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Liang W, Xu F, Li L, Peng C, Sun H, Qiu J, Sun J. Epigenetic control of skeletal muscle atrophy. Cell Mol Biol Lett 2024; 29:99. [PMID: 38978023 PMCID: PMC11229277 DOI: 10.1186/s11658-024-00618-1] [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: 03/25/2024] [Accepted: 06/26/2024] [Indexed: 07/10/2024] Open
Abstract
Skeletal muscular atrophy is a complex disease involving a large number of gene expression regulatory networks and various biological processes. Despite extensive research on this topic, its underlying mechanisms remain elusive, and effective therapeutic approaches are yet to be established. Recent studies have shown that epigenetics play an important role in regulating skeletal muscle atrophy, influencing the expression of numerous genes associated with this condition through the addition or removal of certain chemical modifications at the molecular level. This review article comprehensively summarizes the different types of modifications to DNA, histones, RNA, and their known regulators. We also discuss how epigenetic modifications change during the process of skeletal muscle atrophy, the molecular mechanisms by which epigenetic regulatory proteins control skeletal muscle atrophy, and assess their translational potential. The role of epigenetics on muscle stem cells is also highlighted. In addition, we propose that alternative splicing interacts with epigenetic mechanisms to regulate skeletal muscle mass, offering a novel perspective that enhances our understanding of epigenetic inheritance's role and the regulatory network governing skeletal muscle atrophy. Collectively, advancements in the understanding of epigenetic mechanisms provide invaluable insights into the study of skeletal muscle atrophy. Moreover, this knowledge paves the way for identifying new avenues for the development of more effective therapeutic strategies and pharmaceutical interventions.
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Affiliation(s)
- Wenpeng Liang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, 26001, China
- Department of Prenatal Screening and Diagnosis Center, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, 226001, China
| | - Feng Xu
- Department of Endocrinology, Affiliated Hospital 2 of Nantong University and First People's Hospital of Nantong City, Nantong, 226001, China
| | - Li Li
- Nantong Center for Disease Control and Prevention, Medical School of Nantong University, Nantong, 226001, China
| | - Chunlei Peng
- Department of Medical Oncology, Tumor Hospital Affiliated to Nantong University, Nantong, 226000, China
| | - Hualin Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, 26001, China
| | - Jiaying Qiu
- Department of Prenatal Screening and Diagnosis Center, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, 226001, China.
| | - Junjie Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, 26001, China.
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Zhang X, Xia F, Zhang X, Blumenthal RM, Cheng X. C2H2 Zinc Finger Transcription Factors Associated with Hemoglobinopathies. J Mol Biol 2024; 436:168343. [PMID: 37924864 PMCID: PMC11185177 DOI: 10.1016/j.jmb.2023.168343] [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: 09/04/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023]
Abstract
In humans, specific aberrations in β-globin results in sickle cell disease and β-thalassemia, symptoms of which can be ameliorated by increased expression of fetal globin (HbF). Two recent CRISPR-Cas9 screens, centered on ∼1500 annotated sequence-specific DNA binding proteins and performed in a human erythroid cell line that expresses adult hemoglobin, uncovered four groups of candidate regulators of HbF gene expression. They are (1) members of the nucleosome remodeling and deacetylase (NuRD) complex proteins that are already known for HbF control; (2) seven C2H2 zinc finger (ZF) proteins, including some (ZBTB7A and BCL11A) already known for directly silencing the fetal γ-globin genes in adult human erythroid cells; (3) a few other transcription factors of different structural classes that might indirectly influence HbF gene expression; and (4) DNA methyltransferase 1 (DNMT1) that maintains the DNA methylation marks that attract the MBD2-associated NuRD complex to DNA as well as associated histone H3 lysine 9 methylation. Here we briefly discuss the effects of these regulators, particularly C2H2 ZFs, in inducing HbF expression for treating β-hemoglobin disorders, together with recent advances in developing safe and effective small-molecule therapeutics for the regulation of this well-conserved hemoglobin switch.
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Affiliation(s)
- Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Fangfang Xia
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaotian Zhang
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center Houston, McGovern Medical School, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Uneme Y, Maeda R, Nakayama G, Narita H, Takeda N, Hiramatsu R, Nishihara H, Nakato R, Kanai Y, Araki K, Siomi MC, Yamanaka S. Morc1 reestablishes H3K9me3 heterochromatin on piRNA-targeted transposons in gonocytes. Proc Natl Acad Sci U S A 2024; 121:e2317095121. [PMID: 38502704 PMCID: PMC10990106 DOI: 10.1073/pnas.2317095121] [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: 10/02/2023] [Accepted: 01/23/2024] [Indexed: 03/21/2024] Open
Abstract
To maintain fertility, male mice re-repress transposable elements (TEs) that were de-silenced in the early gonocytes before their differentiation into spermatogonia. However, the mechanism of TE silencing re-establishment remains unknown. Here, we found that the DNA-binding protein Morc1, in cooperation with the methyltransferase SetDB1, deposits the repressive histone mark H3K9me3 on a large fraction of activated TEs, leading to heterochromatin. Morc1 also triggers DNA methylation, but TEs targeted by Morc1-driven DNA methylation only slightly overlapped with those repressed by Morc1/SetDB1-dependent heterochromatin formation, suggesting that Morc1 silences TEs in two different manners. In contrast, TEs regulated by Morc1 and Miwi2, the nuclear PIWI-family protein, almost overlapped. Miwi2 binds to PIWI-interacting RNAs (piRNAs) that base-pair with TE mRNAs via sequence complementarity, while Morc1 DNA binding is not sequence specific, suggesting that Miwi2 selects its targets, and then, Morc1 acts to repress them with cofactors. A high-ordered mechanism of TE repression in gonocytes has been identified.
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Affiliation(s)
- Yuta Uneme
- Department of Biophysics and Biochemistry, Faculty of Science, The University of Tokyo, Tokyo113-0032, Japan
| | - Ryu Maeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
| | - Gen Nakayama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
| | - Haruka Narita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
| | - Naoki Takeda
- Division of Developmental Genetics, Institute of Resource Development and Analysis, Kumamoto University, Kumamoto860-0811, Japan
| | - Ryuji Hiramatsu
- Department of Veterinary Anatomy, The University of Tokyo, Tokyo113-8657, Japan
| | - Hidenori Nishihara
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara631-8505, Japan
| | - Ryuichiro Nakato
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo113-0032, Japan
| | - Yoshiakira Kanai
- Department of Veterinary Anatomy, The University of Tokyo, Tokyo113-8657, Japan
| | - Kimi Araki
- Division of Developmental Genetics, Institute of Resource Development and Analysis, Kumamoto University, Kumamoto860-0811, Japan
- Faculty of Life Sciences, Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Honjo, Kumamoto860-8556, Japan
| | - Mikiko C. Siomi
- Department of Biophysics and Biochemistry, Faculty of Science, The University of Tokyo, Tokyo113-0032, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
| | - Soichiro Yamanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
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Chen J, Wang Y, Yang Z, Liu D, Jin Y, Li X, Deng Y, Wang B, Zhang Z, Ma Y. Identification and validation of the reference genes in the echiuran worm Urechis unicinctus based on transcriptome data. BMC Genomics 2023; 24:248. [PMID: 37165306 PMCID: PMC10170059 DOI: 10.1186/s12864-023-09358-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Real-time quantitative PCR (RT-qPCR) is a crucial and widely used method for gene expression analysis. Selecting suitable reference genes is extremely important for the accuracy of RT-qPCR results. Commonly used reference genes are not always stable in various organisms or under different environmental conditions. With the increasing application of high-throughput sequencing, transcriptome analysis has become an effective method for identifying novel stable reference genes. RESULTS In this study, we identified candidate reference genes based on transcriptome data covering embryos and larvae of early development, normal adult tissues, and the hindgut under sulfide stress using the coefficient of variation (CV) method in the echiuran Urechis unicinctus, resulting in 6834 (15.82%), 7110 (16.85%) and 13880 (35.87%) candidate reference genes, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the candidate reference genes were significantly enriched in cellular metabolic process, protein metabolic process and ribosome in early development and normal adult tissues as well as in cellular localization and endocytosis in the hindgut under sulfide stress. Subsequently, ten genes including five new candidate reference genes and five commonly used reference genes, were validated by RT-qPCR. The expression stability of the ten genes was analyzed using four methods (geNorm, NormFinder, BestKeeper, and ∆Ct). The comprehensive results indicated that the new candidate reference genes were more stable than most commonly used reference genes. The commonly used ACTB was the most unstable gene. The candidate reference genes STX12, EHMT1, and LYAG were the most stable genes in early development, normal adult tissues, and hindgut under sulfide stress, respectively. The log2(TPM) of the transcriptome data was significantly negatively correlated with the Ct values of RT-qPCR (Ct = - 0.5405 log2(TPM) + 34.51), which made it possible to estimate the Ct value before RT-qPCR using transcriptome data. CONCLUSION Our study is the first to select reference genes for RT-qPCR from transcriptome data in Echiura and provides important information for future gene expression studies in U. unicinctus.
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Affiliation(s)
- Jiao Chen
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yunjian Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhi Yang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Danwen Liu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yao Jin
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xixi Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuhang Deng
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Boya Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhifeng Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Yubin Ma
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
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Vinson DA, Stephens KE, O’Meally RN, Bhat S, Dancy BCR, Cole RN, Yegnasubramanian S, Taverna SD. De novo methylation of histone H3K23 by the methyltransferases EHMT1/GLP and EHMT2/G9a. Epigenetics Chromatin 2022; 15:36. [PMID: 36411491 PMCID: PMC9677696 DOI: 10.1186/s13072-022-00468-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 10/15/2022] [Indexed: 11/22/2022] Open
Abstract
Epigenetic modifications to histone proteins serve an important role in regulating permissive and repressive chromatin states, but despite the identification of many histone PTMs and their perceived role, the epigenetic writers responsible for generating these chromatin signatures are not fully characterized. Here, we report that the canonical histone H3K9 methyltransferases EHMT1/GLP and EHMT2/G9a are capable of catalyzing methylation of histone H3 lysine 23 (H3K23). Our data show that while both enzymes can mono- and di-methylate H3K23, only EHMT1/GLP can tri-methylate H3K23. We also show that pharmacologic inhibition or genetic ablation of EHMT1/GLP and/or EHMT2/G9a leads to decreased H3K23 methylation in mammalian cells. Taken together, this work identifies H3K23 as a new direct methylation target of EHMT1/GLP and EHMT2/G9a, and highlights the differential activity of these enzymes on H3K23 as a substrate.
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Affiliation(s)
- David A. Vinson
- grid.21107.350000 0001 2171 9311Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.21107.350000 0001 2171 9311Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Kimberly E. Stephens
- grid.21107.350000 0001 2171 9311Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.21107.350000 0001 2171 9311Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.241054.60000 0004 4687 1637Department of Pediatrics, Division of Infectious Diseases, University of Arkansas for Medical Sciences, Arkansas Children’s Research Institute, Little Rock, AR 72202 USA
| | - Robert N. O’Meally
- grid.21107.350000 0001 2171 9311Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Shri Bhat
- grid.21107.350000 0001 2171 9311Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Blair C. R. Dancy
- grid.21107.350000 0001 2171 9311Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.21107.350000 0001 2171 9311Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.507680.c0000 0001 2230 3166Walter Reed Army Institute of Research, Silver Spring, MD 20910-7500 USA
| | - Robert N. Cole
- grid.21107.350000 0001 2171 9311Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Srinivasan Yegnasubramanian
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Sean D. Taverna
- grid.21107.350000 0001 2171 9311Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.21107.350000 0001 2171 9311Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
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Pribluda A, Daemen A, Lima AN, Wang X, Hafner M, Poon C, Modrusan Z, Katakam AK, Foreman O, Eastham J, Hung J, Haley B, Garcia JT, Jackson EL, Junttila MR. EHMT2 methyltransferase governs cell identity in the lung and is required for KRAS G12D tumor development and propagation. eLife 2022; 11:57648. [PMID: 35983994 PMCID: PMC9439681 DOI: 10.7554/elife.57648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/16/2022] [Indexed: 11/30/2022] Open
Abstract
Lung development, integrity and repair rely on precise Wnt signaling, which is corrupted in diverse diseases, including cancer. Here, we discover that EHMT2 methyltransferase regulates Wnt signaling in the lung by controlling the transcriptional activity of chromatin-bound β-catenin, through a non-histone substrate in mouse lung. Inhibition of EHMT2 induces transcriptional, morphologic, and molecular changes consistent with alveolar type 2 (AT2) lineage commitment. Mechanistically, EHMT2 activity functions to support regenerative properties of KrasG12D tumors and normal AT2 cells—the predominant cell of origin of this cancer. Consequently, EHMT2 inhibition prevents KrasG12D lung adenocarcinoma (LUAD) tumor formation and propagation and disrupts normal AT2 cell differentiation. Consistent with these findings, low gene EHMT2 expression in human LUAD correlates with enhanced AT2 gene expression and improved prognosis. These data reveal EHMT2 as a critical regulator of Wnt signaling, implicating Ehmt2 as a potential target in lung cancer and other AT2-mediated lung pathologies.
