101
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Al Temimi AHK, Teeuwen RS, Tran V, Altunc AJ, Lenstra DC, Ren W, Qian P, Guo H, Mecinović J. Importance of the main chain of lysine for histone lysine methyltransferase catalysis. Org Biomol Chem 2020; 17:5693-5697. [PMID: 31134245 DOI: 10.1039/c9ob01038f] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Histone lysine methyltransferases (KMTs) are biomedicinally important class of epigenetic enzymes that catalyse methylation of lysine residues in histones and other proteins. Enzymatic and computational studies on the simplest lysine analogues that possess a modified main chain demonstrate that the lysine's backbone contributes significantly to functional KMT binding and catalysis.
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Affiliation(s)
- Abbas H K Al Temimi
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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102
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Function of the MYND Domain and C-Terminal Region in Regulating the Subcellular Localization and Catalytic Activity of the SMYD Family Lysine Methyltransferase Set5. Mol Cell Biol 2020; 40:MCB.00341-19. [PMID: 31685550 DOI: 10.1128/mcb.00341-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/01/2019] [Indexed: 11/20/2022] Open
Abstract
SMYD lysine methyltransferases target histones and nonhistone proteins for methylation and are critical regulators of muscle development and implicated in neoplastic transformation. They are characterized by a split catalytic SET domain and an intervening MYND zinc finger domain, as well as an extended C-terminal domain. Saccharomyces cerevisiae contains two SMYD proteins, Set5 and Set6, which share structural elements with the mammalian SMYD enzymes. Set5 is a histone H4 lysine 5, 8, and 12 methyltransferase, implicated in the regulation of stress responses and genome stability. While the SMYD proteins have diverse roles in cells, there are many gaps in our understanding of how these enzymes are regulated. Here, we performed mutational analysis of Set5, combined with phosphoproteomics, to identify regulatory mechanisms for its enzymatic activity and subcellular localization. Our results indicate that the MYND domain promotes Set5 chromatin association in cells and is required for its role in repressing subtelomeric genes. Phosphoproteomics revealed extensive phosphorylation of Set5, and phosphomimetic mutations enhance Set5 catalytic activity but diminish its ability to interact with chromatin in cells. These studies uncover multiple regions within Set5 that regulate its localization and activity and highlight potential avenues for understanding mechanisms controlling the diverse roles of SMYD enzymes.
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103
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Yu C, Zhuang S. Histone Methyltransferases as Therapeutic Targets for Kidney Diseases. Front Pharmacol 2019; 10:1393. [PMID: 31866860 PMCID: PMC6908484 DOI: 10.3389/fphar.2019.01393] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 10/31/2019] [Indexed: 12/31/2022] Open
Abstract
Emerging evidence has demonstrated that epigenetic regulation plays a vital role in gene expression under normal and pathological conditions. Alterations in the expression and activation of histone methyltransferases (HMTs) have been reported in preclinical models of multiple kidney diseases, including acute kidney injury, chronic kidney disease, diabetic nephropathy, polycystic kidney disease, and renal cell carcinoma. Pharmacological inhibition of these enzymes has shown promise in preclinical models of those renal diseases. In this review, we summarize recent knowledge regarding expression and activation of various HMTs and their functional roles in some kidney diseases. The preclinical activity of currently available HMT inhibitors and the mechanisms of their actions are highlighted.
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Affiliation(s)
- Chao Yu
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shougang Zhuang
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Medicine, Rhode Island Hospital and Alpert Medical School, Brown University, Providence, RI, United States
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104
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Watson ZL, Yamamoto TM, McMellen A, Kim H, Hughes CJ, Wheeler LJ, Post MD, Behbakht K, Bitler BG. Histone methyltransferases EHMT1 and EHMT2 (GLP/G9A) maintain PARP inhibitor resistance in high-grade serous ovarian carcinoma. Clin Epigenetics 2019; 11:165. [PMID: 31775874 PMCID: PMC6882350 DOI: 10.1186/s13148-019-0758-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 10/06/2019] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Euchromatic histone-lysine-N-methyltransferases 1 and 2 (EHMT1/2, aka GLP/G9A) catalyze dimethylation of histone H3 lysine 9 (H3K9me2) and have roles in epigenetic silencing of gene expression. EHMT1/2 also have direct roles in DNA repair and are implicated in chemoresistance in several cancers. Resistance to chemotherapy and PARP inhibitors (PARPi) is a major cause of mortality in high-grade serous ovarian carcinoma (HGSOC), but the contribution of the epigenetic landscape is unknown. RESULTS To identify epigenetic mechanisms of PARPi resistance in HGSOC, we utilized unbiased exploratory techniques, including RNA-Seq and mass spectrometry profiling of histone modifications. Compared to sensitive cells, PARPi-resistant HGSOC cells display a global increase of H3K9me2 accompanied by overexpression of EHMT1/2. EHMT1/2 overexpression was also observed in a PARPi-resistant in vivo patient-derived xenograft (PDX) model. Genetic or pharmacologic disruption of EHMT1/2 sensitizes HGSOC cells to PARPi. Cell death assays demonstrate that EHMT1/2 disruption does not increase PARPi-induced apoptosis. Functional DNA repair assays show that disruption of EHMT1/2 ablates homologous recombination (HR) and non-homologous end joining (NHEJ), while immunofluorescent staining of phosphorylated histone H2AX shows large increases in DNA damage. Propidium iodide staining and flow cytometry analysis of cell cycle show that PARPi treatment increases the proportion of PARPi-resistant cells in S and G2 phases, while cells treated with an EHMT1/2 inhibitor remain in G1. Co-treatment with PARPi and EHMT1/2 inhibitor produces an intermediate phenotype. Immunoblot of cell cycle regulators shows that combined EHMT1/2 and PARP inhibition reduces expression of specific cyclins and phosphorylation of mitotic markers. These data suggest DNA damage and altered cell cycle regulation as mechanisms of sensitization. RNA-Seq of PARPi-resistant cells treated with EHMT1/2 inhibitor showed significant gene expression changes enriched in pro-survival pathways that remain unexplored in the context of PARPi resistance, including PI3K, AKT, and mTOR. CONCLUSIONS This study demonstrates that disrupting EHMT1/2 sensitizes HGSOC cells to PARPi, and suggests a potential mechanism through DNA damage and cell cycle dysregulation. RNA-Seq identifies several unexplored pathways that may alter PARPi resistance. Further study of EHMT1/2 and regulated genes will facilitate development of novel therapeutic strategies to successfully treat HGSOC.
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Affiliation(s)
- Zachary L Watson
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Tomomi M Yamamoto
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Alexandra McMellen
- Cancer Biology Graduate Program, University of Colorado, Aurora, CO, 80045, USA
| | - Hyunmin Kim
- Translational Bioinformatics and Cancer Systems Biology Laboratory, Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Connor J Hughes
- Medical Student Training Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Lindsay J Wheeler
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Miriam D Post
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Kian Behbakht
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Benjamin G Bitler
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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105
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Abstract
The epigenetic modifications of histones are versatile marks that are intimately connected to development and disease pathogenesis including human cancers. In this review, we will discuss the many different types of histone modifications and the biological processes with which they are involved. Specifically, we review the enzymatic machineries and modifications that are involved in cancer development and progression, and how to apply currently available small molecule inhibitors for histone modifiers as tool compounds to study the functional significance of histone modifications and their clinical implications.
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Affiliation(s)
- Zibo Zhao
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Simpson Querrey 7th Floor 303 E. Superior Street, Chicago, IL 60611 USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Simpson Querrey 7th Floor 303 E. Superior Street, Chicago, IL 60611 USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
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106
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Abstract
Protein methylation is an important and reversible post-translational modification
that regulates many biological processes in cells. It occurs mainly on lysine and arginine
residues and involves many important biological processes, including transcriptional
activity, signal transduction, and the regulation of gene expression. Protein methylation
and its regulatory enzymes are related to a variety of human diseases, so improved identification
of methylation sites is useful for designing drugs for a variety of related diseases.
In this review, we systematically summarize and analyze the tools used for the prediction
of protein methylation sites on arginine and lysine residues over the last decade.
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Affiliation(s)
- Chunyan Ao
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Shunshan Jin
- Department of Neurology, Heilongjiang Province Land Reclamation Headquarters General Hospital, Harbin, China
| | - Yuan Lin
- Department of System Integration, Sparebanken Vest, Bergen, Norway
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
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107
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Al Temimi AHK, Martin M, Meng Q, Lenstra DC, Qian P, Guo H, Weinhold E, Mecinović J. Lysine Ethylation by Histone Lysine Methyltransferases. Chembiochem 2019; 21:392-400. [PMID: 31287209 PMCID: PMC7064923 DOI: 10.1002/cbic.201900359] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Indexed: 01/16/2023]
Abstract
Biomedicinally important histone lysine methyltransferases (KMTs) catalyze the transfer of a methyl group from S‐adenosylmethionine (AdoMet) cosubstrate to lysine residues in histones and other proteins. Herein, experimental and computational investigations on human KMT‐catalyzed ethylation of histone peptides by using S‐adenosylethionine (AdoEth) and Se‐adenosylselenoethionine (AdoSeEth) cosubstrates are reported. MALDI‐TOF MS experiments reveal that, unlike monomethyltransferases SETD7 and SETD8, methyltransferases G9a and G9a‐like protein (GLP) do have the capacity to ethylate lysine residues in histone peptides, and that cosubstrates follow the efficiency trend AdoMet>AdoSeEth>AdoEth. G9a and GLP can also catalyze AdoSeEth‐mediated ethylation of ornithine and produce histone peptides bearing lysine residues with different alkyl groups, such as H3K9meet and H3K9me2et. Molecular dynamics and free energy simulations based on quantum mechanics/molecular mechanics potential supported the experimental findings by providing an insight into the geometry and energetics of the enzymatic methyl/ethyl transfer process.
