 repressor activity, although the mechanism of repression is not well defined. Here we describe genetic interaction between Gli3 and Enhancer of Zeste 2 (Ezh2) that encodes the histone methyltransferase subunit of Polycomb Repressive Complex 2. Loss of anterior limb identity was evident in both Gli3 and conditional Ezh2 single mutant embryos. This phenotype was enhanced in Ezh2;Gli3 double mutant embryos, but more closely resembled that of Ezh2 single mutants. Absent anterior skeletal elements in the Ezh2 mutant background were not rescued by either reduction of Gli activator or forced expression of Gli repressor. The data imply that Ezh2 is epistatic to Gli3 and suggest the possibility that hedghehog activation is repressed by the recruitment of polycomb repressive complex 2.
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48
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Streubel G, Watson A, Jammula SG, Scelfo A, Fitzpatrick DJ, Oliviero G, McCole R, Conway E, Glancy E, Negri GL, Dillon E, Wynne K, Pasini D, Krogan NJ, Bracken AP, Cagney G. The H3K36me2 Methyltransferase Nsd1 Demarcates PRC2-Mediated H3K27me2 and H3K27me3 Domains in Embryonic Stem Cells. Mol Cell 2018; 70:371-379.e5. [PMID: 29606589 DOI: 10.1016/j.molcel.2018.02.027] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 12/22/2017] [Accepted: 02/23/2018] [Indexed: 12/12/2022]
Abstract
The Polycomb repressor complex 2 (PRC2) is composed of the core subunits Ezh1/2, Suz12, and Eed, and it mediates all di- and tri-methylation of histone H3 at lysine 27 in higher eukaryotes. However, little is known about how the catalytic activity of PRC2 is regulated to demarcate H3K27me2 and H3K27me3 domains across the genome. To address this, we mapped the endogenous interactomes of Ezh2 and Suz12 in embryonic stem cells (ESCs), and we combined this with a functional screen for H3K27 methylation marks. We found that Nsd1-mediated H3K36me2 co-locates with H3K27me2, and its loss leads to genome-wide expansion of H3K27me3. These increases in H3K27me3 occurred at PRC2/PRC1 target genes and as de novo accumulation within what were previously broad H3K27me2 domains. Our data support a model in which Nsd1 is a key modulator of PRC2 function required for regulating the demarcation of genome-wide H3K27me2 and H3K27me3 domains in ESCs.
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Affiliation(s)
- Gundula Streubel
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland; School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Ariane Watson
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Sri Ganesh Jammula
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Andrea Scelfo
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | | | - Giorgio Oliviero
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Rachel McCole
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eric Conway
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eleanor Glancy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Gian Luca Negri
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Eugene Dillon
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Kieran Wynne
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Diego Pasini
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy; Department of Health Sciences, University of Milan, Via A. di Rudinì, 8, 20142 Milan, Italy
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94148, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland.
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Eubanks CG, Dayebgadoh G, Liu X, Washburn MP. Unravelling the biology of chromatin in health and cancer using proteomic approaches. Expert Rev Proteomics 2017; 14:905-915. [PMID: 28895440 DOI: 10.1080/14789450.2017.1374860] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Chromatin remodeling complexes play important roles in the control of genome regulation in both normal and diseased states, and are therefore critical components for the regulation of epigenetic states in cells. Given the role epigenetics plays in cancer, for example, chromatin remodeling complexes are routinely targeted for therapeutic intervention. Areas covered: Protein mass spectrometry and proteomics are powerful technologies used to study and understand chromatin remodeling. While impressive progress has been made in this area, there remain significant challenges in the application of proteomic technologies to the study of chromatin remodeling. As parts of large multi-subunit complexes that can be heavily modified with dynamic post-translational modifications, challenges in the study of chromatin remodeling complexes include defining the content, determining the regulation, and studying the dynamics of the complexes under different cellular states. Expert commentary: Impwortant considerations in the study of chromatin remodeling complexes include the complexity of sample preparation, the choice of proteomic methods for the analysis of samples, and data analysis challenges. Continued research in these three areas promise to yield even greater insights into the biology of chromatin remodeling and epigenetics and the dynamics of these systems in human health and cancer.
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Affiliation(s)
| | | | - Xingyu Liu
- a Stowers Institute for Medical Research , Kansas City , MO , USA
| | - Michael P Washburn
- a Stowers Institute for Medical Research , Kansas City , MO , USA.,b Departments of Pathology & Laboratory Medicine , University of Kansas Medical Center , Kansas City , KS , USA
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50
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Schuettengruber B, Bourbon HM, Di Croce L, Cavalli G. Genome Regulation by Polycomb and Trithorax: 70 Years and Counting. Cell 2017; 171:34-57. [DOI: 10.1016/j.cell.2017.08.002] [Citation(s) in RCA: 611] [Impact Index Per Article: 87.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/17/2017] [Accepted: 08/01/2017] [Indexed: 01/05/2023]
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