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Affiliation(s)
- Ariel Pribluda
- Discovery Biology, Surrozen, South San Francisco, United States
| | - Anneleen Daemen
- Computational biology, Oric Pharma, South San Francisco, United States
| | - Anthony Nelson Lima
- Department of Translational Oncology, Genentech, Inc, South San Francisco, United States
| | - Xi Wang
- Department of Translational Oncology, Genentech, Inc, South San Francisco, United States
| | - Marc Hafner
- Department of Bioinformatics and Computational Biology, Genentech, Inc, South San Francisco, United States
| | - Chungkee Poon
- Department of Immunology, Genentech, Inc, South San Francisco, United States
| | - Zora Modrusan
- Department of Molecular Biology, Genentech, Inc, South San Francisco, United States
| | | | - Oded Foreman
- Department of Pathology, Genentech, Inc, South San Francisco, United States
| | - Jefferey Eastham
- Department of Pathology, Genentech, Inc, South San Francisco, United States
| | - Jefferey Hung
- Department of Pathology, Genentech, Inc, South San Francisco, United States
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, Inc, South San Francisco, United States
| | - Julia T Garcia
- Department of Genetics, Stanford University, Stanford, United States
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Wang L, Chen J, Zuo Q, Wu C, Yu T, Zheng P, Huang H, Deng J, Fang L, Liu H, Li C, Yu P, Zou Q, Zheng J. Calreticulin enhances gastric cancer metastasis by dimethylating H3K9 in the E-cadherin promoter region mediating by G9a. Oncogenesis 2022; 11:29. [PMID: 35641480 PMCID: PMC9156786 DOI: 10.1038/s41389-022-00405-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/18/2022] [Accepted: 05/17/2022] [Indexed: 01/06/2023] Open
Abstract
The latest study shows that gastric cancer (GC) ranked the fifth most common cancer (5.6%) with over 1 million estimated new cases annually and the fourth most common cause of cancer death (7.7%) globally in 2020. Metastasis is the leading cause of GC treatment failure. Therefore, clarifying the regulatory mechanisms for GC metastatic process is necessary. In the current study, we discovered that calreticulin (CALR) was highly expressed in GC tissues and related to lymph node metastasis and patient’s terrible prognosis. The introduction of CALR dramatically promoted GC cell migration in vitro and in vivo, while the repression of CALR got the opposite effects. Cell migration is a functional consequence of the epithelial-mesenchymal transition (EMT) and is related to adhesion of cells. Additionally, we observed that CALR inhibition or overexpression regulated the expression of EMT markers (E-cadherin, ZO-1, Snail, N-cadherin, and ZEB1) and cellular adhesive moleculars (Fibronectin, integrin β1and MMP2). Mechanistically, our data indicated that CALR could mediate DNA methylation of E-cadherin promoter by interacting with G9a, a major euchromatin methyltransferase responsible for methylation of histone H3 on lysine 9(H3K9me2) and recruiting G9a to the E-cadherin promoter. Knockdown of G9a in CALR overexpressing models restored E-cadherin expression and blocked the stimulatory effects of CALR on GC cell migration. Taken together, these findings not only reveal critical roles of CALR medicated GC metastasis but also provide novel treatment strategies for GC.
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Affiliation(s)
- Lina Wang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, No. 30 Gaotanyan Street, 400038, Chongqing, China
| | - Jun Chen
- Department of General Surgery and Center of Minimal Invasive Gastrointestinal Surgery, Southwest Hospital, Army Medical University, No. 30 Gaotanyan Street, 400038, Chongqing, China
| | - Qianfei Zuo
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, No. 30 Gaotanyan Street, 400038, Chongqing, China
| | - Chunmei Wu
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, No. 30 Gaotanyan Street, 400038, Chongqing, China
| | - Ting Yu
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, No. 30 Gaotanyan Street, 400038, Chongqing, China
| | - Pengfei Zheng
- Department of medicinal chemistry, College of Pharmacy, Army Medical University, No. 30 Gaotanyan Street, 400038, Chongqing, China
| | - Hui Huang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, No. 30 Gaotanyan Street, 400038, Chongqing, China
| | - Jun Deng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, No. 30 Gaotanyan Street, 400038, Chongqing, China
| | - Lichao Fang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, No. 30 Gaotanyan Street, 400038, Chongqing, China
| | - Huamin Liu
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, No. 30 Gaotanyan Street, 400038, Chongqing, China
| | - Chenghong Li
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, No. 30 Gaotanyan Street, 400038, Chongqing, China
| | - Peiwu Yu
- Department of General Surgery and Center of Minimal Invasive Gastrointestinal Surgery, Southwest Hospital, Army Medical University, No. 30 Gaotanyan Street, 400038, Chongqing, China.
| | - Quanming Zou
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Army Medical University, No. 30 Gaotanyan Street, 400038, Chongqing, China.
| | - Junsong Zheng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, No. 30 Gaotanyan Street, 400038, Chongqing, China.
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Guo Y, Zhao YR, Liu H, Xin Y, Yu JZ, Zang YJ, Xu QG. EHMT2 promotes the pathogenesis of hepatocellular carcinoma by epigenetically silencing APC expression. Cell Biosci 2021; 11:152. [PMID: 34344448 PMCID: PMC8335875 DOI: 10.1186/s13578-021-00663-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 07/22/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC), the second leading cause of cancer death worldwide, alone accounts for over half (466,100) of new cancer cases and 422,100 deaths based on the average year incidence rates of 2009 to 2011 in China. Due to unclear and complex underlying mechanisms for HCC development, effective therapy for HCC is still unavailable. The Wnt-β-catenin pathway is a critical contributor of HCC pathogenesis: 40-70% of HCCs from patients harbor the nuclear accumulation of β-catenin protein. However, the mechanisms for β-catenin activation are not fully understood. METHODS The deletion of EHMT2 in Hep3B and Huh1 cells was achieved by transiently transfecting cells with pX459 plasmids, which carry EHMT2 specific small guide RNA (sgRNA) sequences for Cas9 protein. All experiments were performed in triplicate and repeated more than three times. RESULTS In the present study, we observed that EHMT2 (but not EHMT1) mRNA and protein levels were significantly elevated in HCC compared with normal controls. Next, the results of Ki67 staining, as well as MTT, soft-agar and xenograft assays, in wild-type and EHMT2-/- Hep3B and Huh1 cancer stem cells collectively revealed that the elevation of EHMT2 expression is required for the tumorigenesis of HCC. Meanwhile, we found that elevated EHMT2 expression contributes to the activation of Wnt-β-catenin signaling: deletion of EHMT2 in Hep3B or Huh1 cells promoted the cytoplasmic localization of β-catenin and restrained the expression of Wnt-β-catenin signaling targets such as Myc, CCND1, MMP-7, etc. We demonstrated that EMHT2 directly mediates the H3K9me2 methylation of the APC promoter to epigenetically silence its expression. More intriguingly, our findings also showed that UNC0642, a specific inhibitor of EHMT2, exhibits anti-tumorigenesis effects in HCC both in vitro and in vivo, which were largely abolished by deletion of EHMT2 or overexpression of APC in Hep3B and Huh1 cells. CONCLUSION Altogether, our observations emphasize that the EHMT2-APC axis is a critical contributor to Wnt-β-catenin pathway activation in HCC, and UNC0642 may be a potential candidate for target drug treatment of HCC.
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Affiliation(s)
- Yuan Guo
- Liver Disease Center, The Affiliated Hospital of Qingdao University, 59 Haier Blvd, Qingdao, 266000, Shandong, China
| | - Yan-Rong Zhao
- Liver Disease Center, The Affiliated Hospital of Qingdao University, 59 Haier Blvd, Qingdao, 266000, Shandong, China
| | - Huan Liu
- Organ Transplantation Center, The Affiliated Hospital of Qingdao University, 59 Haier Blvd, Qingdao, 266000, Shandong, China
| | - Yang Xin
- Liver Disease Center, The Affiliated Hospital of Qingdao University, 59 Haier Blvd, Qingdao, 266000, Shandong, China
| | - Jian-Zhi Yu
- Liver Disease Center, The Affiliated Hospital of Qingdao University, 59 Haier Blvd, Qingdao, 266000, Shandong, China
| | - Yun-Jin Zang
- Liver Disease Center, The Affiliated Hospital of Qingdao University, 59 Haier Blvd, Qingdao, 266000, Shandong, China.
| | - Qing-Guo Xu
- Organ Transplantation Center, The Affiliated Hospital of Qingdao University, 59 Haier Blvd, Qingdao, 266000, Shandong, China. .,Lead Contact, The Affiliated Hospital of Qingdao University, 59 Haier Blvd, Qingdao, 266000, Shandong, China.
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9
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Padeken J, Methot S, Zeller P, Delaney CE, Kalck V, Gasser SM. Argonaute NRDE-3 and MBT domain protein LIN-61 redundantly recruit an H3K9me3 HMT to prevent embryonic lethality and transposon expression. Genes Dev 2021; 35:82-101. [PMID: 33303642 PMCID: PMC7778263 DOI: 10.1101/gad.344234.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/05/2020] [Indexed: 12/30/2022]
Abstract
The establishment and maintenance of chromatin domains shape the epigenetic memory of a cell, with the methylation of histone H3 lysine 9 (H3K9me) defining transcriptionally silent heterochromatin. We show here that the C. elegans SET-25 (SUV39/G9a) histone methyltransferase (HMT), which catalyzes H3K9me1, me2 and me3, can establish repressed chromatin domains de novo, unlike the SETDB1 homolog MET-2. Thus, SET-25 is needed to silence novel insertions of RNA or DNA transposons, and repress tissue-specific genes de novo during development. We identify two partially redundant pathways that recruit SET-25 to its targets. One pathway requires LIN-61 (L3MBTL2), which uses its four MBT domains to bind the H3K9me2 deposited by MET-2. The second pathway functions independently of MET-2 and involves the somatic Argonaute NRDE-3 and small RNAs. This pathway targets primarily highly conserved RNA and DNA transposons. These redundant SET-25 targeting pathways (MET-2-LIN-61-SET-25 and NRDE-3-SET-25) ensure repression of intact transposons and de novo insertions, while MET-2 can act alone to repress simple and satellite repeats. Removal of both pathways in the met-2;nrde-3 double mutant leads to the loss of somatic H3K9me2 and me3 and the synergistic derepression of transposons in embryos, strongly elevating embryonic lethality.