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Affiliation(s)
- Abbas H K Al Temimi
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Michael Martin
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056, Aachen, Germany
| | - Qingxi Meng
- Chemistry and Material Science Faculty, Shandong Agricultural University, Daizong Road No.61, Tai'an, 271018, P.R. China
| | - Danny C Lenstra
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Ping Qian
- Chemistry and Material Science Faculty, Shandong Agricultural University, Daizong Road No.61, Tai'an, 271018, P.R. China
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN, 37996, USA.,UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37830, USA
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056, Aachen, Germany
| | - Jasmin Mecinović
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.,Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
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108
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The nucleophilic amino group of lysine is central for histone lysine methyltransferase catalysis. Commun Chem 2019. [DOI: 10.1038/s42004-019-0210-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Abstract
Histone lysine methyltransferases (KMTs) are biomedically important epigenetic enzymes that catalyze the transfer of methyl group from S-adenosylmethionine to lysine’s nucleophilic ε-amino group in histone tails and core histones. Understanding the chemical basis of KMT catalysis is important for discerning its complex biology in disease, structure-function relationship, and for designing specific inhibitors with therapeutic potential. Here we examine histone peptides, which possess simplest lysine analogs with different nucleophilic character, as substrates for human KMTs. Combined MALDI-TOF MS experiments, NMR analyses and molecular dynamics and free-energy simulations based on quantum mechanics/molecular mechanics (QM/MM) potential provide experimental and theoretical evidence that KMTs do have an ability to catalyze methylation of primary amine-containing N-nucleophiles, but do not methylate related amide/guanidine-containing N-nucleophiles as well as simple O- and C-nucleophiles. The results demonstrate a broader, but still limited, substrate scope for KMT catalysis, and contribute to rational design of selective epigenetic inhibitors.
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109
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Soshnikova N. Functions of SETD7 during development, homeostasis and cancer. Stem Cell Investig 2019; 6:26. [PMID: 31620473 DOI: 10.21037/sci.2019.06.10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 06/19/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Natalia Soshnikova
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
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110
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Lund PJ, Lehman SM, Garcia BA. Quantitative analysis of global protein lysine methylation by mass spectrometry. Methods Enzymol 2019; 626:475-498. [PMID: 31606088 DOI: 10.1016/bs.mie.2019.07.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Since protein activity is often regulated by posttranslational modifications, the qualitative and quantitative analysis of modification sites is critical for understanding the regulation of biological pathways that control cell function and phenotype. Methylation constitutes one of the many types of posttranslational modifications that target lysine residues. Although lysine methylation is perhaps most commonly associated with histone proteins and the epigenetic regulation of processes involving chromatin, methylation has also been observed as an important regulatory modification on other proteins, which has spurred the development of methods to profile lysine methylation sites more globally. As with many posttranslational modifications, tandem mass spectrometry represents an ideal platform for the high-throughput analysis of lysine methylation due to its high sensitivity and resolving power. The following protocol outlines a general method to assay lysine methylation across the proteome using SILAC and quantitative proteomics. First, cells are labeled by SILAC to allow for relative quantitation across different experimental conditions, such as cells with or without ectopic expression of a methyltransferase. Next, cells are lysed and proteins are digested into peptides. Methylated peptides are then enriched by immunoprecipitation with pan-specific antibodies against methylated lysine. Finally, the enriched peptides are analyzed by LC-MS/MS to identify methylated peptides and their modification sites and to compare the relative abundance of methylation events between different conditions. This approach should yield detection of a couple hundred lysine methylation sites, and those showing differential abundance may then be prioritized for further study.
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Affiliation(s)
- Peder J Lund
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Stephanie M Lehman
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Penn Epigenetics Institute, Smilow Center for Translational Research, University of Pennsylvania School of Medicine, Philadelphia, PA, United States.
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111
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Batham J, Lim PS, Rao S. SETDB-1: A Potential Epigenetic Regulator in Breast Cancer Metastasis. Cancers (Basel) 2019; 11:cancers11081143. [PMID: 31405032 PMCID: PMC6721492 DOI: 10.3390/cancers11081143] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 02/06/2023] Open
Abstract
The full epigenetic repertoire governing breast cancer metastasis is not completely understood. Here, we discuss the histone methyltransferase SET Domain Bifurcated Histone Lysine Methyltransferase 1 (SETDB1) and its role in breast cancer metastasis. SETDB1 serves as an exemplar of the difficulties faced when developing therapies that not only specifically target cancer cells but also the more elusive and aggressive stem cells that contribute to metastasis via epithelial-to-mesenchymal transition and confer resistance to therapies.
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Affiliation(s)
- Jacob Batham
- Melanie Swan Memorial Translational Centre, Faculty of Sci-Tech, University of Canberra, Bruce ACT 2617, Australia
| | - Pek Siew Lim
- Melanie Swan Memorial Translational Centre, Faculty of Sci-Tech, University of Canberra, Bruce ACT 2617, Australia.
| | - Sudha Rao
- Melanie Swan Memorial Translational Centre, Faculty of Sci-Tech, University of Canberra, Bruce ACT 2617, Australia.
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112
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Structural basis for the target specificity of actin histidine methyltransferase SETD3. Nat Commun 2019; 10:3541. [PMID: 31388018 PMCID: PMC6684798 DOI: 10.1038/s41467-019-11554-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/22/2019] [Indexed: 12/26/2022] Open
Abstract
SETD3 is an actin histidine-N3 methyltransferase, whereas other characterized SET-domain enzymes are protein lysine methyltransferases. We report that in a pre-reactive complex SETD3 binds the N3-protonated form (N3-H) of actin His73, and in a post-reactive product complex, SETD3 generates the methylated histidine in an N1-protonated (N1-H) and N3-methylated form. During the reaction, the imidazole ring of His73 rotates ~105°, which shifts the proton from N3 to N1, thus ensuring that the target atom N3 is deprotonated prior to the methyl transfer. Under the conditions optimized for lysine deprotonation, SETD3 has weak lysine methylation activity on an actin peptide in which the target His73 is substituted by a lysine. The structure of SETD3 with Lys73-containing peptide reveals a bent conformation of Lys73, with its side chain aliphatic carbons tracing along the edge of imidazole ring and the terminal ε-amino group occupying a position nearly identical to the N3 atom of unmethylated histidine. SETD3 is the first known metazoan protein histidine methyltransferase but the molecular basis for its target specificity is unclear. Here, the authors elucidate the structural and molecular determinants for the histidine specificity of SETD3.
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113
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Ye S, Ding YF, Jia WH, Liu XL, Feng JY, Zhu Q, Cai SL, Yang YS, Lu QY, Huang XT, Yang JS, Jia SN, Ding GP, Wang YH, Zhou JJ, Chen YD, Yang WJ. SET Domain-Containing Protein 4 Epigenetically Controls Breast Cancer Stem Cell Quiescence. Cancer Res 2019; 79:4729-4743. [PMID: 31308046 DOI: 10.1158/0008-5472.can-19-1084] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/06/2019] [Accepted: 07/10/2019] [Indexed: 12/31/2022]
Abstract
Quiescent cancer stem cells (CSC) play important roles in tumorigenesis, relapse, and resistance to chemoradiotherapy. However, the determinants of CSC quiescence and how they sustain themselves to generate tumors and relapse beyond resistance to chemoradiotherapy remains unclear. Here, we found that SET domain-containing protein 4 (SETD4) epigenetically controls breast CSC (BCSC) quiescence by facilitating heterochromatin formation via H4K20me3 catalysis. H4K20me3 localized to the promoter regions and regulated the expression of a set of genes in quiescent BCSCs (qBCSC). SETD4-defined qBCSCs were resistant to chemoradiotherapy and promoted tumor relapse in a mouse model. Upon activation, a SETD4-defined qBCSC sustained itself in a quiescent state by asymmetric division and concurrently produced an active daughter cell that proliferated to produce a cancer cell population. Single-cell sequence analysis indicated that SETD4+ qBCSCs clustered together as a distinct cell type within the heterogeneous BCSC population. SETD4-defined quiescent CSCs were present in multiple cancer types including gastric, cervical, ovarian, liver, and lung cancers and were resistant to chemotherapy. SETD4-defined qBCSCs had a high tumorigenesis potential and correlated with malignancy and chemotherapy resistance in clinical breast cancer patients. Taken together, the results from our previous study and current study on six cancer types reveal an evolutionarily conserved mechanism of cellular quiescence epigenetically controlled by SETD4. Our findings provide insights into the mechanism of tumorigenesis and relapse promoted by SETD4-defined quiescent CSCs and have broad implications for clinical therapies. SIGNIFICANCE: These findings advance our knowledge on the epigenetic determinants of quiescence in cancer stem cell populations and pave the way for future pharmacologic developments aimed at targeting drug-resistant quiescent stem cells.
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Affiliation(s)
- Sen Ye
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yan-Fu Ding
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wen-Huan Jia
- Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiao-Li Liu
- Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jing-Yi Feng
- Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qian Zhu
- Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Sun-Li Cai
- Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yao-Shun Yang
- Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qian-Yun Lu
- Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xue-Ting Huang
- Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jin-Shu Yang
- Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Sheng-Nan Jia
- Department of General Surgery, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Guo-Ping Ding
- Department of General Surgery, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yue-Hong Wang
- Department of Respiratory Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jiao-Jiao Zhou
- Department of Surgical Oncology, The Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yi-Ding Chen
- Department of Surgical Oncology, The Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Wei-Jun Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China. .,Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
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114
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PRDM16s transforms megakaryocyte-erythroid progenitors into myeloid leukemia-initiating cells. Blood 2019; 134:614-625. [PMID: 31270104 DOI: 10.1182/blood.2018888255] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 06/26/2019] [Indexed: 12/11/2022] Open
Abstract
Oncogenic mutations confer on cells the ability to propagate indefinitely, but whether oncogenes alter the cell fate of these cells is unknown. Here, we show that the transcriptional regulator PRDM16s causes oncogenic fate conversion by transforming cells fated to form platelets and erythrocytes into myeloid leukemia stem cells (LSCs). Prdm16s expression in megakaryocyte-erythroid progenitors (MEPs), which normally lack the potential to generate granulomonocytic cells, caused AML by converting MEPs into LSCs. Prdm16s blocked megakaryocytic/erythroid potential by interacting with super enhancers and activating myeloid master regulators, including PU.1. A CRISPR dropout screen confirmed that PU.1 is required for Prdm16s-induced leukemia. Ablating PU.1 attenuated leukemogenesis and reinstated the megakaryocytic/erythroid potential of leukemic MEPs in mouse models and human AML with PRDM16 rearrangement. Thus, oncogenic PRDM16 s expression gives MEPs an LSC fate by activating myeloid gene regulatory networks.