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Affiliation(s)
- Jan Padeken
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Stephen Methot
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Peter Zeller
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
- Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
| | - Colin E Delaney
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Veronique Kalck
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
- Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
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10
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Jan S, Dar MI, Wani R, Sandey J, Mushtaq I, Lateef S, Syed SH. Targeting EHMT2/ G9a for cancer therapy: Progress and perspective. Eur J Pharmacol 2020; 893:173827. [PMID: 33347828 DOI: 10.1016/j.ejphar.2020.173827] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/12/2020] [Accepted: 12/16/2020] [Indexed: 12/11/2022]
Abstract
Euchromatic histone lysine methyltransferase-2, also known as G9a, is a ubiquitously expressed SET domain-containing histone lysine methyltransferase linked with both facultative and constitutive heterochromatin formation and transcriptional repression. It is an essential developmental gene and reported to play role in embryonic development, establishment of proviral silencing in ES cells, tumor cell growth, metastasis, T-cell immune response, cocaine induced neural plasticity and cognition and adaptive behavior. It is mainly responsible for carrying out mono, di and tri methylation of histone H3K9 in euchromatin. G9a levels are elevated in many cancers and its selective inhibition is known to reduce the cell growth and induce autophagy, apoptosis and senescence. We carried out a thorough search of online literature databases including Pubmed, Scopus, Journal websites, Clinical trials etc to gather the maximum possible information related to the G9a. The main messages from the cited papers are presented in a systematic manner. Chemical structures were drawn by Chemdraw software. In this review, we shed light on current understanding of structure and biological activity of G9a, the molecular events directing its targeting to genomic regions and its post-translational modification. Finally, we discuss the current strategies to target G9a in different cancers and evaluate the available compounds and agents used to inhibit G9a functions. The review provides the present status and future directions of research in targeting G9a and provides the basis to persuade the development of novel strategies to target G9a -related effects in cancer cells.
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Affiliation(s)
- Suraya Jan
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Mohd Ishaq Dar
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rubiada Wani
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jagjeet Sandey
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Iqra Mushtaq
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sammar Lateef
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sajad Hussain Syed
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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11
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See K, Kiseleva AA, Smith CL, Liu F, Li J, Poleshko A, Epstein JA. Histone methyltransferase activity programs nuclear peripheral genome positioning. Dev Biol 2020; 466:90-98. [PMID: 32712024 DOI: 10.1016/j.ydbio.2020.07.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 11/26/2022]
Abstract
Spatial organization of the genome in the nucleus plays a critical role in development and regulation of transcription. A genomic region that resides at the nuclear periphery is part of the chromatin layer marked with histone H3 lysine 9 dimethyl (H3K9me2), but chromatin reorganization during cell differentiation can cause movement in and out of this nuclear compartment with patterns specific for individual cell fates. Here we describe a CRISPR-based system that allows visualization coupled with forced spatial relocalization of a target genomic locus in live cells. We demonstrate that a specified locus can be tethered to the nuclear periphery through direct binding to a dCas9-Lap2β fusion protein at the nuclear membrane, or via targeting of a histone methyltransferase (HMT), G9a fused to dCas9, that promotes H3K9me2 labeling and localization to the nuclear periphery. The enzymatic activity of the HMT is sufficient to promote this repositioning, while disruption of the catalytic activity abolishes the localization effect. We further demonstrate that dCas9-G9a-mediated localization to the nuclear periphery is independent of nuclear actin polymerization. Our data suggest a function for epigenetic histone modifying enzymes in spatial chromatin organization and provide a system for tracking and labeling targeted genomic regions in live cells.
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Affiliation(s)
- Kelvin See
- Department of Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anna A Kiseleva
- Department of Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Cheryl L Smith
- Department of Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Feiyan Liu
- Department of Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jun Li
- Department of Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrey Poleshko
- Department of Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan A Epstein
- Department of Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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12
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Salas-Pérez F, Ramos-Lopez O, Mansego ML, Milagro FI, Santos JL, Riezu-Boj JI, Martínez JA. DNA methylation in genes of longevity-regulating pathways: association with obesity and metabolic complications. Aging (Albany NY) 2020; 11:1874-1899. [PMID: 30926763 PMCID: PMC6461164 DOI: 10.18632/aging.101882] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/20/2019] [Indexed: 12/28/2022]
Abstract
Aging is the main risk factor for most chronic diseases. Epigenetic mechanisms, such as DNA methylation (DNAm) plays a pivotal role in the regulation of physiological responses that can vary along lifespan. The aim of this research was to analyze the association between leukocyte DNAm in genes involved in longevity and the occurrence of obesity and related metabolic alterations in an adult population. Subjects from the MENA cohort (n=474) were categorized according to age (<45 vs 45>) and the presence of metabolic alterations: increased waist circumference, hypercholesterolemia, insulin resistance, and metabolic syndrome. The methylation levels of 58 CpG sites located at genes involved in longevity-regulating pathways were strongly correlated (FDR-adjusted< 0.0001) with BMI. Fifteen of them were differentially methylated (p<0.05) between younger and older subjects that exhibited at least one metabolic alteration. Six of these CpG sites, located at MTOR (cg08862778), ULK1 (cg07199894), ADCY6 (cg11658986), IGF1R (cg01284192), CREB5 (cg11301281), and RELA (cg08128650), were common to the metabolic traits, and CREB5, RELA, and ULK1 were statistically associated with age. In summary, leukocyte DNAm levels of several CpG sites located at genes involved in longevity-regulating pathways were associated with obesity and metabolic syndrome traits, suggesting a role of DNAm in aging-related metabolic alterations.
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Affiliation(s)
- Francisca Salas-Pérez
- Department of Nutrition, Food Science and Physiology; Center for Nutrition Research, University of Navarra, Pamplona, 31008, Spain
| | - Omar Ramos-Lopez
- Department of Nutrition, Food Science and Physiology; Center for Nutrition Research, University of Navarra, Pamplona, 31008, Spain
| | - María L Mansego
- Department of Bioinformatics, Making Genetics S.L, Pamplona, 31002, Spain
| | - Fermín I Milagro
- Department of Nutrition, Food Science and Physiology; Center for Nutrition Research, University of Navarra, Pamplona, 31008, Spain.,CIBERobn, Fisiopatología de la Obesidad y la Nutrición, Carlos III Health Institute, Madrid, 28029, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, 31008, Spain
| | - José L Santos
- IdiSNA, Navarra Institute for Health Research, Pamplona, 31008, Spain
| | - José I Riezu-Boj
- Department of Nutrition, Food Science and Physiology; Center for Nutrition Research, University of Navarra, Pamplona, 31008, Spain.,CIBERobn, Fisiopatología de la Obesidad y la Nutrición, Carlos III Health Institute, Madrid, 28029, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, 31008, Spain
| | - J Alfredo Martínez
- Department of Nutrition, Food Science and Physiology; Center for Nutrition Research, University of Navarra, Pamplona, 31008, Spain.,CIBERobn, Fisiopatología de la Obesidad y la Nutrición, Carlos III Health Institute, Madrid, 28029, Spain.,Department of Nutrition, Diabetes and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile.,Institute IMDEA Food, Madrid, 28049, Spain
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13
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Iacono G, Dubos A, Méziane H, Benevento M, Habibi E, Mandoli A, Riet F, Selloum M, Feil R, Zhou H, Kleefstra T, Kasri NN, van Bokhoven H, Herault Y, Stunnenberg HG. Increased H3K9 methylation and impaired expression of Protocadherins are associated with the cognitive dysfunctions of the Kleefstra syndrome. Nucleic Acids Res 2019; 46:4950-4965. [PMID: 29554304 PMCID: PMC6007260 DOI: 10.1093/nar/gky196] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 03/09/2018] [Indexed: 12/13/2022] Open
Abstract
Kleefstra syndrome, a disease with intellectual disability, autism spectrum disorders and other developmental defects is caused in humans by haploinsufficiency of EHMT1. Although EHMT1 and its paralog EHMT2 were shown to be histone methyltransferases responsible for deposition of the di-methylated H3K9 (H3K9me2), the exact nature of epigenetic dysfunctions in Kleefstra syndrome remains unknown. Here, we found that the epigenome of Ehmt1+/- adult mouse brain displays a marked increase of H3K9me2/3 which correlates with impaired expression of protocadherins, master regulators of neuronal diversity. Increased H3K9me3 was present already at birth, indicating that aberrant methylation patterns are established during embryogenesis. Interestingly, we found that Ehmt2+/- mice do not present neither the marked increase of H3K9me2/3 nor the cognitive deficits found in Ehmt1+/- mice, indicating an evolutionary diversification of functions. Our finding of increased H3K9me3 in Ehmt1+/- mice is the first one supporting the notion that EHMT1 can quench the deposition of tri-methylation by other Histone methyltransferases, ultimately leading to impaired neurocognitive functioning. Our insights into the epigenetic pathophysiology of Kleefstra syndrome may offer guidance for future developments of therapeutic strategies for this disease.
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Affiliation(s)
- Giovanni Iacono
- Radboud University, Department of Molecular Biology, Faculty of Science, 6500 HB Nijmegen, the Netherlands
- To whom correspondence should be addressed. Tel: +31 24 3610524; . Correspondence may also be addressed to Giovanni Iacono.
| | - Aline Dubos
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, 1 rue Laurent Fries, 67404 Illkirch, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
| | - Hamid Méziane
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Marco Benevento
- Department of Cognitive Neuroscience, Radboudumc, 6500 HB Nijmegen, the Netherlands
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, 6525 AJ Nijmegen, the Netherlands
| | - Ehsan Habibi
- Radboud University, Department of Molecular Biology, Faculty of Science, 6500 HB Nijmegen, the Netherlands
| | - Amit Mandoli
- Radboud University, Department of Molecular Biology, Faculty of Science, 6500 HB Nijmegen, the Netherlands
| | - Fabrice Riet
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Mohammed Selloum
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), UMR5535, Centre National de Recherche Scientifique (CNRS), 1919 Route de Mende, 34293 Montpellier, France
- The University of Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Huiqing Zhou
- Radboud University, Department of Molecular Biology, Faculty of Science, 6500 HB Nijmegen, the Netherlands
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, the Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, 6525 AJ Nijmegen, the Netherlands
| | - Nael Nadif Kasri
- Department of Cognitive Neuroscience, Radboudumc, 6500 HB Nijmegen, the Netherlands
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, 6525 AJ Nijmegen, the Netherlands
| | - Hans van Bokhoven
- Department of Cognitive Neuroscience, Radboudumc, 6500 HB Nijmegen, the Netherlands
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, 6525 AJ Nijmegen, the Netherlands
| | - Yann Herault
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, 1 rue Laurent Fries, 67404 Illkirch, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
| | - Hendrik G Stunnenberg
- Radboud University, Department of Molecular Biology, Faculty of Science, 6500 HB Nijmegen, the Netherlands
- To whom correspondence should be addressed. Tel: +31 24 3610524; . Correspondence may also be addressed to Giovanni Iacono.
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14
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Li Z, Jiao X, Di Sante G, Ertel A, Casimiro MC, Wang M, Katiyar S, Ju X, Klopfenstein DV, Tozeren A, Dampier W, Chepelev I, Jeltsch A, Pestell RG. Cyclin D1 integrates G9a-mediated histone methylation. Oncogene 2019; 38:4232-4249. [PMID: 30718920 PMCID: PMC6542714 DOI: 10.1038/s41388-019-0723-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 12/03/2018] [Accepted: 01/08/2019] [Indexed: 12/26/2022]
Abstract
Lysine methylation of histones and non-histone substrates by the SET domain containing protein lysine methyltransferase (KMT) G9a/EHMT2 governs transcription contributing to apoptosis, aberrant cell growth, and pluripotency. The positioning of chromosomes within the nuclear three-dimensional space involves interactions between nuclear lamina (NL) and the lamina-associated domains (LAD). Contact of individual LADs with the NL are dependent upon H3K9me2 introduced by G9a. The mechanisms governing the recruitment of G9a to distinct subcellular sites, into chromatin or to LAD, is not known. The cyclin D1 gene product encodes the regulatory subunit of the holoenzyme that phosphorylates pRB and NRF1 thereby governing cell-cycle progression and mitochondrial metabolism. Herein, we show that cyclin D1 enhanced H3K9 dimethylation though direct association with G9a. Endogenous cyclin D1 was required for the recruitment of G9a to target genes in chromatin, for G9a-induced H3K9me2 of histones, and for NL-LAD interaction. The finding that cyclin D1 is required for recruitment of G9a to target genes in chromatin and for H3K9 dimethylation, identifies a novel mechanism coordinating protein methylation.