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115
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Alsulami M, Munawar N, Dillon E, Oliviero G, Wynne K, Alsolami M, Moss C, Ó Gaora P, O'Meara F, Cotter D, Cagney G. SETD1A Methyltransferase Is Physically and Functionally Linked to the DNA Damage Repair Protein RAD18. Mol Cell Proteomics 2019; 18:1428-1436. [PMID: 31076518 PMCID: PMC6601208 DOI: 10.1074/mcp.ra119.001518] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Indexed: 12/13/2022] Open
Abstract
SETD1A is a SET domain-containing methyltransferase involved in epigenetic regulation of transcription. It is the main catalytic component of a multiprotein complex that methylates lysine 4 of histone H3, a histone mark associated with gene activation. In humans, six related protein complexes with partly nonredundant cellular functions share several protein subunits but are distinguished by unique catalytic SET-domain proteins. We surveyed physical interactions of the SETD1A-complex using endogenous immunoprecipitation followed by label-free quantitative proteomics on three subunits: SETD1A, RBBP5, and ASH2L. Surprisingly, SETD1A, but not RBBP5 or ASH2L, was found to interact with the DNA damage repair protein RAD18. Reciprocal RAD18 immunoprecipitation experiments confirmed the interaction with SETD1A, whereas size exclusion and protein network analysis suggested an interaction independent of the main SETD1A complex. We found evidence of SETD1A and RAD18 influence on mutual gene expression levels. Further, knockdown of the genes individually showed a DNA damage repair phenotype, whereas simultaneous knockdown resulted in an epistatic effect. This adds to a growing body of work linking epigenetic enzymes to processes involved in genome stability.
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Affiliation(s)
- Manal Alsulami
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Nayla Munawar
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; ¶Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
| | - Eugene Dillon
- §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Giorgio Oliviero
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kieran Wynne
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; ‖Maine Medical Center Research Institute, 81 Research Drive, Scarborough, Maine 04074
| | - Mona Alsolami
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Catherine Moss
- §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Peadar Ó Gaora
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Fergal O'Meara
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - David Cotter
- **Department of Psychiatry, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Gerard Cagney
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland;.
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116
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Alsulami M, Munawar N, Dillon E, Oliviero G, Wynne K, Alsolami M, Moss C, Ó Gaora P, O'Meara F, Cotter D, Cagney G. SETD1A Methyltransferase Is Physically and Functionally Linked to the DNA Damage Repair Protein RAD18. Mol Cell Proteomics 2019. [DOI: https://doi.org/10.1074/mcp.ra119.001518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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117
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Al Temimi AHK, van der Wekken-de Bruijne R, Proietti G, Guo H, Qian P, Mecinović J. γ-Thialysine versus Lysine: An Insight into the Epigenetic Methylation of Histones. Bioconjug Chem 2019; 30:1798-1804. [DOI: 10.1021/acs.bioconjchem.9b00313] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Abbas H. K. Al Temimi
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | | | - Giordano Proietti
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Ping Qian
- Chemistry and Material Science Faculty, Shandong Agricultural University, Tai’an 271018, P.R. China
| | - Jasmin Mecinović
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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Rao RA, Ketkar AA, Kedia N, Krishnamoorthy VK, Lakshmanan V, Kumar P, Mohanty A, Kumar SD, Raja SO, Gulyani A, Chaturvedi CP, Brand M, Palakodeti D, Rampalli S. KMT1 family methyltransferases regulate heterochromatin-nuclear periphery tethering via histone and non-histone protein methylation. EMBO Rep 2019; 20:e43260. [PMID: 30858340 PMCID: PMC6501005 DOI: 10.15252/embr.201643260] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 02/07/2019] [Accepted: 02/12/2019] [Indexed: 12/31/2022] Open
Abstract
Euchromatic histone methyltransferases (EHMTs), members of the KMT1 family, methylate histone and non-histone proteins. Here, we uncover a novel role for EHMTs in regulating heterochromatin anchorage to the nuclear periphery (NP) via non-histone methylation. We show that EHMTs methylate and stabilize LaminB1 (LMNB1), which associates with the H3K9me2-marked peripheral heterochromatin. Loss of LMNB1 methylation or EHMTs abrogates heterochromatin anchorage at the NP We further demonstrate that the loss of EHMTs induces many hallmarks of aging including global reduction of H3K27methyl marks and altered nuclear morphology. Consistent with this, we observe a gradual depletion of EHMTs, which correlates with loss of methylated LMNB1 and peripheral heterochromatin in aging human fibroblasts. Restoration of EHMT expression reverts peripheral heterochromatin defects in aged cells. Collectively, our work elucidates a new mechanism by which EHMTs regulate heterochromatin domain organization and reveals their impact on fundamental changes associated with the intrinsic aging process.
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Affiliation(s)
- Radhika Arasala Rao
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
- Sastra University, Tirumalaisamudram, Thanjavur, Tamilnadu, India
| | - Alhad Ashok Ketkar
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Neelam Kedia
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Vignesh K Krishnamoorthy
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Vairavan Lakshmanan
- Sastra University, Tirumalaisamudram, Thanjavur, Tamilnadu, India
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Pankaj Kumar
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Abhishek Mohanty
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Shilpa Dilip Kumar
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Sufi O Raja
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Akash Gulyani
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Chandra Prakash Chaturvedi
- Department of Hematology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Marjorie Brand
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Dasaradhi Palakodeti
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Shravanti Rampalli
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
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119
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Small-molecule inhibitors of lysine methyltransferases SMYD2 and SMYD3: current trends. Future Med Chem 2019; 11:901-921. [DOI: 10.4155/fmc-2018-0380] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Lysine methyltransferases SMYD2 and SMYD3 are involved in the epigenetic regulation of cell differentiation and functioning. Overexpression and deregulation of these enzymes have been correlated to the insurgence and progression of different tumors, making them promising molecular targets in cancer therapy even if their role in tumors is not yet fully understood. In this light, selective small-molecule inhibitors are required to fully understand and validate these enzymes, as this is a prerequisite for the development of successful targeted therapeutic strategies. The present review gives a systematic overview of the chemical probes developed to selectively target SMYD2 and SMYD3, with particular focus on the structural features important for high inhibitory activity, on the mode of inhibition and on the efficacy in cell-based and in in vivo models.
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120
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Li W, Wang HY, Zhao X, Duan H, Cheng B, Liu Y, Zhao M, Shu W, Mei Y, Wen Z, Tang M, Guo L, Li G, Chen Q, Liu X, Du HN. A methylation-phosphorylation switch determines Plk1 kinase activity and function in DNA damage repair. SCIENCE ADVANCES 2019; 5:eaau7566. [PMID: 30854428 PMCID: PMC6402851 DOI: 10.1126/sciadv.aau7566] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/23/2019] [Indexed: 05/27/2023]
Abstract
Polo-like kinase 1 (Plk1) is a crucial regulator of cell cycle progression; but the mechanism of regulation of Plk1 activity is not well understood. We present evidence that Plk1 activity is controlled by a balanced methylation and phosphorylation switch. The methyltransferase G9a monomethylates Plk1 at Lys209, which antagonizes phosphorylation of T210 to inhibit Plk1 activity. We found that the methyl-deficient Plk1 mutant K209A affects DNA replication, whereas the methyl-mimetic Plk1 mutant K209M prolongs metaphase-to-anaphase duration through the inability of sister chromatids separation. We detected accumulation of Plk1 K209me1 when cells were challenged with DNA damage stresses. Ablation of K209me1 delays the timely removal of RPA2 and RAD51 from DNA damage sites, indicating the critical role of K209me1 in guiding the machinery of DNA damage repair. Thus, our study highlights the importance of a methylation-phosphorylation switch of Plk1 in determining its kinase activity and functioning in DNA damage repair.
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Affiliation(s)
- Weizhe Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Hong-Yan Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Xiaolu Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Hongguo Duan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Binghua Cheng
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan 430071, China
| | - Yafei Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Mengjie Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Wenjie Shu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Yuchao Mei
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Zengqi Wen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences ,Beijing 100101, China
| | - Mingliang Tang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Lin Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences ,Beijing 100101, China
| | - Qiang Chen
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan 430071, China
| | - Xiaoqi Liu
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Hai-Ning Du
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
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121
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Yan L, Zhang Y, Ding B, Zhou H, Yao W, Xu H. Genetic alteration of histone lysine methyltransferases and their significance in renal cell carcinoma. PeerJ 2019; 7:e6396. [PMID: 30755832 PMCID: PMC6368835 DOI: 10.7717/peerj.6396] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 01/05/2019] [Indexed: 12/26/2022] Open
Abstract
Background Histone lysine methyltransferases (HMTs), a category of enzymes, play essential roles in regulating transcription, cellular differentiation, and chromatin construction. The genomic landscape and clinical significance of HMTs in renal cell carcinoma (RCC) remain uncovered. Methods We conducted an integrative analysis of 50 HMTs in RCC and discovered the internal relations among copy number alterations (CNAs), expressive abundance, mutations, and clinical outcome. Results We confirmed 12 HMTs with the highest frequency of genetic alterations, including seven HMTs with high-level amplification, two HMTs with somatic mutation, and three HMTs with putative homozygous deletion. Patterns of copy number and expression varied among different subtypes of RCC, including clear cell renal cell carcinoma, papillary cell carcinoma, and chromophobe renal carcinoma. Kaplan-Meier survival analysis and multivariate analysis identified that CNA or mRNA expression in some HMTs were significantly associated with shorter overall patient survival. Systematic analysis identified six HMTs (ASH1L, PRDM6, NSD1, EZH2, WHSC1L1, SETD2) which were dysregulated by genetic alterations as candidate therapeutic targets. Discussion In summary, our findings strongly evidenced that genetic alteration of HMTs may play an important role in generation and development of RCC, which lays a solid foundation for the mechanism for further research in the future.