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Affiliation(s)
- Zhiping Li
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Pennsylvania Biotechnology Center, 3805 Old Easton Rd., Doylestown, PA, 18902, USA
| | - Xuanmao Jiao
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Pennsylvania Biotechnology Center, 3805 Old Easton Rd., Doylestown, PA, 18902, USA
| | - Gabriele Di Sante
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Pennsylvania Biotechnology Center, 3805 Old Easton Rd., Doylestown, PA, 18902, USA
| | - Adam Ertel
- Department of Cancer Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA, 19107, USA
| | - Mathew C Casimiro
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Pennsylvania Biotechnology Center, 3805 Old Easton Rd., Doylestown, PA, 18902, USA
| | - Min Wang
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Pennsylvania Biotechnology Center, 3805 Old Easton Rd., Doylestown, PA, 18902, USA
| | - Sanjay Katiyar
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Pennsylvania Biotechnology Center, 3805 Old Easton Rd., Doylestown, PA, 18902, USA
| | - Xiaoming Ju
- Department of Cancer Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA, 19107, USA
| | - D V Klopfenstein
- Center for Integrated Bioinformatics, School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Aydin Tozeren
- Center for Integrated Bioinformatics, School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - William Dampier
- Department of Microbiology & Immunology, Drexel University College of Medicine, Philadelphia, PA, 19104, USA
| | - Iouri Chepelev
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, D-70569, Stuttgart, Germany
| | - Richard G Pestell
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Pennsylvania Biotechnology Center, 3805 Old Easton Rd., Doylestown, PA, 18902, USA. .,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 637551, Singapore.
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15
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Anderson EM, Penrod RD, Barry SM, Hughes BW, Taniguchi M, Cowan CW. It is a complex issue: emerging connections between epigenetic regulators in drug addiction. Eur J Neurosci 2018; 50:2477-2491. [PMID: 30251397 DOI: 10.1111/ejn.14170] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/04/2018] [Accepted: 09/11/2018] [Indexed: 02/06/2023]
Abstract
Drug use leads to addiction in some individuals, but the underlying brain mechanisms that control the transition from casual drug use to an intractable substance use disorder (SUD) are not well understood. Gene x environment interactions such as the frequency of drug use and the type of substance used likely to promote maladaptive plastic changes in brain regions that are critical for controlling addiction-related behavior. Epigenetics encompasses a broad spectrum of mechanisms important for regulating gene transcription that are not dependent on changes in DNA base pair sequences. This review focuses on the proteins and complexes contributing to epigenetic modifications in the nucleus accumbens (NAc) following drug experience. We discuss in detail the three major mechanisms: histone acetylation and deacetylation, histone methylation, and DNA methylation. We discuss how drug use alters the regulation of the associated proteins regulating these processes and highlight how experimental manipulations of these proteins in the NAc can alter drug-related behaviors. Finally, we discuss the ways that histone modifications and DNA methylation coordinate actions by recruiting large epigenetic enzyme complexes to aid in transcriptional repression. Targeting these multiprotein epigenetic enzyme complexes - and the individual proteins that comprise them - might lead to effective therapeutics to reverse or treat SUDs in patients.
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Affiliation(s)
- Ethan M Anderson
- Departments of Neuroscience and Psychiatry and Behavioral Sciences, Medical University of South Carolina, 173 Ashley Ave, MSC 510, Charleston, SC, 29425-2030, USA
| | - Rachel D Penrod
- Departments of Neuroscience and Psychiatry and Behavioral Sciences, Medical University of South Carolina, 173 Ashley Ave, MSC 510, Charleston, SC, 29425-2030, USA
| | - Sarah M Barry
- Departments of Neuroscience and Psychiatry and Behavioral Sciences, Medical University of South Carolina, 173 Ashley Ave, MSC 510, Charleston, SC, 29425-2030, USA
| | - Brandon W Hughes
- Departments of Neuroscience and Psychiatry and Behavioral Sciences, Medical University of South Carolina, 173 Ashley Ave, MSC 510, Charleston, SC, 29425-2030, USA
| | - Makoto Taniguchi
- Departments of Neuroscience and Psychiatry and Behavioral Sciences, Medical University of South Carolina, 173 Ashley Ave, MSC 510, Charleston, SC, 29425-2030, USA
| | - Christopher W Cowan
- Departments of Neuroscience and Psychiatry and Behavioral Sciences, Medical University of South Carolina, 173 Ashley Ave, MSC 510, Charleston, SC, 29425-2030, USA
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16
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Barraza A, Coss-Navarrete EL, Vizuet-de-Rueda JC, Martínez-Aguilar K, Hernández-Chávez JL, Ordaz-Ortiz JJ, Winkler R, Tiessen A, Alvarez-Venegas R. Down-regulation of PvTRX1h increases nodule number and affects auxin, starch, and metabolic fingerprints in the common bean (Phaseolus vulgaris L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:45-58. [PMID: 30080634 DOI: 10.1016/j.plantsci.2018.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/09/2018] [Accepted: 05/14/2018] [Indexed: 06/08/2023]
Abstract
The legume-rhizobium symbiotic relationship has been widely studied and characterized. However, little information is available about the role of histone lysine methyltransferases in the legume-rhizobium interaction and in the formation of nitrogen-fixing nodules in the common bean. Thus, this study aimed to gain a better understanding of the epigenetic control of nodulation in the common bean. Specifically, we studied the role of PvTRX1h, a histone lysine methyltransferase coding gene, in nodule development and auxin biosynthesis. Through a reverse genetics approach, we generated common bean composite plants to knock-down PvTRX1h expression. Here we found that the down-regulation of PvTRX1h increased the number of nodules per plant, but reduced the number of colony-forming units recovered from nodules. Genes coding for enzymes involved in the synthesis of the indole-3-acetic acid were up-regulated, as was the concentration of this hormone. In addition, PvTRX1h down-regulation altered starch accumulation as determined by the number of amyloplasts per nodule. Metabolic fingerprinting by direct liquid introduction-electrospray ionization-mass spectrometry (DLI-ESI-MS) revealed that the root nodules were globally affected by PvTRX1h down-regulation. Therefore, PvTRX1h likely acts through chromatin histone modifications that alter the auxin signaling network to determine bacterial colonization, nodule number, starch accumulation, hormone levels, and cell proliferation.
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Affiliation(s)
- Aarón Barraza
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Guanajuato, C.P. 36824, Mexico
| | - Evelia Lorena Coss-Navarrete
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Guanajuato, C.P. 36824, Mexico
| | - Juan Carlos Vizuet-de-Rueda
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Guanajuato, C.P. 36824, Mexico
| | - Keren Martínez-Aguilar
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Guanajuato, C.P. 36824, Mexico
| | - José Luis Hernández-Chávez
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Guanajuato, C.P. 36824, Mexico
| | - José Juan Ordaz-Ortiz
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad de Genómica Avanzada, Guanajuato, Mexico
| | - Robert Winkler
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Guanajuato, C.P. 36824, Mexico
| | - Axel Tiessen
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Guanajuato, C.P. 36824, Mexico
| | - Raúl Alvarez-Venegas
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Guanajuato, C.P. 36824, Mexico.
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Antidepressant administration modulates stress-induced DNA methylation and DNA methyltransferase expression in rat prefrontal cortex and hippocampus. Behav Brain Res 2018; 343:8-15. [PMID: 29378290 DOI: 10.1016/j.bbr.2018.01.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 12/23/2022]
Abstract
Stress and antidepressant treatment can modulate DNA methylation in promoter region of genes related to neuroplasticity and mood regulation, thus implicating this epigenetic mechanism in depression neurobiology and treatment. Accordingly, systemic administration of DNA methyltransferase (DNMT) inhibitors induces antidepressant-like effects in rodents. DNA methylation is conveyed by DNMT 1, 3a and 3b isoforms, which are differentially expressed in the brain. In order to investigate if the behavioral effects of antidepressants could be associated with changes in DNA methylation and DNMT expression, we investigated the effects induced by acute and repeated antidepressant treatment on DNA methylation and DNMT expression (1, 3a and 3b isoforms) in different brain regions of rats exposed to a stress model of depression, the learned helplessness (LH). Therefore, rats were exposed to pretest and treated with one or seven injections of vehicle or imipramine (15 mg kg-1), with test session performed one hour after the last injection. Chronic, but not acute, imipramine administration attenuated escape failures during the test, a well described antidepressant-like effect in this model. DNA methylation and DNMT (1, 3a and 3b) levels were measured in the dorsal and ventral hippocampus (dHPC, vHPC) and in the prefrontal cortex (PFC) of rats exposed to stress and treatment. Stress increased DNA methylation, DNMT3a and DNMT3b expression in the dHPC and PFC. Chronic, but not acute, imipramine administration attenuated stress effects only in the PFC. These results suggest the regulation of DNA methylation in the PFC may be an important mechanism for antidepressant-like effects in the LH model.
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18
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Daiwile AP, Sivanesan S, Tarale P, Naoghare PK, Bafana A, Parmar D, Kannan K. Role of fluoride induced histone trimethylation in development of skeletal fluorosis. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2018; 57:159-165. [PMID: 29275289 DOI: 10.1016/j.etap.2017.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 10/25/2017] [Accepted: 12/16/2017] [Indexed: 05/19/2023]
Abstract
Chronic exposure to fluoride has been associated with the development of skeletal fluorosis. Limited reports are available on fluoride induced histone modification. However, the role of histone modification in the pathogenesis of skeletal fluorosis is not investigated. In the present study, we have investigated the role of fluoride induced histone modification on fluorosis development using human osteosarcoma (HOS) cell line. The expression of histone methyltransferases (EHMT1 and EHZ2) and level of global histone trimethylation (H3K9 and H3K27) have been assessed and observed to be increased significantly after fluoride exposure (8 mg/L). EpiTect chromatin immunoprecipitation (CHIP) qPCR Array (Human TGFβ/BMP signaling pathway) was performed to assess the H3K9 trimethylation at promoter regions of pathway-specific genes. H3K9 ChIP PCR array analysis identified hyper H3K9 trimethylation in promoter regions of TGFBR2 and SMAD3. qPCR and STRING analysis was carried out to determine the repressive epigenetic effect of H3K9 trimethylation on expression pattern and functional association of identified genes. Identified genes (TGFBR2 and SMAD3) showed down-regulation which confirms the repressive epigenetic effect of promoter H3K9 hyper trimethylation. Expression of two other vital genes COL1A1 and MMP13 involved in TGFBR2-SMAD signaling pathway was also found to be down-regulated with a decrease in expression of TGFBR2 and SMAD3. STRING analysis revealed functional association and involvement of identified genes TGFBR2, SMAD3, COL1A1 and MMP13 in the collagen and cartilage development/morphogenesis, connective tissue formation, bio-mineral tissue development, endochondral bone formation, bone and skeletal morphogenesis. In conclusion, present investigation is a first attempt to link fluoride induced hyper H3K9 tri-methylation mediated repression of TGFBR2 and SMAD3 with the development of skeletal fluorosis.
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Affiliation(s)
- Atul P Daiwile
- Environmental Impact Sustainability Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, 440020, India
| | - Saravanadevi Sivanesan
- Environmental Impact Sustainability Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, 440020, India.
| | - Prashant Tarale
- Environmental Impact Sustainability Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, 440020, India
| | - Pravin K Naoghare
- Environmental Impact Sustainability Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, 440020, India
| | - Amit Bafana
- Environmental Impact Sustainability Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, 440020, India
| | - Devendra Parmar
- Developmental Toxicology Division, CSIR-Indian Institute of Toxicology Research (IITR), Lucknow 226001, India
| | - Krishnamurthi Kannan
- Environmental Impact Sustainability Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, 440020, India
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19
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Huang Y, Jiang X, Yu M, Huang R, Yao J, Li M, Zheng F, Yang X. Beneficial effects of diazepin-quinazolin-amine derivative (BIX-01294) on preimplantation development and molecular characteristics of cloned mouse embryos. Reprod Fertil Dev 2017; 29:1260-1269. [DOI: 10.1071/rd15463] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 06/04/2016] [Indexed: 12/19/2022] Open
Abstract
Somatic cell nuclear transfer is frequently associated with abnormal epigenetic modifications that may lead to the developmental failure of cloned embryos. BIX-01294 (a diazepine–quinazoline–amine derivative) is a specific inhibitor of the histone methyltransferase G9a. The aim of the present study was to investigate the effects of BIX-01294 on development, dimethylation of histone H3 at lysine 9 (H3K9), DNA methylation and the expression of imprinted genes in cloned mouse preimplantation embryos. There were no significant differences in blastocyst rates of cloned embryos treated with or without 0.1 μM BIX-01294. Relative to clone embryos treated without 0.1 μM BIX-01294, exposure of embryos to BIX-01294 decreased histone H3K9 dimethylation and DNA methylation in cloned embryos to levels that were similar to those of in vivo-fertilised embryos at the 2-cell and blastocyst stages. Cloned embryos had lower expression of octamer-binding transcription factor 4 (Oct4) and small nuclear ribonucleoprotein N (Snrpn), but higher expression of imprinted maternally expressed transcript (non-protein coding) (H19) and growth factor receptor-bound protein 10 (Grb10) compared with in vivo-fertilised counterparts. The addition of 0.1 μM BIX-01294 to the activation and culture medium resulted in lower H19 expression and higher cyclin dependent kinase inhibitor 1C (Cdkn1c) and delta-like 1 homolog (Dlk1) expression, but had no effect on the expression of Oct4, Snrpn and Grb10. The loss of methylation at the Grb10 cytosine–phosphorous–guanine (CpG) islands in cloned embryos was partially corrected by BIX-01294. These results indicate that BIX-01294 treatment of cloned embryos has beneficial effects in terms of correcting abnormal epigenetic modifications, but not on preimplantation development.
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20
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Targeting the histone methyltransferase G9a activates imprinted genes and improves survival of a mouse model of Prader-Willi syndrome. Nat Med 2016; 23:213-222. [PMID: 28024084 DOI: 10.1038/nm.4257] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/29/2016] [Indexed: 12/13/2022]
Abstract
Prader-Willi syndrome (PWS) is an imprinting disorder caused by a deficiency of paternally expressed gene(s) in the 15q11-q13 chromosomal region. The regulation of imprinted gene expression in this region is coordinated by an imprinting center (PWS-IC). In individuals with PWS, genes responsible for PWS on the maternal chromosome are present, but repressed epigenetically, which provides an opportunity for the use of epigenetic therapy to restore expression from the maternal copies of PWS-associated genes. Through a high-content screen (HCS) of >9,000 small molecules, we discovered that UNC0638 and UNC0642-two selective inhibitors of euchromatic histone lysine N-methyltransferase-2 (EHMT2, also known as G9a)-activated the maternal (m) copy of candidate genes underlying PWS, including the SnoRNA cluster SNORD116, in cells from humans with PWS and also from a mouse model of PWS carrying a paternal (p) deletion from small nuclear ribonucleoprotein N (Snrpn (S)) to ubiquitin protein ligase E3A (Ube3a (U)) (mouse model referred to hereafter as m+/pΔS-U). Both UNC0642 and UNC0638 caused a selective reduction of the dimethylation of histone H3 lysine 9 (H3K9me2) at PWS-IC, without changing DNA methylation, when analyzed by bisulfite genomic sequencing. This indicates that histone modification is essential for the imprinting of candidate genes underlying PWS. UNC0642 displayed therapeutic effects in the PWS mouse model by improving the survival and the growth of m+/pΔS-U newborn pups. This study provides the first proof of principle for an epigenetics-based therapy for PWS.
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Carlson SM, Gozani O. Nonhistone Lysine Methylation in the Regulation of Cancer Pathways. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a026435. [PMID: 27580749 DOI: 10.1101/cshperspect.a026435] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Proteins are regulated by an incredible array of posttranslational modifications (PTMs). Methylation of lysine residues on histone proteins is a PTM with well-established roles in regulating chromatin and epigenetic processes. The recent discovery that hundreds and likely thousands of nonhistone proteins are also methylated at lysine has opened a tremendous new area of research. Major cellular pathways involved in cancer, such as growth signaling and the DNA damage response, are regulated by lysine methylation. Although the field has developed quickly in recent years many fundamental questions remain to be addressed. We review the history and molecular functions of lysine methylation. We then discuss the enzymes that catalyze methylation of lysine residues, the enzymes that remove lysine methylation, and the cancer pathways known to be regulated by lysine methylation. The rest of the article focuses on two open questions that we suggest as a roadmap for future research. First is understanding the large number of candidate methyltransferase and demethylation enzymes whose enzymatic activity is not yet defined and which are potentially associated with cancer through genetic studies. Second is investigating the biological processes and cancer mechanisms potentially regulated by the multitude of lysine methylation sites that have been recently discovered.
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Affiliation(s)
- Scott M Carlson
- Department of Biology, Stanford University, Stanford, California 94305
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, California 94305
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22
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Human EHMT2/G9a activates p53 through methylation-independent mechanism. Oncogene 2016; 36:922-932. [PMID: 27452519 DOI: 10.1038/onc.2016.258] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 05/01/2016] [Accepted: 05/23/2016] [Indexed: 12/23/2022]
Abstract
p53 is a critical tumor suppressor in humans. It functions mostly as a transcriptional factor and its activity is regulated by numerous post-translational modifications. Among different covalent modifications found on p53 the most controversial one is lysine methylation. We found that human G9a (hG9a) unlike its mouse orthologue (mG9a) potently stimulated p53 transcriptional activity. Both ectopic and endogenous hG9a augmented p53-dependent transcription of pro-apoptotic genes, including Bax and Puma, resulting in enhanced apoptosis and reduced colony formation. Significantly, shRNA-mediated knockdown of hG9a attenuated p53-dependent activation of Puma. On the molecular level, hG9a interacted with histone acetyltransferase, p300/CBP, resulting in increased histone acetylation at the promoter of Puma. The bioinformatics data substantiated our findings showing that positive correlation between G9a and p53 expression is associated with better survival of lung cancer patients. Collectively, this study demonstrates that depending on the cellular and organismal context, orthologous proteins may exert both overlapping and opposing functions. Furthermore, this finding has important ramifications on the use of G9a inhibitors in combination with genotoxic drugs to treat p53-positive tumors.
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23
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Lin X, Huang Y, Zou Y, Chen X, Ma X. Depletion of G9a gene induces cell apoptosis in human gastric carcinoma. Oncol Rep 2016; 35:3041-9. [PMID: 27081761 DOI: 10.3892/or.2016.4692] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/12/2016] [Indexed: 11/06/2022] Open
Abstract
G9a is a mammalian histone methyltransferase that contributes to the epigenetic silencing of tumor suppressor genes. Evidence suggests that G9a is required to maintain the malignant phenotype, but little documentation show the role of G9a function in mediating tumor growth. We retrospectively analyzed the protein of G9a and monomethylated histone H3 lysine 9 (H3K9 me1), and dimethylated histone H3 lysine 9 (H3K9 me2) in 175 cases of gastric carcinoma by immunohistochemistry. RNAi-based inhibition of G9a in MGC803 cancer cell line was studied. G9a depletion was done by transient transfection using Lipofectamine 2000. Depletion efficiency of G9a was tested using real-time PCR and western blot analysis. Cell apoptosis and proliferation were detected by TUNEL assay and MTT, respectively. The proteins of H3K9 me1, me2, trimethylation of H3K9 (H3K9 me3), monomethylated histone H3 lysine 27 (H3K27 me1), dimethylated histone H3 lysine 27 (H3K27 me2) and histone acetylated H3, apoptotic proteins were studied by western blot analysis. G9a and H3K9 me2 expression was higher in gastric cancer cells compared to the control (p<0.05). Both G9a and H3K9 me2 were positively correlated with the degree of differentiation, depth of infiltration, lymphatic invasions and tumor-node-metastasis stage in gastric carcinoma, (p<0.05). RNAi-mediated knockdown of G9a induced cell apoptosis and inhibited cell proliferation. Depletion of G9a reduced the levels of H3K9 me1 and me2, H3K27 me1 and me2. Nonetheless, it did not activate acetylation of H3 and H3K9 me3. These data suggest that G9a is required in tumorigenesis, and correlated with prognosis. Furthermore, G9a plays a critical role in regulating epigenetics. Depletion of G9a inhibits cell growth and induces cells apoptosis in gastric cancer. It might be of therapeutic benefit in gastric cancers.
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Affiliation(s)
- Xiaolei Lin
- Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, Fujian 363000, P.R. China
| | - Yiqun Huang
- Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, Fujian 363000, P.R. China
| | - Yong Zou
- Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, Fujian 363000, P.R. China
| | - Xingsheng Chen
- United Hospital of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Xudong Ma
- Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, Fujian 363000, P.R. China
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24
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Simon JM, Parker JS, Liu F, Rothbart SB, Ait-Si-Ali S, Strahl BD, Jin J, Davis IJ, Mosley AL, Pattenden SG. A Role for Widely Interspaced Zinc Finger (WIZ) in Retention of the G9a Methyltransferase on Chromatin. J Biol Chem 2015; 290:26088-102. [PMID: 26338712 PMCID: PMC4646261 DOI: 10.1074/jbc.m115.654459] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 08/23/2015] [Indexed: 11/06/2022] Open
Abstract
G9a and GLP lysine methyltransferases form a heterodimeric complex that is responsible for the majority of histone H3 lysine 9 mono- and di-methylation (H3K9me1/me2). Widely interspaced zinc finger (WIZ) associates with the G9a-GLP protein complex, but its role in mediating lysine methylation is poorly defined. Here, we show that WIZ regulates global H3K9me2 levels by facilitating the interaction of G9a with chromatin. Disrupting the association of G9a-GLP with chromatin by depleting WIZ resulted in altered gene expression and protein-protein interactions that were distinguishable from that of small molecule-based inhibition of G9a/GLP, supporting discrete functions of the G9a-GLP-WIZ chromatin complex in addition to H3K9me2 methylation.
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Affiliation(s)
- Jeremy M Simon
- From the Carolina Institute for Developmental Disabilities, Department of Cell Biology and Physiology, and the Department of Genetics, Curriculum in Bioinformatics and Computational Biology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Joel S Parker
- the Department of Genetics and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Feng Liu
- the Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599
| | - Scott B Rothbart
- the Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan 49503
| | - Slimane Ait-Si-Ali
- the Laboratoire Epigénétique et Destin Cellulaire, UMR7216, CNRS, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Brian D Strahl
- the Lineberger Comprehensive Cancer Center, the Curriculum in Genetics and Molecular Biology, and the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Jian Jin
- the Department of Structural and Chemical Biology, the Department of Oncological Sciences, and the Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Ian J Davis
- the Department of Genetics, the Lineberger Comprehensive Cancer Center, the Department of Pediatrics, and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, and
| | - Amber L Mosley
- the Department of Biochemistry and Molecular Biology and the Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Samantha G Pattenden
- the Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599,
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25
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Casciello F, Windloch K, Gannon F, Lee JS. Functional Role of G9a Histone Methyltransferase in Cancer. Front Immunol 2015; 6:487. [PMID: 26441991 PMCID: PMC4585248 DOI: 10.3389/fimmu.2015.00487] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 09/07/2015] [Indexed: 11/13/2022] Open
Abstract
Post-translational modifications of DNA and histones are epigenetic mechanisms, which affect the chromatin structure, ultimately leading to gene expression changes. A number of different epigenetic enzymes are actively involved in the addition or the removal of various covalent modifications, which include acetylation, methylation, phosphorylation, ubiquitination, and sumoylation. Deregulation of these processes is a hallmark of cancer. For instance, G9a, a histone methyltransferase responsible for histone H3 lysine 9 (H3K9) mono- and dimethylation, has been observed to be upregulated in different types of cancer and its overexpression has been associated with poor prognosis. Key roles played by these enzymes in various diseases have led to the hypothesis that these molecules represent valuable targets for future therapies. Several small molecule inhibitors have been developed to specifically block the epigenetic activity of these enzymes, representing promising therapeutic tools in the treatment of human malignancies, such as cancer. In this review, the role of one of these epigenetic enzymes, G9a, is discussed, focusing on its functional role in regulating gene expression as well as its implications in cancer initiation and progression. We also discuss important findings from recent studies using epigenetic inhibitors in cell systems in vitro as well as experimental tumor growth and metastasis assays in vivo.