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Affiliation(s)
- Libin Yan
- Urology, Tongji Hospital,Tongji Medical College, Huazhong University of Science Technology, Wuhan, Hubei, China.,Institute of Urology of Hubei Province, Wuhan, China
| | - Yangjun Zhang
- Urology, Tongji Hospital,Tongji Medical College, Huazhong University of Science Technology, Wuhan, Hubei, China.,Institute of Urology of Hubei Province, Wuhan, China
| | - Beichen Ding
- Urology, Tongji Hospital,Tongji Medical College, Huazhong University of Science Technology, Wuhan, Hubei, China.,Institute of Urology of Hubei Province, Wuhan, China
| | - Hui Zhou
- Urology, Tongji Hospital,Tongji Medical College, Huazhong University of Science Technology, Wuhan, Hubei, China.,Institute of Urology of Hubei Province, Wuhan, China
| | - Weimin Yao
- Urology, Tongji Hospital,Tongji Medical College, Huazhong University of Science Technology, Wuhan, Hubei, China.,Institute of Urology of Hubei Province, Wuhan, China
| | - Hua Xu
- Urology, Tongji Hospital,Tongji Medical College, Huazhong University of Science Technology, Wuhan, Hubei, China.,Institute of Urology of Hubei Province, Wuhan, China
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122
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Zhang Y, Yan L, Yao W, Chen K, Xu H, Ye Z. Integrated Analysis of Genetic Abnormalities of the Histone Lysine Methyltransferases in Prostate Cancer. Med Sci Monit 2019; 25:193-239. [PMID: 30616239 PMCID: PMC6330996 DOI: 10.12659/msm.912294] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background The histone methyltransferase (HMT) family includes histone lysine methyltransferases (HKMTs) and histone/protein arginine methyltransferases (PRMTs). The role of HMT gene variants in prostate cancer remains unknown. Therefore, this study aimed to evaluate HMT gene variants in the pathogenesis and prognosis of human prostate cancer, using in vitro cell studies and bioinformatics analysis. Material/Methods Integrative bioinformatics analysis of the expression of 51 HMT genes in human prostate cancer was based on datasets from the Cancer Genome Atlas (TCGA). Correlation and regression analysis were used to identify critical HMTs in prostate cancer. Kaplan-Meier and the area under the receiver operating characteristics curve (AUROC) were performed to evaluate the function of the HMTs on prognosis. Gene expression and function of 22Rv1 human prostate carcinoma cells were studied. Results The HMT genes identified to have a role in the pathogenesis of prostate cancer included the EZH2, SETD5, PRDM12, NSD1, SETD6, SMYD1, and the WHSC1L1 gene. The EZH2, SETD5, and SMYD1 genes were selected as a prognostic panel, with the SUV420H2 HMT gene. SETD2, NSD1, and ASH1L were identified as critical genes in the development of castration-resistant prostate cancer (CRPC), similar to mixed-lineage leukemia (MLL) complex family members. Knockdown of the SETD5 gene in 22Rv1 prostate carcinoma cells in vitro inhibited cancer cell growth and migration. Conclusions HMT gene variants may have a role in the pathogenesis of prostate cancer. Future studies may determine the role of HMT genes as prognostic biomarkers in patients with prostate cancer.
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Affiliation(s)
- Yangjun Zhang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, AL, China (mainland).,Institute of Urology of Hubei Province, Wuhan, Hubei, China (mainland)
| | - Libin Yan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (mainland).,Institute of Urology of Hubei Province, Wuhan, Hubei, China (mainland)
| | - Weimin Yao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, AL, China (mainland).,Institute of Urology of Hubei Province, Wuhan, Hubei, China (mainland)
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, AL, China (mainland).,Institute of Urology of Hubei Province, Wuhan, Hubei, China (mainland)
| | - Hua Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, AL, China (mainland).,Institute of Urology of Hubei Province, Wuhan, Hubei, China (mainland)
| | - Zhangqun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, AL, China (mainland).,Institute of Urology of Hubei Province, Wuhan, Hubei, China (mainland)
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123
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Kwiatkowski S, Seliga AK, Vertommen D, Terreri M, Ishikawa T, Grabowska I, Tiebe M, Teleman AA, Jagielski AK, Veiga-da-Cunha M, Drozak J. SETD3 protein is the actin-specific histidine N-methyltransferase. eLife 2018; 7:37921. [PMID: 30526847 PMCID: PMC6289574 DOI: 10.7554/elife.37921] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 11/06/2018] [Indexed: 01/02/2023] Open
Abstract
Protein histidine methylation is a rare post-translational modification of unknown biochemical importance. In vertebrates, only a few methylhistidine-containing proteins have been reported, including β-actin as an essential example. The evolutionary conserved methylation of β-actin H73 is catalyzed by an as yet unknown histidine N-methyltransferase. We report here that the protein SETD3 is the actin-specific histidine N-methyltransferase. In vitro, recombinant rat and human SETD3 methylated β-actin at H73. Knocking-out SETD3 in both human HAP1 cells and in Drosophila melanogaster resulted in the absence of methylation at β-actin H73 in vivo, whereas β-actin from wildtype cells or flies was > 90% methylated. As a consequence, we show that Setd3-deficient HAP1 cells have less cellular F-actin and an increased glycolytic phenotype. In conclusion, by identifying SETD3 as the actin-specific histidine N-methyltransferase, our work pioneers new research into the possible role of this modification in health and disease and questions the substrate specificity of SET-domain-containing enzymes.
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Affiliation(s)
- Sebastian Kwiatkowski
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Agnieszka K Seliga
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Didier Vertommen
- Protein Phosphorylation Unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Marianna Terreri
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Takao Ishikawa
- Department of Molecular Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Iwona Grabowska
- Department of Cytology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Marcel Tiebe
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg University, Heidelberg, Germany
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg University, Heidelberg, Germany
| | - Adam K Jagielski
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Maria Veiga-da-Cunha
- Metabolic Research Unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Jakub Drozak
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Warsaw, Poland
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124
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Małecki JM, Willemen HLDM, Pinto R, Ho AYY, Moen A, Kjønstad IF, Burgering BMT, Zwartkruis F, Eijkelkamp N, Falnes PØ. Lysine methylation by the mitochondrial methyltransferase FAM173B optimizes the function of mitochondrial ATP synthase. J Biol Chem 2018; 294:1128-1141. [PMID: 30530489 DOI: 10.1074/jbc.ra118.005473] [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: 08/22/2018] [Revised: 12/05/2018] [Indexed: 01/23/2023] Open
Abstract
Lysine methylation is an important post-translational modification that is also present on mitochondrial proteins, but the mitochondrial lysine-specific methyltransferases (KMTs) responsible for modification are in most cases unknown. Here, we set out to determine the function of human family with sequence similarity 173 member B (FAM173B), a mitochondrial methyltransferase (MTase) reported to promote chronic pain. Using bioinformatics analyses and biochemical assays, we found that FAM173B contains an atypical, noncleavable mitochondrial targeting sequence responsible for its localization to mitochondria. Interestingly, CRISPR/Cas9-mediated KO of FAM173B in mammalian cells abrogated trimethylation of Lys-43 in ATP synthase c-subunit (ATPSc), a modification previously reported as ubiquitous among metazoans. ATPSc methylation was restored by complementing the KO cells with enzymatically active human FAM173B or with a putative FAM173B orthologue from the nematode Caenorhabditis elegans Interestingly, lack of Lys-43 methylation caused aberrant incorporation of ATPSc into the ATP synthase complex and resulted in decreased ATP-generating ability of the complex, as well as decreased mitochondrial respiration. In summary, we have identified FAM173B as the long-sought KMT responsible for methylation of ATPSc, a key protein in cellular ATP production, and have demonstrated functional significance of ATPSc methylation. We suggest renaming FAM173B to ATPSc-KMT (gene name ATPSCKMT).
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Affiliation(s)
- Jędrzej M Małecki
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway.
| | | | - Rita Pinto
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Angela Y Y Ho
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Anders Moen
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Ingrid F Kjønstad
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Boudewijn M T Burgering
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, The Netherlands
| | - Fried Zwartkruis
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, The Netherlands
| | - Niels Eijkelkamp
- Laboratory of Translational Immunology (LTI), 3584 EA Utrecht, The Netherlands
| | - Pål Ø Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway.
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125
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Xing J, Jing W, Zhang Y, Liu L, Xu J, Chen X. Identification of differentially expressed genes in broiler offspring under maternal folate deficiency. Physiol Genomics 2018; 50:1015-1025. [DOI: 10.1152/physiolgenomics.00086.2018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Folate plays an important role in DNA and RNA synthesis by donating methyl groups. To investigate the effects of maternal folate deficiency (FD) on the abdominal adipose transcriptome and on the accumulation of lipid droplets in the liver tissue of chicken offspring, differentially expressed genes (DEGs) of FD were identified with digital gene expression tag profiling. Ultramicroscopy suggested that the size of lipid droplets in hepatocytes increased with FD, while the lipid droplets population number was largely not affected. The serum parameters assay showed that the concentrations of MTHFR (476.57 vs. 395.27), DHFR (45.056 vs. 38.952), LPL (50.408 vs. 48.677), HCY (4.354 vs. 3.836), LEP (9.951 vs. 8.673), and IGF2 (1209.4 vs. 1027.7) in offspring serum of the FD group were significantly higher than those of the normal folate (NF) group ( P < 0.01). The 442 DEGs between NF and FD groups were identified by digital gene expression profiling. Considering the DEGs in the FD groups vs. NF groups, 179 genes were upregulated while 263 downregulated, and in particular, 145 upregulated and 214 downregulated DEGs were successfully annotated with the nonredundant database. Gene Ontology analysis showed that FD mainly affected cellular processes, cell part and binding, cell killing, virions, and receptor regulator activity. With pathway analysis, it indicated that 123 unigenes were assigned to 115 KEGG pathways, but only five of 115 these pathways were significantly enriched with P values ≤ 0.05. Taken together, these results provide a foundation for further studying the responses of offspring to maternal FD in breeding chickens.