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Affiliation(s)
- Francesco Casciello
- Control of Gene Expression Laboratory, QIMR Berghofer Medical Research Institute , Herston, QLD , Australia ; School of Natural Sciences, Griffith University , Nathan, QLD , Australia
| | - Karolina Windloch
- Control of Gene Expression Laboratory, QIMR Berghofer Medical Research Institute , Herston, QLD , Australia
| | - Frank Gannon
- Control of Gene Expression Laboratory, QIMR Berghofer Medical Research Institute , Herston, QLD , Australia
| | - Jason S Lee
- Control of Gene Expression Laboratory, QIMR Berghofer Medical Research Institute , Herston, QLD , Australia ; Faculty of Health, School of Biomedical Sciences, Queensland University of Technology , Kelvin Grove, QLD , Australia ; School of Chemistry and Molecular Biosciences, University of Queensland , Brisbane, QLD , Australia
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26
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Mozzetta C, Pontis J, Ait-Si-Ali S. Functional Crosstalk Between Lysine Methyltransferases on Histone Substrates: The Case of G9A/GLP and Polycomb Repressive Complex 2. Antioxid Redox Signal 2015; 22:1365-81. [PMID: 25365549 PMCID: PMC4432786 DOI: 10.1089/ars.2014.6116] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
SIGNIFICANCE Methylation of histone H3 on lysine 9 and 27 (H3K9 and H3K27) are two epigenetic modifications that have been linked to several crucial biological processes, among which are transcriptional silencing and cell differentiation. RECENT ADVANCES Deposition of these marks is catalyzed by H3K9 lysine methyltransferases (KMTs) and polycomb repressive complex 2, respectively. Increasing evidence is emerging in favor of a functional crosstalk between these two major KMT families. CRITICAL ISSUES Here, we review the current knowledge on the mechanisms of action and function of these enzymes, with particular emphasis on their interplay in the regulation of chromatin states and biological processes. We outline their crucial roles played in tissue homeostasis, by controlling the fate of embryonic and tissue-specific stem cells, highlighting how their deregulation is often linked to the emergence of a number of malignancies and neurological disorders. FUTURE DIRECTIONS Histone methyltransferases are starting to be tested as drug targets. A new generation of highly selective chemical inhibitors is starting to emerge. These hold great promise for a rapid translation of targeting epigenetic drugs into clinical practice for a number of aggressive cancers and neurological disorders.
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Affiliation(s)
- Chiara Mozzetta
- Laboratoire Epigénétique et Destin Cellulaire, UMR7216, Centre National de la Recherche Scientifique CNRS, Université Paris Diderot , Sorbonne Paris Cité, Paris, France
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27
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Kim KB, Son HJ, Choi S, Hahm JY, Jung H, Baek HJ, Kook H, Hahn Y, Kook H, Seo SB. H3K9 methyltransferase G9a negatively regulates UHRF1 transcription during leukemia cell differentiation. Nucleic Acids Res 2015; 43:3509-23. [PMID: 25765655 PMCID: PMC4402520 DOI: 10.1093/nar/gkv183] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 02/23/2015] [Indexed: 01/03/2023] Open
Abstract
Histone H3K9 methyltransferase (HMTase) G9a-mediated transcriptional repression is a major epigenetic silencing mechanism. UHRF1 (ubiquitin-like with PHD and ring finger domains 1) binds to hemimethylated DNA and plays an essential role in the maintenance of DNA methylation. Here, we provide evidence that UHRF1 is transcriptionally downregulated by H3K9 HMTase G9a. We found that increased expression of G9a along with transcription factor YY1 specifically represses UHRF1 transcription during TPA-mediated leukemia cell differentiation. Using ChIP analysis, we found that UHRF1 was among the transcriptionally silenced genes during leukemia cell differentiation. Using a DNA methylation profiling array, we discovered that the UHRF1 promoter was hypomethylated in samples from leukemia patients, further supporting its overexpression and oncogenic activity. Finally, we showed that G9a regulates UHRF1-mediated H3K23 ubiquitination and proper DNA replication maintenance. Therefore, we propose that H3K9 HMTase G9a is a specific epigenetic regulator of UHRF1.
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Affiliation(s)
- Kee-Beom Kim
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 156-756
| | - Hye-Ju Son
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 156-756
| | - Sulji Choi
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 156-756
| | - Ja Young Hahm
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 156-756
| | - Hyeonsoo Jung
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 156-756
| | - Hee Jo Baek
- Environmental Health Center for Childhood Leukemia and Cancer, Department of Pediatrics, Chonnam National University Hwasun Hospital, Hwasun 519-809
| | - Hoon Kook
- Environmental Health Center for Childhood Leukemia and Cancer, Department of Pediatrics, Chonnam National University Hwasun Hospital, Hwasun 519-809
| | - Yoonsoo Hahn
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 156-756
| | - Hyun Kook
- Medical Research Center for Gene Regulation and Department of Pharmacology, Chonnam National University, Gwangju 501-746, Republic of Korea
| | - Sang-Beom Seo
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 156-756
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28
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Liu N, Zhang Z, Wu H, Jiang Y, Meng L, Xiong J, Zhao Z, Zhou X, Li J, Li H, Zheng Y, Chen S, Cai T, Gao S, Zhu B. Recognition of H3K9 methylation by GLP is required for efficient establishment of H3K9 methylation, rapid target gene repression, and mouse viability. Genes Dev 2015; 29:379-93. [PMID: 25637356 PMCID: PMC4335294 DOI: 10.1101/gad.254425.114] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
GLP and G9a are major H3K9 dimethylases essential for mouse early embryonic development. Here, Liu et al. report that the histone methyltransferase activities of GLP and G9a are stimulated by neighboring nucleosomes that are premethylated at H3K9. In mouse embryonic stem cells harboring a mutant GLP that lacks H3K9me1-binding activity, critical pluripotent genes displayed inefficient establishment of H3K9me2 and delayed gene silencing during differentiation. Mice carrying the H3K9me1-binding mutant form of GLP displayed embryonic growth retardation and defects in calvaria bone formation. GLP and G9a are major H3K9 dimethylases and are essential for mouse early embryonic development. GLP and G9a both harbor ankyrin repeat domains that are capable of binding H3K9 methylation. However, the functional significance of their recognition of H3K9 methylation is unknown. Here, we report that the histone methyltransferase activities of GLP and G9a are stimulated by neighboring nucleosomes that are premethylated at H3K9. These stimulation events function in cis and are dependent on the H3K9 methylation binding activities of ankyrin repeat domains of GLP and G9a. Disruption of the H3K9 methylation-binding activity of GLP in mice causes growth retardation of embryos, ossification defects of calvaria, and postnatal lethality due to starvation of the pups. In mouse embryonic stem cells (ESCs) harboring a mutant GLP that lacks H3K9me1-binding activity, critical pluripotent genes, including Oct4 and Nanog, display inefficient establishment of H3K9me2 and delayed gene silencing during differentiation. Collectively, our study reveals a new activation mechanism for GLP and G9a that plays an important role in ESC differentiation and mouse viability.
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Affiliation(s)
- Nan Liu
- College of Life Sciences, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences, Beijing 102206, China; National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhuqiang Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hui Wu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province 130012, China;
| | - Yonghua Jiang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Lingjun Meng
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jun Xiong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Zuodong Zhao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xiaohua Zhou
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jia Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - Hong Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yong Zheng
- National Institute of Biological Sciences, Beijing 102206, China
| | - She Chen
- National Institute of Biological Sciences, Beijing 102206, China
| | - Tao Cai
- National Institute of Biological Sciences, Beijing 102206, China
| | - Shaorong Gao
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Bing Zhu
- National Institute of Biological Sciences, Beijing 102206, China; National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
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29
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Role of epigenetic mechanisms in epithelial-to-mesenchymal transition of breast cancer cells. Transl Res 2015; 165:126-42. [PMID: 24768944 DOI: 10.1016/j.trsl.2014.04.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 03/26/2014] [Accepted: 04/03/2014] [Indexed: 02/06/2023]
Abstract
The epithelial-to-mesenchymal transition (EMT) is a crucial process during normal development that allows dynamic and reversible shifts between epithelial and mesenchymal cell states. Cancer cells take advantage of the complex, interrelated cellular networks that regulate EMT to promote their migratory and invasive capabilities. During the past few years, evidence has accumulated that indicates that genetic mutations and changes to epigenetic mechanisms are key drivers of EMT in cancer cells. Recent studies have begun to shed light on the epigenetic reprogramming in cancer cells that enables them to switch from a noninvasive form to an invasive, metastatic form. The authors review the current knowledge of alterations of epigenetic machinery, including DNA methylation, histone modifications, nucleosome remodeling and expression of microRNAs, associated with EMT and tumor progression of breast cancer cells. Last, existing and upcoming drug therapies targeting epigenetic regulators and their potential benefit for developing novel treatment strategies are discussed.
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30
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EZH2, the moderator in the discussion between methyltransferases at histone H3? J Cell Commun Signal 2014; 9:77-9. [PMID: 25381642 DOI: 10.1007/s12079-014-0256-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 11/03/2014] [Indexed: 10/24/2022] Open
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31
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Cheng X. Structural and functional coordination of DNA and histone methylation. Cold Spring Harb Perspect Biol 2014; 6:6/8/a018747. [PMID: 25085914 DOI: 10.1101/cshperspect.a018747] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
One of the most fundamental questions in the control of gene expression in mammals is how epigenetic methylation patterns of DNA and histones are established, erased, and recognized. This central process in controlling gene expression includes coordinated covalent modifications of DNA and its associated histones. This article focuses on structural aspects of enzymatic activities of histone (arginine and lysine) methylation and demethylation and functional links between the methylation status of the DNA and histones. An interconnected network of methyltransferases, demethylases, and accessory proteins is responsible for changing or maintaining the modification status of specific regions of chromatin.
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Affiliation(s)
- Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
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32
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Guan X, Zhong X, Men W, Gong S, Zhang L, Han Y. Analysis of EHMT1 expression and its correlations with clinical significance in esophageal squamous cell cancer. Mol Clin Oncol 2013; 2:76-80. [PMID: 24649311 DOI: 10.3892/mco.2013.207] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 08/28/2013] [Indexed: 01/25/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a highly aggressive malignancy, requiring effective biomarkers for prognosis and therapeutic responsiveness. Histone H3K9 methyltransferases (EHMT1 and EHMT2) are global genome organizers, which are crucial for maintaining the balance state of cells in a tissue-specific manner. It was previously suggested that EHMT1 expression is a predictor of prognosis in several malignant tumors; however, the prognostic significance of EHMT1 expression in ESCC has not been determined. A cohort of 50 ESCC cases and 46 paired normal esophageal tissue samples were evaluated to assess the levels of EHMT1 expression by immunohistochemistry and reverse transcription-polymerase chain reaction. The SPSS software package was used for statistical data analysis. A significantly upregulated EHMT1 expression was observed in squamous preinvasive lesions and ESCC compared to the matched normal esophageal epithelia (52.0 vs. 21.7%, respectively). The expression of EHMT1 was correlated with tumor grade (G), depth of invasion (T) and lymph node metastasis (N) in ESCC. EHMT1 overexpression was found to be associated with poor cancer-specific survival in squamous cell carcinomas (χ2=3.922, P=0.048). The expression of EHMT1 was identified as an independent prognostic factor for overall survival in ESCC patients. In conclusion, EHMT1 expression is upregulated in ESCC and early preinvasive esophageal squamous lesions and the overexpression of EHMT1 is associated with poor prognosis in ESCC. Therefore, the expression of EHMT1 may be an effective prognostic biomarker for ESCC.