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Affiliation(s)
- Jinyi Xing
- School of Life Sciences, Linyi University, Linyi, China
| | - Wenqian Jing
- School of Agriculture and Forestry Sciences, Linyi University, Linyi, China
| | - Yujie Zhang
- School of Life Sciences, Linyi University, Linyi, China
| | - Lin Liu
- School of Pharmacy, Linyi University, Linyi, China
| | - Junjie Xu
- School of Pharmacy, Linyi University, Linyi, China
| | - Xianwei Chen
- School of Agriculture and Forestry Sciences, Linyi University, Linyi, China
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126
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Sohtome Y, Sodeoka M. Development of Chaetocin and
S
‐Adenosylmethionine Analogues as Tools for Studying Protein Methylation. CHEM REC 2018; 18:1660-1671. [DOI: 10.1002/tcr.201800118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/25/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Yoshihiro Sohtome
- Synthetic Organic Chemistry LaboratoryRIKEN Cluster for Pioneering Research 2-1 Hirosawa, Wako Saitama Japan
- RIKEN Center for Sustainable Resource Science
- AMED-CREST, Japan Agency for Medical Research and Development
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry LaboratoryRIKEN Cluster for Pioneering Research 2-1 Hirosawa, Wako Saitama Japan
- RIKEN Center for Sustainable Resource Science
- AMED-CREST, Japan Agency for Medical Research and Development
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127
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Penn BH, Netter Z, Johnson JR, Von Dollen J, Jang GM, Johnson T, Ohol YM, Maher C, Bell SL, Geiger K, Golovkine G, Du X, Choi A, Parry T, Mohapatra BC, Storck MD, Band H, Chen C, Jäger S, Shales M, Portnoy DA, Hernandez R, Coscoy L, Cox JS, Krogan NJ. An Mtb-Human Protein-Protein Interaction Map Identifies a Switch between Host Antiviral and Antibacterial Responses. Mol Cell 2018; 71:637-648.e5. [PMID: 30118682 PMCID: PMC6329589 DOI: 10.1016/j.molcel.2018.07.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 04/24/2018] [Accepted: 07/11/2018] [Indexed: 11/29/2022]
Abstract
Although macrophages are armed with potent antibacterial functions, Mycobacterium tuberculosis (Mtb) replicates inside these innate immune cells. Determinants of macrophage intrinsic bacterial control, and the Mtb strategies to overcome them, are poorly understood. To further study these processes, we used an affinity tag purification mass spectrometry (AP-MS) approach to identify 187 Mtb-human protein-protein interactions (PPIs) involving 34 secreted Mtb proteins. This interaction map revealed two factors involved in Mtb pathogenesis-the secreted Mtb protein, LpqN, and its binding partner, the human ubiquitin ligase CBL. We discovered that an lpqN Mtb mutant is attenuated in macrophages, but growth is restored when CBL is removed. Conversely, Cbl-/- macrophages are resistant to viral infection, indicating that CBL regulates cell-intrinsic polarization between antibacterial and antiviral immunity. Collectively, these findings illustrate the utility of this Mtb-human PPI map for developing a deeper understanding of the intricate interactions between Mtb and its host.
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Affiliation(s)
- Bennett H Penn
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Zoe Netter
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jeffrey R Johnson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94148, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - John Von Dollen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94148, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Gwendolyn M Jang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94148, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Tasha Johnson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94148, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Yamini M Ohol
- Department of Microbiology and Immunology, Program in Microbial Pathogenesis and Host Defense, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Cyrus Maher
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Samantha L Bell
- Department of Microbiology and Immunology, Program in Microbial Pathogenesis and Host Defense, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kristina Geiger
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Guillaume Golovkine
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xiaotang Du
- Department of Microbiology and Immunology, Program in Microbial Pathogenesis and Host Defense, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alex Choi
- Department of Microbiology and Immunology, Program in Microbial Pathogenesis and Host Defense, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Trevor Parry
- Department of Microbiology and Immunology, Program in Microbial Pathogenesis and Host Defense, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Bhopal C Mohapatra
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska, Omaha, NE 68182, USA
| | - Matthew D Storck
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska, Omaha, NE 68182, USA
| | - Hamid Band
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska, Omaha, NE 68182, USA
| | - Chen Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Stefanie Jäger
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94148, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94148, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Dan A Portnoy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ryan Hernandez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Laurent Coscoy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jeffery S Cox
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Microbiology and Immunology, Program in Microbial Pathogenesis and Host Defense, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94148, USA; Gladstone Institutes, San Francisco, CA 94158, USA.
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128
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Mutlu B, Chen HM, Moresco JJ, Orelo BD, Yang B, Gaspar JM, Keppler-Ross S, Yates JR, Hall DH, Maine EM, Mango SE. Regulated nuclear accumulation of a histone methyltransferase times the onset of heterochromatin formation in C. elegans embryos. SCIENCE ADVANCES 2018; 4:eaat6224. [PMID: 30140741 PMCID: PMC6105299 DOI: 10.1126/sciadv.aat6224] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 07/18/2018] [Indexed: 05/19/2023]
Abstract
Heterochromatin formation during early embryogenesis is timed precisely, but how this process is regulated remains elusive. We report the discovery of a histone methyltransferase complex whose nuclear accumulation and activation establish the onset of heterochromatin formation in Caenorhabditis elegans embryos. We find that the inception of heterochromatin generation coincides with the accumulation of the histone H3 lysine 9 (H3K9) methyltransferase MET-2 (SETDB) into nuclear hubs. The absence of MET-2 results in delayed and disturbed heterochromatin formation, whereas accelerated nuclear localization of the methyltransferase leads to precocious H3K9 methylation. We identify two factors that bind to and function with MET-2: LIN-65, which resembles activating transcription factor 7-interacting protein (ATF7IP) and localizes MET-2 into nuclear hubs, and ARLE-14, which is orthologous to adenosine 5'-diphosphate-ribosylation factor-like 14 effector protein (ARL14EP) and promotes stable association of MET-2 with chromatin. These data reveal that nuclear accumulation of MET-2 in conjunction with LIN-65 and ARLE-14 regulates timing of heterochromatin domains during embryogenesis.
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Affiliation(s)
- Beste Mutlu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Huei-Mei Chen
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - James J. Moresco
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, San Diego, CA 92037, USA
| | - Barbara D. Orelo
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, San Diego, CA 92037, USA
| | - Bing Yang
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
| | - John M. Gaspar
- Informatics Group, Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Sabine Keppler-Ross
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, San Diego, CA 92037, USA
| | - David H. Hall
- Center for C. elegans Anatomy, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Eleanor M. Maine
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
| | - Susan E. Mango
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Corresponding author.
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129
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Phenotypic characterization of SETD3 knockout Drosophila. PLoS One 2018; 13:e0201609. [PMID: 30067821 PMCID: PMC6070285 DOI: 10.1371/journal.pone.0201609] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/18/2018] [Indexed: 01/14/2023] Open
Abstract
Lysine methylation is a reversible post-translational modification that affects protein function. Lysine methylation is involved in regulating the function of both histone and non-histone proteins, thereby influencing both cellular transcription and the activation of signaling pathways. To date, only a few lysine methyltransferases have been studied in depth. Here, we study the Drosophila homolog of the human lysine methyltransferase SETD3, CG32732/dSETD3. Since mammalian SETD3 is involved in cell proliferation, we tested the effect of dSETD3 on proliferation and growth of Drosophila S2 cells and whole flies. Knockdown of dSETD3 did not alter mTORC1 activity nor proliferation rate of S2 cells. Complete knock-out of dSETD3 in Drosophila flies did not affect their weight, growth rate or fertility. dSETD3 KO flies showed normal responses to starvation and hypoxia. In sum, we could not identify any clear phenotypes for SETD3 knockout animals, indicating that additional work will be required to elucidate the molecular and physiological function of this highly conserved enzyme.
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130
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Horton JR, Liu X, Wu L, Zhang K, Shanks J, Zhang X, Rai G, Mott BT, Jansen DJ, Kales SC, Henderson MJ, Pohida K, Fang Y, Hu X, Jadhav A, Maloney DJ, Hall MD, Simeonov A, Fu H, Vertino PM, Yan Q, Cheng X. Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A. J Med Chem 2018; 61:3193-3208. [PMID: 29537847 PMCID: PMC6322411 DOI: 10.1021/acs.jmedchem.8b00261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Isomers of chiral drugs can exhibit marked differences in biological activities. We studied the binding and inhibitory activities of 12 compounds against KDM5A. Among them are two pairs of enantiomers representing two distinct inhibitor chemotypes, namely, ( R)- and ( S)-2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)methyl)-1 H-pyrrolo[3,2- b]pyridine-7-carboxylic acid (compounds N51 and N52) and ( R) - and ( S) -N-(1-(3-isopropyl-1 H-pyrazole-5-carbonyl)pyrrolidin-3-yl)cyclopropanecarboxamide (compounds N54 and N55). In vitro, the S enantiomer of the N51/N52 pair (N52) and the R enantiomer of the N54/N55 pair (N54) exhibited about 4- to 5-fold greater binding affinity. The more potent enzyme inhibition of KDM5A by the R-isoform for the cell-permeable N54/N55 pair translated to differences in growth inhibitory activity. We determined structures of the KDM5A catalytic domain in complex with all 12 inhibitors, which revealed the interactions (or lack thereof) responsible for the differences in binding affinity. These results provide insights to guide improvements in binding potency and avenues for development of cell permeable inhibitors of the KDM5 family.