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Affiliation(s)
- Xiaojiao Guan
- Department of Pathology, Basic Science College, China Medical University, Shenyang, Liaoning, P.R. China
| | - Xinwen Zhong
- Departments of Thoracic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, P.R. China
| | - Wanfu Men
- Departments of Thoracic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, P.R. China
| | - Shulei Gong
- Departments of Thoracic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, P.R. China
| | - Lin Zhang
- Departments of Thoracic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, P.R. China
| | - Yuchen Han
- Department of Pathology, Basic Science College, China Medical University, Shenyang, Liaoning, P.R. China ; ; Pathology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, P.R. China
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Shin HM, Kapoor V, Guan T, Kaech SM, Welsh RM, Berg LJ. Epigenetic modifications induced by Blimp-1 Regulate CD8⁺ T cell memory progression during acute virus infection. Immunity 2013; 39:661-75. [PMID: 24120360 PMCID: PMC3808842 DOI: 10.1016/j.immuni.2013.08.032] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 06/24/2013] [Indexed: 11/29/2022]
Abstract
The transcription factor Blimp-1 regulates the overall accumulation of virus-specific CD8⁺ T cells during acute viral infections. We found that increased proliferation and survival of Blimp-1-deficient CD8⁺ T cells resulted from sustained expression of CD25 and CD27 and persistent cytokine responsiveness. Silencing of Il2ra and Cd27 reduced the Blimp-1-deficient CD8⁺ T cell response. Genome-wide chromatin immunoprecipitation (ChIP) sequencing analysis identified Il2ra and Cd27 as direct targets of Blimp-1. At the peak of the antiviral response, but not earlier, Blimp-1 recruited the histone-modifying enzymes G9a and HDAC2 to the Il2ra and Cd27 loci, thereby repressing expression of these genes. In the absence of Blimp-1, Il2ra and Cd27 exhibited enhanced histone H3 acetylation and reduced histone H3K9 trimethylation. These data elucidate a central mechanism by which Blimp-1 acts as an epigenetic regulator and enhances the numbers of short-lived effector cells while suppressing the development of memory-precursor CD8⁺ T cells.
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Affiliation(s)
- Hyun Mu Shin
- Dept. of Pathology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Varun Kapoor
- Dept. of Pathology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Tianxia Guan
- Dept. of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA and Howard Hughes Medical Institute
| | - Susan M. Kaech
- Dept. of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA and Howard Hughes Medical Institute
| | - Raymond M. Welsh
- Dept. of Pathology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Leslie J. Berg
- Dept. of Pathology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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Southall SM, Cronin NB, Wilson JR. A novel route to product specificity in the Suv4-20 family of histone H4K20 methyltransferases. Nucleic Acids Res 2013; 42:661-71. [PMID: 24049080 PMCID: PMC3874154 DOI: 10.1093/nar/gkt776] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The delivery of site-specific post-translational modifications to histones generates an epigenetic regulatory network that directs fundamental DNA-mediated processes and governs key stages in development. Methylation of histone H4 lysine-20 has been implicated in DNA repair, transcriptional silencing, genomic stability and regulation of replication. We present the structure of the histone H4K20 methyltransferase Suv4-20h2 in complex with its histone H4 peptide substrate and S-adenosyl methionine cofactor. Analysis of the structure reveals that the Suv4-20h2 active site diverges from the canonical SET domain configuration and generates a high degree of both substrate and product specificity. Together with supporting biochemical data comparing Suv4-20h1 and Suv4-20h2, we demonstrate that the Suv4-20 family enzymes take a previously mono-methylated H4K20 substrate and generate an exclusively di-methylated product. We therefore predict that other enzymes are responsible for the tri-methylation of histone H4K20 that marks silenced heterochromatin.
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Affiliation(s)
- Stacey M Southall
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, London, SW3 6JB, UK
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Abstract
The discovery of epigenetic processes as possible pivotal regulatory mechanisms in psychiatric diseases raised the question of how psychoactive drugs may impact the epigenetic machinery. In the present study we set out to explore the specificity and the mode of action of the reported inhibitory effect of the TCA (tricyclic antidepressant) amitriptyline on DNMT (DNA methyltransferase) activity in primary astrocytes from the rat cortex. We found that the impact on DNMT was shared by another TCA, imipramine, and by paroxetine, but not by venlafaxine or the mood stabilizers carbamazepine and valproic acid. DNMT activity in subventricular neural stem cells was refractory to the action of ADs (antidepressants). Among the established DNMTs, ADs primarily targeted DNMT1. The reduction of enzymatic DNMT1 activity was neither due to reduced DNMT1 expression nor due to direct drug interference. We tested putative DNMT1-inhibitory mechanisms and discovered that a known stimulator of DNMT1, the histone methyltransferase G9a, exhibited decreased protein levels and interactions with DNMT1 upon AD exposure. Adding recombinant G9a completely reversed the AD repressive effect on DNMT1 function. In conclusion, the present study presents a model where distinct ADs affect DNMT1 activity via G9a with important repercussions for possible novel treatment regimes.
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36
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Maintenance of gene silencing by the coordinate action of the H3K9 methyltransferase G9a/KMT1C and the H3K4 demethylase Jarid1a/KDM5A. Proc Natl Acad Sci U S A 2012; 109:18845-50. [PMID: 23112189 DOI: 10.1073/pnas.1213951109] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Chromatin remodeling is essential for controlling the expression of genes during development. The histone-modifying enzyme G9a/KMT1C can act both as a coactivator and a corepressor of transcription. Here, we show that the dual function of G9a as a coactivator vs. a corepressor entails its association within two distinct protein complexes, one containing the coactivator Mediator and one containing the corepressor Jarid1a/KDM5A. Functionally, G9a is important in stabilizing the Mediator complex for gene activation, whereas its repressive function entails a coordinate action with the histone H3 lysine 4 (H3K4) demethylase Jarid1a for the maintenance of gene repression. The essential nature of cross-talk between the histone methyltransferase G9a and the demethylase Jarid1a is demonstrated on the embryonic E(y)-globin gene, where the concurrent introduction of repressive histone marks (dimethylated H3K9 and dimethylated H3K27) and removal of activating histone mark (trimethylated H3K4) is required for maintenance of gene silencing. Taken together with our previous demonstration of cross-talk between UTX and MLL2 to mediate activation of the adult β(maj)-globin gene, these data suggest a model where "active" and "repressive" cross-talk between histone-modifying enzymes coexist on the same multigene locus and play a crucial role in the precise control of developmentally regulated gene expression.
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37
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Chen X, Skutt-Kakaria K, Davison J, Ou YL, Choi E, Malik P, Loeb K, Wood B, Georges G, Torok-Storb B, Paddison PJ. G9a/GLP-dependent histone H3K9me2 patterning during human hematopoietic stem cell lineage commitment. Genes Dev 2012; 26:2499-511. [PMID: 23105005 DOI: 10.1101/gad.200329.112] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
G9a and GLP are conserved protein methyltransferases that play key roles during mammalian development through mono- and dimethylation of histone H3 Lys 9 (H3K9me1/2), modifications associated with transcriptional repression. During embryogenesis, large H3K9me2 chromatin territories arise that have been proposed to reinforce lineage choice by affecting high-order chromatin structure. Here we report that in adult human hematopoietic stem and progenitor cells (HSPCs), H3K9me2 chromatin territories are absent in primitive cells and are formed de novo during lineage commitment. In committed HSPCs, G9a/GLP activity nucleates H3K9me2 marks at CpG islands and other genomic sites within genic regions, which then spread across most genic regions during differentiation. Immunofluorescence assays revealed the emergence of H3K9me2 nuclear speckles in committed HSPCs, consistent with progressive marking. Moreover, gene expression analysis indicated that G9a/GLP activity suppresses promiscuous transcription of lineage-affiliated genes and certain gene clusters, suggestive of regulation of HSPC chromatin structure. Remarkably, HSPCs continuously treated with UNC0638, a G9a/GLP small molecular inhibitor, better retain stem cell-like phenotypes and function during in vitro expansion. These results suggest that G9a/GLP activity promotes progressive H3K9me2 patterning during HSPC lineage specification and that its inhibition delays HSPC lineage commitment. They also inform clinical manipulation of donor-derived HSPCs.
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Affiliation(s)
- Xiaoji Chen
- Molecular and Cell Biology (MCB) Program, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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38
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Hashimoto H, Vertino PM, Cheng X. Molecular coupling of DNA methylation and histone methylation. Epigenomics 2012; 2:657-69. [PMID: 21339843 DOI: 10.2217/epi.10.44] [Citation(s) in RCA: 207] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The combinatorial pattern of DNA and histone modifications constitutes an epigenetic 'code' that shapes gene-expression patterns by enabling or restricting the transcriptional potential of genomic domains. DNA methylation is associated with histone modifications, particularly the absence of histone H3 lysine 4 methylation (H3K4me0) and the presence of H3K9 methylation. This article focuses on three protein domains (ATRX-Dnmt3-Dnmt3L [ADD], Cys-X-X-Cys [CXXC] and the methyl-CpG-binding domain [MBD]) and the functional implications of domain architecture in the mechanisms linking histone methylation and DNA methylation in mammalian cells. The DNA methyltransferase DNMT3a and its accessory protein Dnmt 3L contain a H3K4me0-interacting ADD domain that links the DNA methylation reaction with unmodified H3K4. The H3K4 methyltransferase MLL1 contains a CpG-interacting CXXC domain that may couple the H3K4 methylation reaction to unmethylated DNA. Another H3K4 methyltransferase, SET1, although lacking an intrinsic CXXC domain, interacts directly with an accessory protein CFP1 that contains the same domain. The H3K9 methyltransferase SETDB1 contains a putative MBD that potentially links the H3K4 methylation reaction to methylated DNA or may do so through the interaction with the MBD containing protein MBD1. Finally, we consider the domain structure of the DNA methyltransferase DNMT1, its accessory protein UHRF1 and their associated proteins, and propose a mechanism by which DNA methylation and histone methylation may be coordinately maintained through mitotic cell division, allowing for the transmission of parental DNA and for the histone methylation patterns to be copied to newly replicated chromatin.
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Affiliation(s)
- Hideharu Hashimoto
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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39
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Dong C, Wu Y, Yao J, Wang Y, Yu Y, Rychahou PG, Evers BM, Zhou BP. G9a interacts with Snail and is critical for Snail-mediated E-cadherin repression in human breast cancer. J Clin Invest 2012; 122:1469-86. [PMID: 22406531 DOI: 10.1172/jci57349] [Citation(s) in RCA: 360] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 01/18/2012] [Indexed: 12/23/2022] Open
Abstract
Breast cancers are highly heterogeneous but can be grouped into subtypes based on several criteria, including level of expression of certain markers. Claudin-low breast cancer (CLBC) is associated with early metastasis and resistance to chemotherapy, while gene profiling indicates it is characterized by the expression of markers of epithelial-mesenchymal transition (EMT) - a phenotypic conversion linked with metastasis. Although the epigenetic program controlling the phenotypic and cellular plasticity of EMT remains unclear, one contributor may be methylation of the E-cadherin promoter, resulting in decreased E-cadherin expression, a hallmark of EMT. Indeed, reduced E-cadherin often occurs in CLBC and may contribute to the early metastasis and poor patient survival associated with this disease. Here, we have determined that methylation of histone H3 on lysine 9 (H3K9me2) is critical for promoter DNA methylation of E-cadherin in three TGF-β-induced EMT model cell lines, as well as in CLBC cell lines. Further, Snail interacted with G9a, a major euchromatin methyltransferase responsible for H3K9me2, and recruited G9a and DNA methyltransferases to the E-cadherin promoter for DNA methylation. Knockdown of G9a restored E-cadherin expression by suppressing H3K9me2 and blocking DNA methylation. This resulted in inhibition of cell migration and invasion in vitro and suppression of tumor growth and lung colonization in in vivo models of CLBC metastasis. Our study not only reveals a critical mechanism underlying the epigenetic regulation of EMT but also paves a way for the development of new treatment strategies for CLBC.