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Affiliation(s)
- John R. Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Xu Liu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Lizhen Wu
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, United States
| | - Kai Zhang
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, United States
| | - John Shanks
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Bryan T. Mott
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Daniel J. Jansen
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Stephen C. Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Mark J. Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Katherine Pohida
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Yuhong Fang
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - David J. Maloney
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Haian Fu
- Department of Pharmacology, Emory University, Atlanta, Georgia 30322, United States
- Department of Hematology and Medical Oncology, Emory University, Atlanta, Georgia 30322, United States
- Emory Chemical Biology Discovery Center, Emory University, Atlanta, Georgia 30322, United States
- The Winship Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
| | - Paula M. Vertino
- The Winship Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
- Department of Radiation Oncology, Emory University, Atlanta, Georgia 30322, United States
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, United States
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
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131
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Jiang F, Liu Q, Wang Y, Zhang J, Wang H, Song T, Yang M, Wang X, Kang L. Comparative genomic analysis of SET domain family reveals the origin, expansion, and putative function of the arthropod-specific SmydA genes as histone modifiers in insects. Gigascience 2018; 6:1-16. [PMID: 28444351 PMCID: PMC5459927 DOI: 10.1093/gigascience/gix031] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 04/19/2017] [Indexed: 02/07/2023] Open
Abstract
The SET domain is an evolutionarily conserved motif present in histone lysine methyltransferases, which are important in the regulation of chromatin and gene expression in animals. In this study, we searched for SET domain–containing genes (SET genes) in all of the 147 arthropod genomes sequenced at the time of carrying out this experiment to understand the evolutionary history by which SET domains have evolved in insects. Phylogenetic and ancestral state reconstruction analysis revealed an arthropod-specific SET gene family, named SmydA, that is ancestral to arthropod animals and specifically diversified during insect evolution. Considering that pseudogenization is the most probable fate of the new emerging gene copies, we provided experimental and evolutionary evidence to demonstrate their essential functions. Fluorescence in situ hybridization analysis and in vitro methyltransferase activity assays showed that the SmydA-2 gene was transcriptionally active and retained the original histone methylation activity. Expression knockdown by RNA interference significantly increased mortality, implying that the SmydA genes may be essential for insect survival. We further showed predominantly strong purifying selection on the SmydA gene family and a potential association between the regulation of gene expression and insect phenotypic plasticity by transcriptome analysis. Overall, these data suggest that the SmydA gene family retains essential functions that may possibly define novel regulatory pathways in insects. This work provides insights into the roles of lineage-specific domain duplication in insect evolution.
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Affiliation(s)
- Feng Jiang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Qing Liu
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanli Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
| | - Jie Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Huimin Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Tianqi Song
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
| | - Meiling Yang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xianhui Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Le Kang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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132
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Jakobsson ME, Małecki J, Falnes PØ. Regulation of eukaryotic elongation factor 1 alpha (eEF1A) by dynamic lysine methylation. RNA Biol 2018; 15:314-319. [PMID: 29447067 DOI: 10.1080/15476286.2018.1440875] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Lysine methylation is a frequent post-translational protein modification, which has been intensively studied in the case of histone proteins. Lysine methylations are also found on many non-histone proteins, and one prominent example is eukaryotic elongation factor 1 alpha (eEF1A). Besides its essential role in the protein synthesis machinery, a number of non-canonical functions have also been described for eEF1A, such as regulation of the actin cytoskeleton and the promotion of viral replication. The functional significance of the extensive lysine methylations on eEF1A, as well as the identity of the responsible lysine methyltransferases (KMTs), have until recently remained largely elusive. However, recent discoveries and characterizations of human eEF1A-specific KMTs indicate that lysine methylation of eEF1A can be dynamic and inducible, and modulates mRNA translation in a codon-specific fashion. Here, we give a general overview of eEF1A lysine methylation and discuss its possible functional and regulatory significance, with particular emphasis on newly discovered human KMTs.
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Affiliation(s)
- Magnus E Jakobsson
- a Department of Biosciences , Faculty of Mathematics and Natural Sciences, University of Oslo , Oslo , Norway.,b Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research (NNF-CPR) , University of Copenhagen , Copenhagen , Denmark
| | - Jędrzej Małecki
- a Department of Biosciences , Faculty of Mathematics and Natural Sciences, University of Oslo , Oslo , Norway
| | - Pål Ø Falnes
- a Department of Biosciences , Faculty of Mathematics and Natural Sciences, University of Oslo , Oslo , Norway
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133
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Ding H, Lu WC, Hu JC, Liu YC, Zhang CH, Lian FL, Zhang NX, Meng FW, Luo C, Chen KX. Identification and Characterizations of Novel, Selective Histone Methyltransferase SET7 Inhibitors by Scaffold Hopping- and 2D-Molecular Fingerprint-Based Similarity Search. Molecules 2018; 23:molecules23030567. [PMID: 29498708 PMCID: PMC6017732 DOI: 10.3390/molecules23030567] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 02/23/2018] [Accepted: 02/28/2018] [Indexed: 12/17/2022] Open
Abstract
SET7, serving as the only histone methyltransferase that monomethylates 'Lys-4' of histone H3, has been proved to function as a key regulator in diverse biological processes, such as cell proliferation, transcriptional network regulation in embryonic stem cell, cell cycle control, protein stability, heart morphogenesis and development. What's more, SET7 is involved inthe pathogenesis of alopecia aerate, breast cancer, tumor and cancer progression, atherosclerosis in human carotid plaques, chronic renal diseases, diabetes, obesity, ovarian cancer, prostate cancer, hepatocellular carcinoma, and pulmonary fibrosis. Therefore, there is urgent need to develop novel SET7 inhibitors. In this paper, based on DC-S239 which has been previously reported in our group, we employed scaffold hopping- and 2D fingerprint-based similarity searches and identified DC-S285 as the new hit compound targeting SET7 (IC50 = 9.3 μM). Both radioactive tracing and NMR experiments validated the interactions between DC-S285 and SET7 followed by the second-round similarity search leading to the identification ofDC-S303 with the IC50 value of 1.1 μM. In cellular level, DC-S285 retarded tumor cell proliferation and showed selectivity against MCF7 (IC50 = 21.4 μM), Jurkat (IC50 = 2.2 μM), THP1 (IC50 = 3.5 μM), U937 (IC50 = 3.9 μM) cell lines. Docking calculations suggested that DC-S303 share similar binding mode with the parent compoundDC-S239. What's more, it presented good selectivity against other epigenetic targets, including SETD1B, SETD8, G9a, SMYD2 and EZH2. DC-S303 can serve as a drug-like scaffold which may need further optimization for drug development, and can be used as chemical probe to help the community to better understand the SET7 biology.
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Affiliation(s)
- Hong Ding
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China.
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Wen Chao Lu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Jun Chi Hu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Yu-Chih Liu
- Shanghai ChemPartner Co., Ltd., #5 Building, 998 Halei Road, Shanghai 201203, China.
| | - Chen Hua Zhang
- Shanghai ChemPartner Co., Ltd., #5 Building, 998 Halei Road, Shanghai 201203, China.
| | - Fu Lin Lian
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Nai Xia Zhang
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Fan Wang Meng
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada.
| | - Cheng Luo
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Kai Xian Chen
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China.
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
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134
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Khan S, Iqbal M, Tariq M, Baig SM, Abbas W. Epigenetic regulation of HIV-1 latency: focus on polycomb group (PcG) proteins. Clin Epigenetics 2018; 10:14. [PMID: 29441145 PMCID: PMC5800276 DOI: 10.1186/s13148-018-0441-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/05/2018] [Indexed: 01/10/2023] Open
Abstract
HIV-1 latency allows the virus to persist until reactivation, in a transcriptionally silent form in its cellular reservoirs despite the presence of effective cART. Such viral persistence represents a major barrier to HIV eradication since treatment interruption leads to rebound plasma viremia. Polycomb group (PcG) proteins have recently got a considerable attention in regulating HIV-1 post-integration latency as they are involved in the repression of proviral gene expression through the methylation of histones. This epigenetic regulation plays an important role in the establishment and maintenance of HIV-1 latency. In fact, PcG proteins act in complexes and modulate the epigenetic signatures of integrated HIV-1 promoter. Key role played by PcG proteins in the molecular control of HIV-1 latency has led to hypothesize that PcG proteins may represent a valuable target for future HIV-1 therapy in purging HIV-1 reservoirs. In this regard, various small molecules have been synthesized or explored to specifically block the epigenetic activity of PcG. In this review, we will highlight the possible therapeutic approaches to achieve either a functional or sterilizing cure of HIV-1 infection with special focus on histone methylation by PcG proteins together with current and novel pharmacological approaches to reactivate HIV-1 from latency that could ultimately lead towards a better clearance of viral latent reservoirs.
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Affiliation(s)
- Sheraz Khan
- Health Biotechnology Division (HBD), National Institute for Biotechnology and Genetic Engineering (NIBGE), PO Box 577, Jhang road, Faisalabad, 38000 Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Mazhar Iqbal
- Health Biotechnology Division (HBD), National Institute for Biotechnology and Genetic Engineering (NIBGE), PO Box 577, Jhang road, Faisalabad, 38000 Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Muhammad Tariq
- Department of Biology (Epigenetics group), SBA School of Science and Engineering, LUMS, Lahore, 54792 Pakistan
| | - Shahid M. Baig
- Health Biotechnology Division (HBD), National Institute for Biotechnology and Genetic Engineering (NIBGE), PO Box 577, Jhang road, Faisalabad, 38000 Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Wasim Abbas
- Health Biotechnology Division (HBD), National Institute for Biotechnology and Genetic Engineering (NIBGE), PO Box 577, Jhang road, Faisalabad, 38000 Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
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135
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Catarino RR, Stark A. Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation. Genes Dev 2018; 32:202-223. [PMID: 29491135 PMCID: PMC5859963 DOI: 10.1101/gad.310367.117] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Enhancers are important genomic regulatory elements directing cell type-specific transcription. They assume a key role during development and disease, and their identification and functional characterization have long been the focus of scientific interest. The advent of next-generation sequencing and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-based genome editing has revolutionized the means by which we study enhancer biology. In this review, we cover recent developments in the prediction of enhancers based on chromatin characteristics and their identification by functional reporter assays and endogenous DNA perturbations. We discuss that the two latter approaches provide different and complementary insights, especially in assessing enhancer sufficiency and necessity for transcription activation. Furthermore, we discuss recent insights into mechanistic aspects of enhancer function, including findings about cofactor requirements and the role of post-translational histone modifications such as monomethylation of histone H3 Lys4 (H3K4me1). Finally, we survey how these approaches advance our understanding of transcription regulation with respect to promoter specificity and transcriptional bursting and provide an outlook covering open questions and promising developments.
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Affiliation(s)
- Rui R Catarino
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
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136
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Dynamic regulation of six histone H3 lysine (K) methyltransferases in response to prolonged anoxia exposure in a freshwater turtle. Gene 2018; 649:50-57. [PMID: 29382574 DOI: 10.1016/j.gene.2018.01.086] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 01/03/2018] [Accepted: 01/26/2018] [Indexed: 12/26/2022]
Abstract
The importance of histone lysine methylation is well established in health, disease, early development, aging, and cancer. However, the potential role of histone H3 methylation in regulating gene expression in response to extended periods of oxygen deprivation (anoxia) in a natural, anoxia-tolerant model system is underexplored. Red-eared sliders (Trachemys scripta elegans) can tolerate and survive three months of absolute anoxia and recover without incurring detrimental cellular damage, mainly by reducing the overall metabolic rate by 90% when compared to normoxia. Stringent regulation of gene expression is a vital aspect of metabolic rate depression in red-eared sliders, and as such we examined the anoxia-responsive regulation of histone lysine methylation in the liver during 5 h and 20 h anoxia exposure. Interestingly, this is the first study to illustrate the existence of histone lysine methyltransferases (HKMTs) and corresponding histone H3 lysine methylation levels in the liver of anoxia-tolerant red-eared sliders. In brief, H3K4me1, a histone mark associated with active transcription, and two corresponding histone lysine methyltransferases that modify H3K4me1 site, significantly increased in response to anoxia. On the contrary, H3K27me1, another transcriptionally active histone mark, significantly decreased during 20 h anoxia, and a transcriptionally repressive histone mark, H3K9me3, and the corresponding KMTs, similarly increased during 20 h anoxia. Overall, the results suggest a dynamic regulation of histone H3 lysine methylation in the liver of red-eared sliders that could theoretically aid in the selective upregulation of genes that are necessary for anoxia survival, while globally suppressing others to conserve energy.
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137
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Deng W, Wang Y, Ma L, Zhang Y, Ullah S, Xue Y. Computational prediction of methylation types of covalently modified lysine and arginine residues in proteins. Brief Bioinform 2017; 18:647-658. [PMID: 27241573 DOI: 10.1093/bib/bbw041] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Indexed: 11/14/2022] Open
Abstract
Protein methylation is an essential posttranslational modification (PTM) mostly occurs at lysine and arginine residues, and regulates a variety of cellular processes. Owing to the rapid progresses in the large-scale identification of methylation sites, the available data set was dramatically expanded, and more attention has been paid on the identification of specific methylation types of modification residues. Here, we briefly summarized the current progresses in computational prediction of methylation sites, which provided an accurate, rapid and efficient approach in contrast with labor-intensive experiments. We collected 5421 methyllysines and methylarginines in 2592 proteins from the literature, and classified most of the sites into different types. Data analyses demonstrated that different types of methylated proteins were preferentially involved in different biological processes and pathways, whereas a unique sequence preference was observed for each type of methylation sites. Thus, we developed a predictor of GPS-MSP, which can predict mono-, di- and tri-methylation types for specific lysines, and mono-, symmetric di- and asymmetrical di-methylation types for specific arginines. We critically evaluated the performance of GPS-MSP, and compared it with other existing tools. The satisfying results exhibited that the classification of methylation sites into different types for training can considerably improve the prediction accuracy. Taken together, we anticipate that our study provides a new lead for future computational analysis of protein methylation, and the prediction of methylation types of covalently modified lysine and arginine residues can generate more useful information for further experimental manipulation.
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138
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Ginjala V, Rodriguez-Colon L, Ganguly B, Gangidi P, Gallina P, Al-Hraishawi H, Kulkarni A, Tang J, Gheeya J, Simhadri S, Yao M, Xia B, Ganesan S. Protein-lysine methyltransferases G9a and GLP1 promote responses to DNA damage. Sci Rep 2017; 7:16613. [PMID: 29192276 PMCID: PMC5709370 DOI: 10.1038/s41598-017-16480-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 11/09/2017] [Indexed: 11/30/2022] Open
Abstract
Upon induction of DNA breaks, ATM activation leads to a cascade of local chromatin modifications that promote efficient recruitment of DNA repair proteins. Errors in this DNA repair pathway lead to genomic instability and cancer predisposition. Here, we show that the protein lysine methyltransferase G9a (also known as EHMT2) and GLP1 (also known as EHMT1) are critical components of the DNA repair pathway. G9a and GLP1 rapidly localizes to DNA breaks, with GLP1 localization being dependent on G9a. ATM phosphorylation of G9a on serine 569 is required for its recruitment to DNA breaks. G9a catalytic activity is required for the early recruitment of DNA repair factors including 53BP and BRCA1 to DNA breaks. Inhibition of G9a catalytic activity disrupts DNA repair pathways and increases sensitivity to ionizing radiation. Thus, G9a is a potential therapeutic target in the DNA repair pathway.
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Affiliation(s)
- Vasudeva Ginjala
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany street, New Brunswick, New Jersey, 08903, USA.
| | - Lizahira Rodriguez-Colon
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany street, New Brunswick, New Jersey, 08903, USA
| | - Bratati Ganguly
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany street, New Brunswick, New Jersey, 08903, USA
| | - Prawallika Gangidi
- Cornell University, College of Engineering, Department of Biological Engineering, 111 Wing Drive, Ithaca, NY, 14853-5701, USA
| | - Paul Gallina
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany street, New Brunswick, New Jersey, 08903, USA
| | - Husam Al-Hraishawi
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany street, New Brunswick, New Jersey, 08903, USA
| | - Atul Kulkarni
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany street, New Brunswick, New Jersey, 08903, USA
| | - Jeremy Tang
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany street, New Brunswick, New Jersey, 08903, USA
| | - Jinesh Gheeya
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany street, New Brunswick, New Jersey, 08903, USA
| | - Srilatha Simhadri
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany street, New Brunswick, New Jersey, 08903, USA
| | - Ming Yao
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany street, New Brunswick, New Jersey, 08903, USA
| | - Bing Xia
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany street, New Brunswick, New Jersey, 08903, USA
| | - Shridar Ganesan
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany street, New Brunswick, New Jersey, 08903, USA.
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139
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140
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Moritz LE, Trievel RC. Structure, mechanism, and regulation of polycomb-repressive complex 2. J Biol Chem 2017; 293:13805-13814. [PMID: 28912274 DOI: 10.1074/jbc.r117.800367] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Polycomb repressive complex 2 (PRC2) methylates lysine 27 in histone H3, a modification associated with epigenetic gene silencing. This complex plays a fundamental role in regulating cellular differentiation and development, and PRC2 overexpression and mutations have been implicated in numerous cancers. In this Minireview, we examine recent studies elucidating the first crystal structures of the PRC2 core complex, yielding seminal insights into its catalytic mechanism, substrate specificity, allosteric regulation, and inhibition by a class of small molecules that are currently undergoing cancer clinical trials. We conclude by exploring unresolved questions and future directions for inquiry regarding PRC2 structure and function.
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Affiliation(s)
| | - Raymond C Trievel
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
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141
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Malecki J, Aileni VK, Ho AYY, Schwarz J, Moen A, Sørensen V, Nilges BS, Jakobsson ME, Leidel SA, Falnes PØ. The novel lysine specific methyltransferase METTL21B affects mRNA translation through inducible and dynamic methylation of Lys-165 in human eukaryotic elongation factor 1 alpha (eEF1A). Nucleic Acids Res 2017; 45:4370-4389. [PMID: 28108655 PMCID: PMC5416902 DOI: 10.1093/nar/gkx002] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 01/02/2017] [Indexed: 12/25/2022] Open
Abstract
Lysine methylation is abundant on histone proteins, representing a dynamic regulator of chromatin state and gene activity, but is also frequent on many non-histone proteins, including eukaryotic elongation factor 1 alpha (eEF1A). However, the functional significance of eEF1A methylation remains obscure and it has remained unclear whether eEF1A methylation is dynamic and subject to active regulation. We here demonstrate, using a wide range of in vitro and in vivo approaches, that the previously uncharacterized human methyltransferase METTL21B specifically targets Lys-165 in eEF1A in an aminoacyl-tRNA- and GTP-dependent manner. Interestingly, METTL21B-mediated eEF1A methylation showed strong variation across different tissues and cell lines, and was induced by altering growth conditions or by treatment with certain ER-stress-inducing drugs, concomitant with an increase in METTL21B gene expression. Moreover, genetic ablation of METTL21B function in mammalian cells caused substantial alterations in mRNA translation, as measured by ribosomal profiling. A non-canonical function for eEF1A in organization of the cellular cytoskeleton has been reported, and interestingly, METTL21B accumulated in centrosomes, in addition to the expected cytosolic localization. In summary, the present study identifies METTL21B as the enzyme responsible for methylation of eEF1A on Lys-165 and shows that this modification is dynamic, inducible and likely of regulatory importance.