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Affiliation(s)
- Chenfang Dong
- Department of Molecular and Cellular Biochemistry, The University of Kentucky, College of Medicine, Lexington, Kentucky 40506-0509, USA
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40
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Sharma S, Gerke DS, Han HF, Jeong S, Stallcup MR, Jones PA, Liang G. Lysine methyltransferase G9a is not required for DNMT3A/3B anchoring to methylated nucleosomes and maintenance of DNA methylation in somatic cells. Epigenetics Chromatin 2012; 5:3. [PMID: 22284370 PMCID: PMC3292817 DOI: 10.1186/1756-8935-5-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 01/27/2012] [Indexed: 12/31/2022] Open
Abstract
Background DNA methylation, histone modifications and nucleosome occupancy act in concert for regulation of gene expression patterns in mammalian cells. Recently, G9a, a H3K9 methyltransferase, has been shown to play a role in establishment of DNA methylation at embryonic gene targets in ES cells through recruitment of de novo DNMT3A/3B enzymes. However, whether G9a plays a similar role in maintenance of DNA methylation in somatic cells is still unclear. Results Here we show that G9a is not essential for maintenance of DNA methylation in somatic cells. Knockdown of G9a has no measurable effect on DNA methylation levels at G9a-target loci. DNMT3A/3B remain stably anchored to nucleosomes containing methylated DNA even in the absence of G9a, ensuring faithful propagation of methylated states in cooperation with DNMT1 through somatic divisions. Moreover, G9a also associates with nucleosomes in a DNMT3A/3B and DNA methylation-independent manner. However, G9a knockdown synergizes with pharmacologic inhibition of DNMTs resulting in increased hypomethylation and inhibition of cell proliferation. Conclusions Taken together, these data suggest that G9a is not involved in maintenance of DNA methylation in somatic cells but might play a role in re-initiation of de novo methylation after treatment with hypomethylating drugs, thus serving as a potential target for combinatorial treatments strategies involving DNMTs inhibitors.
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Affiliation(s)
- Shikhar Sharma
- Department of Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9181, USA.
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Sharma RP, Gavin DP, Chase KA. Heterochromatin as an incubator for pathology and treatment non-response: implication for neuropsychiatric illness. THE PHARMACOGENOMICS JOURNAL 2012; 12:361-7. [PMID: 22249356 DOI: 10.1038/tpj.2011.64] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Heterochromatin is a higher order assembly that is characterized by a genome-wide distribution, gene-repression, durability and potential to spread. In this light, it is an appealing mechanism to interpret the neurobiology of complex brain disorders such as schizophrenia where downregulation of expression appears to be the norm. H3K9 methylation (H3K9me) can initiate the seeding of a heterochromatin assembly on an inactive or poorly coordinated promoter as a consequence of a decline in transactivators either from disuse or from misuse. H3K9me can extend its influence by spatial spreading through the mechanism of recursively recruiting adapters, such as heterochromatin protein 1 (HP1) homodimers. HP1 itself serves as a platform for other repressive proteins such as DNA methyltransferases. In full color, heterochromatin can occupy genome-wide gene networks, tissue specific ontologies and even rearrange the nuclear architecture. Heterochromatin in the brain is modified by small molecule pharmacology and serves a physiological role in the functioning of dopamine neurons and the construction of memory. From a therapeutic perspective, the durable nature of heterochromatin implies that it may require disassembly before the full genomic-potential of standard pharmacotherapies is achieved, especially in treatment resistant patients.
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Affiliation(s)
- R P Sharma
- The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL 60612, USA.
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42
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Rowbotham SP, Barki L, Neves-Costa A, Santos F, Dean W, Hawkes N, Choudhary P, Will WR, Webster J, Oxley D, Green CM, Varga-Weisz P, Mermoud JE. Maintenance of silent chromatin through replication requires SWI/SNF-like chromatin remodeler SMARCAD1. Mol Cell 2011; 42:285-96. [PMID: 21549307 DOI: 10.1016/j.molcel.2011.02.036] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 01/11/2011] [Accepted: 02/25/2011] [Indexed: 01/20/2023]
Abstract
Epigenetic marks such as posttranslational histone modifications specify the functional states of underlying DNA sequences, though how they are maintained after their disruption during DNA replication remains a critical question. We identify the mammalian SWI/SNF-like protein SMARCAD1 as a key factor required for the re-establishment of repressive chromatin. The ATPase activity of SMARCAD1 is necessary for global deacetylation of histones H3/H4. In this way, SMARCAD1 promotes methylation of H3K9, the establishment of heterochromatin, and faithful chromosome segregation. SMARCAD1 associates with transcriptional repressors including KAP1, histone deacetylases HDAC1/2 and the histone methyltransferase G9a/GLP and modulates the interaction of HDAC1 and KAP1 with heterochromatin. SMARCAD1 directly interacts with PCNA, a central component of the replication machinery, and is recruited to sites of DNA replication. Our findings suggest that chromatin remodeling by SMARCAD1 ensures that silenced loci, such as pericentric heterochromatin, are correctly perpetuated.
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Affiliation(s)
- Samuel P Rowbotham
- Nuclear Dynamics and Function, Babraham Institute, Cambridge CB22 3AT, UK
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Shinkai Y, Tachibana M. H3K9 methyltransferase G9a and the related molecule GLP. Genes Dev 2011; 25:781-8. [PMID: 21498567 DOI: 10.1101/gad.2027411] [Citation(s) in RCA: 402] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The discovery of Suv39h1, the first SET domain-containing histone lysine methyltransferase (HKMT), was reported in 2000. Since then, research on histone methylation has progressed rapidly. Among the identified HKMTs in mammals, G9a and GLP are the primary enzymes for mono- and dimethylation at Lys 9 of histone H3 (H3K9me1 and H3K9me2), and exist predominantly as a G9a-GLP heteromeric complex that appears to be a functional H3K9 methyltransferase in vivo. Recently, many important studies have reported that G9a and GLP play critical roles in various biological processes. The physiological relevance of G9a/GLP-mediated epigenetic gene regulation is discussed.
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Affiliation(s)
- Yoichi Shinkai
- Institute for Virus Research, Kyoto University, Kawara-cho, Sakyo-ku, Kyoto, Kyoto 606-8507, Japan.
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44
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Abstract
The DNA in our bodies is wrapped around octamers of histone proteins to form nucleosomes. This structural organization facilitates packaging of the entire genome into a single nucleus but is also a platform for post-translational modifications which have functional roles within the cell. Over the last few years, modifications of histone residues have been identified and potential roles of individual modifications in processes such as DNA repair, replication and gene transcription have been uncovered. However, we know much less about the combinatorial action of the individual marks and how one modification impacts on the function of another. Recent developments in quantitative proteomics methodology and increasing amounts of genomic data generated using high-throughput techniques are allowing insights into how multiple modifications are interpreted by the cell.
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Affiliation(s)
- Ian C Wood
- Institute of Membrane & Systems Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
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45
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Abstract
Eukaryotic chromatin can be highly dynamic and can continuously exchange between an open transcriptionally active conformation and a compacted silenced one. Post-translational modifications of histones have a pivotal role in regulating chromatin states, thus influencing all chromatin dependent processes. Methylation is currently one of the best characterized histone modification and occurs on arginine and lysine residues. Histone methylation can regulate other modifications (e.g. acetylation, phosphorylation and ubiquitination) in order to define a precise functional chromatin environment. In this review we focus on histone methylation and demethylation, as well as on the enzymes responsible for setting these marks. In particular we are describing novel concepts on the interdependence of histone modifications marks and discussing the molecular mechanisms governing this cross-talks.
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46
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Abstract
Recent advances in chromatin biology have identified a role for epigenetic mechanisms in the regulation of neuronal gene expression changes, a necessary process for proper synaptic plasticity and memory formation. Experimental evidence for dynamic chromatin remodeling influencing gene transcription in postmitotic neurons grew from initial reports describing posttranslational modifications of histones, including phosphorylation and acetylation occurring in various brain regions during memory consolidation. An accumulation of recent studies, however, has also highlighted the importance of other epigenetic modifications, such as DNA methylation and histone methylation, as playing a role in memory formation. This present review examines learning-induced gene transcription by chromatin remodeling underlying long-lasting changes in neurons, with direct implications for the study of epigenetic mechanisms in long-term memory formation and behavior. Furthermore, the study of epigenetic gene regulation, in conjunction with transcription factor activation, can provide complementary lines of evidence to further understanding transcriptional mechanisms subserving memory storage.
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Affiliation(s)
- Farah D. Lubin
- Evelyn F. McKnight Brain Institute, Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Swati Gupta
- Evelyn F. McKnight Brain Institute, Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - R. Ryley Parrish
- Evelyn F. McKnight Brain Institute, Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nicola M. Grissom
- Evelyn F. McKnight Brain Institute, Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robin L. Davis
- Evelyn F. McKnight Brain Institute, Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA
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47
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Aravind L, Abhiman S, Iyer LM. Natural history of the eukaryotic chromatin protein methylation system. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 101:105-76. [PMID: 21507350 DOI: 10.1016/b978-0-12-387685-0.00004-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In eukaryotes, methylation of nucleosomal histones and other nuclear proteins is a central aspect of chromatin structure and dynamics. The past 15 years have seen an enormous advance in our understanding of the biochemistry of these modifications, and of their role in establishing the epigenetic code. We provide a synthetic overview, from an evolutionary perspective, of the main players in the eukaryotic chromatin protein methylation system, with an emphasis on catalytic domains. Several components of the eukaryotic protein methylation system had their origins in bacteria. In particular, the Rossmann fold protein methylases (PRMTs and DOT1), and the LSD1 and jumonji-related demethylases and oxidases, appear to have emerged in the context of bacterial peptide methylation and hydroxylation systems. These systems were originally involved in synthesis of peptide secondary metabolites, such as antibiotics, toxins, and siderophores. The peptidylarginine deiminases appear to have been acquired by animals from bacterial enzymes that modify cell-surface proteins. SET domain methylases, which display the β-clip fold, apparently first emerged in prokaryotes from the SAF superfamily of carbohydrate-binding domains. However, even in bacteria, a subset of the SET domains might have evolved a chromatin-related role in conjunction with a BAF60a/b-like SWIB domain protein and topoisomerases. By the time of the last eukaryotic common ancestor, multiple SET and PRMT methylases were already in place and are likely to have mediated methylation at the H3K4, H3K9, H3K36, and H4K20 positions, and carried out both asymmetric and symmetric arginine dimethylation. Inference of H3K27 methylation in the ancestral eukaryote appears uncertain, though it was certainly in place a little later in eukaryotic evolution. Current data suggest that unlike SET methylases, which are universally present in eukaryotes, demethylases are not. They appear to be absent in the earliest-branching eukaryotic lineages, and emerged later along with several other chromatin proteins, such as the Dot1-methylase, prior to divergence of the kinetoplastid-heterolobosean lineage from the remaining eukaryotes. This period also corresponds to the point of origin of DNA cytosine methylation by DNMT1. Origin of major lineages of SET domains such as the Trithorax, Su(var)3-9, Ash1, SMYD, and TTLL12 and E(Z) might have played the initial role in the establishment of multiple distinct heterochromatic and euchromatic states that are likely to have been present, in some form, through much of eukaryotic evolution. Elaboration of these chromatin states might have gone hand-in-hand with acquisition of multiple jumonji-related and LSD1-like demethylases, and functional linkages with the DNA methylation and RNAi systems. Throughout eukaryotic evolution, there were several lineage-specific expansions of SET domain proteins, which might be related to a special transcription regulation process in trypanosomes, acquisition of new meiotic recombination hotspots in animals, and methylation and associated modifications of the diatom silaffin proteins involved in silica biomineralization. The use of specific domains to "read" the methylation marks appears to have been present in the ancestral eukaryote itself. Of these the chromo-like domains appear to have been acquired from bacterial secreted proteins that might have a role in binding cell-surface peptides or peptidoglycan. Domain architectures of the primary enzymes involved in the eukaryotic protein methylation system indicate key features relating to interactions with each other and other modifications in chromatin, such as acetylation. They also emphasize the profound functional distinction between the role of demethylation and deacetylation in regulation of chromatin dynamics.
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Affiliation(s)
- L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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