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Affiliation(s)
- Jedrzej Malecki
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Vinay Kumar Aileni
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Angela Y Y Ho
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Juliane Schwarz
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
| | - Anders Moen
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Vigdis Sørensen
- Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway
| | - Benedikt S Nilges
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
| | - Magnus E Jakobsson
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
| | - Pål Ø Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
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142
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Affiliation(s)
- Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
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143
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Małecki J, Jakobsson ME, Ho AYY, Moen A, Rustan AC, Falnes PØ. Uncovering human METTL12 as a mitochondrial methyltransferase that modulates citrate synthase activity through metabolite-sensitive lysine methylation. J Biol Chem 2017; 292:17950-17962. [PMID: 28887308 DOI: 10.1074/jbc.m117.808451] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/28/2017] [Indexed: 01/23/2023] Open
Abstract
Lysine methylation is an important and much-studied posttranslational modification of nuclear and cytosolic proteins but is present also in mitochondria. However, the responsible mitochondrial lysine-specific methyltransferases (KMTs) remain largely elusive. Here, we investigated METTL12, a mitochondrial human S-adenosylmethionine (AdoMet)-dependent methyltransferase and found it to methylate a single protein in mitochondrial extracts, identified as citrate synthase (CS). Using several in vitro and in vivo approaches, we demonstrated that METTL12 methylates CS on Lys-395, which is localized in the CS active site. Interestingly, the METTL12-mediated methylation inhibited CS activity and was blocked by the CS substrate oxaloacetate. Moreover, METTL12 was strongly inhibited by the reaction product S-adenosylhomocysteine (AdoHcy). In summary, we have uncovered a novel human mitochondrial KMT that introduces a methyl modification into a metabolic enzyme and whose activity can be modulated by metabolic cues. Based on the established naming nomenclature for similar enzymes, we suggest that METTL12 be renamed CS-KMT (gene name CSKMT).
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Affiliation(s)
| | | | | | | | - Arild C Rustan
- School of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
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144
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Li QL, Lei PJ, Zhao QY, Li L, Wei G, Wu M. Epigenomic analysis in a cell-based model reveals the roles of H3K9me3 in breast cancer transformation. Epigenomics 2017; 9:1077-1092. [DOI: 10.2217/epi-2016-0183] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Aim: Epigenetic marks are critical regulators of chromatin and gene activity. Their roles in normal physiology and disease states, including cancer development, still remain elusive. Herein, the epigenomic change of H3K9me3, as well as its potential impacts on gene activity and genome stability, was investigated in an in vitro breast cancer transformation model. Methods: The global H3K9me3 level was studied with western blotting. The distribution of H3K9me3 on chromatin and gene expression was studied with ChIP-Seq and RNA-Seq, respectively. Results: The global H3K9me3 level decreases during transformation and its distribution on chromatin is reprogrammed. By combining with TCGA data, we identified 67 candidate oncogenes, among which five genes are totally novel. Our analysis further links H3K9me3 with transposon activity, and suggests H3K9me3 reduction increases the cell’s sensitivity to DNA damage reagents. Conclusion: H3K9me3 reduction is possibly related with breast cancer transformation by regulating gene expression and chromatin stability during transformation.
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Affiliation(s)
- Qing-Lan Li
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Department of Biochemistry & Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Pin-Ji Lei
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Department of Biochemistry & Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Quan-Yi Zhao
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Department of Biochemistry & Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Lianyun Li
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Department of Biochemistry & Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Gang Wei
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute of Computational Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Min Wu
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Department of Biochemistry & Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
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145
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Hamey JJ, Wienert B, Quinlan KGR, Wilkins MR. METTL21B Is a Novel Human Lysine Methyltransferase of Translation Elongation Factor 1A: Discovery by CRISPR/Cas9 Knockout. Mol Cell Proteomics 2017; 16:2229-2242. [PMID: 28663172 DOI: 10.1074/mcp.m116.066308] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 06/28/2017] [Indexed: 02/03/2023] Open
Abstract
Lysine methylation is widespread on human proteins, however the enzymes that catalyze its addition remain largely unknown. This limits our capacity to study the function and regulation of this modification. Here we used the CRISPR/Cas9 system to knockout putative protein methyltransferases METTL21B and METTL23 in K562 cells, to determine if they methylate elongation factor eEF1A. The known eEF1A methyltransferase EEF1AKMT1 was also knocked out as a control. Targeted mass spectrometry revealed the loss of lysine 165 methylation upon knockout of METTL21B, and the expected loss of lysine 79 methylation on knockout of EEF1AKMT1 No loss of eEF1A methylation was seen in the METTL23 knockout. Recombinant METTL21B was shown in vitro to catalyze methylation on lysine 165 in eEF1A1 and eEF1A2, confirming it as the methyltransferase responsible for this methylation site. Proteomic analysis by SILAC revealed specific upregulation of large ribosomal subunit proteins in the METTL21B knockout, and changes to further processes related to eEF1A function in knockouts of both METTL21B and EEF1AKMT1 This indicates that the methylation of lysine 165 in human eEF1A has a very specific role. METTL21B exists only in vertebrates, with its target lysine showing similar evolutionary conservation. We suggest METTL21B be renamed eEF1A-KMT3. This is the first study to specifically generate CRISPR/Cas9 knockouts of putative protein methyltransferase genes, for substrate discovery and site mapping. Our approach should prove useful for the discovery of further novel methyltransferases, and more generally for the discovery of sites for other protein-modifying enzymes.
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Affiliation(s)
- Joshua J Hamey
- From the ‡School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia
| | - Beeke Wienert
- From the ‡School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia
| | - Kate G R Quinlan
- From the ‡School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia
| | - Marc R Wilkins
- From the ‡School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia
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146
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Kaniskan HÜ, Jin J. Recent progress in developing selective inhibitors of protein methyltransferases. Curr Opin Chem Biol 2017; 39:100-108. [PMID: 28662389 DOI: 10.1016/j.cbpa.2017.06.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 06/14/2017] [Indexed: 10/19/2022]
Abstract
Mounting evidence suggests that protein methyltransferases (PMTs), which catalyze methylation of histones as well as non-histone proteins, play a crucial role in diverse biological pathways and human diseases. In particular, PMTs have been recognized as major players in regulating gene expression and chromatin state. There has been an increasingly growing interest in these enzymes as potential therapeutic targets and over the past two years tremendous progress has been made in the discovery of selective, small molecule inhibitors of protein lysine and arginine methyltransferases. Inhibitors of PMTs have been used extensively in oncology studies as tool compounds, and inhibitors of EZH2, DOT1L and PRMT5 are currently in clinical trials.
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Affiliation(s)
- H Ümit Kaniskan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
| | - Jian Jin
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
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147
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Eichenberger RM, Ramakrishnan C, Russo G, Deplazes P, Hehl AB. Genome-wide analysis of gene expression and protein secretion of Babesia canis during virulent infection identifies potential pathogenicity factors. Sci Rep 2017; 7:3357. [PMID: 28611446 PMCID: PMC5469757 DOI: 10.1038/s41598-017-03445-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 04/27/2017] [Indexed: 12/14/2022] Open
Abstract
Infections of dogs with virulent strains of Babesia canis are characterized by rapid onset and high mortality, comparable to complicated human malaria. As in other apicomplexan parasites, most Babesia virulence factors responsible for survival and pathogenicity are secreted to the host cell surface and beyond where they remodel and biochemically modify the infected cell interacting with host proteins in a very specific manner. Here, we investigated factors secreted by B. canis during acute infections in dogs and report on in silico predictions and experimental analysis of the parasite’s exportome. As a backdrop, we generated a fully annotated B. canis genome sequence of a virulent Hungarian field isolate (strain BcH-CHIPZ) underpinned by extensive genome-wide RNA-seq analysis. We find evidence for conserved factors in apicomplexan hemoparasites involved in immune-evasion (e.g. VESA-protein family), proteins secreted across the iRBC membrane into the host bloodstream (e.g. SA- and Bc28 protein families), potential moonlighting proteins (e.g. profilin and histones), and uncharacterized antigens present during acute crisis in dogs. The combined data provides a first predicted and partially validated set of potential virulence factors exported during fatal infections, which can be exploited for urgently needed innovative intervention strategies aimed at facilitating diagnosis and management of canine babesiosis.
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Affiliation(s)
| | | | | | - Peter Deplazes
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
| | - Adrian B Hehl
- Institute of Parasitology, University of Zurich, Zurich, Switzerland.
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148
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Yu SE, Kim MS, Park SH, Yoo BC, Kim KH, Jang YK. SET domain-containing protein 5 is required for expression of primordial germ cell specification-associated genes in murine embryonic stem cells. Cell Biochem Funct 2017; 35:247-253. [DOI: 10.1002/cbf.3269] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 05/15/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Seung Eun Yu
- Department of Systems Biology, College of Life Science and Biotechnology; Yonsei University; Seoul Korea
- Initiative for Biological Function and Systems; Yonsei University; Seoul Korea
| | - Min Seong Kim
- Department of Systems Biology, College of Life Science and Biotechnology; Yonsei University; Seoul Korea
- Initiative for Biological Function and Systems; Yonsei University; Seoul Korea
| | - Su Hyung Park
- Department of Systems Biology, College of Life Science and Biotechnology; Yonsei University; Seoul Korea
- Initiative for Biological Function and Systems; Yonsei University; Seoul Korea
| | - Byong Chul Yoo
- Colorectal Cancer Branch, Research Institute; National Cancer Center; Goyang Korea
| | - Kyung Hee Kim
- Colorectal Cancer Branch, Research Institute; National Cancer Center; Goyang Korea
- Omics Core Laboratory, Research Institute; National Cancer Center; Goyang Korea
| | - Yeun Kyu Jang
- Department of Systems Biology, College of Life Science and Biotechnology; Yonsei University; Seoul Korea
- Initiative for Biological Function and Systems; Yonsei University; Seoul Korea
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149
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Chen Y, Anastassiadis K, Kranz A, Stewart AF, Arndt K, Waskow C, Yokoyama A, Jones K, Neff T, Lee Y, Ernst P. MLL2, Not MLL1, Plays a Major Role in Sustaining MLL-Rearranged Acute Myeloid Leukemia. Cancer Cell 2017; 31:755-770.e6. [PMID: 28609655 PMCID: PMC5598468 DOI: 10.1016/j.ccell.2017.05.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 03/09/2017] [Accepted: 05/05/2017] [Indexed: 01/11/2023]
Abstract
The MLL1 histone methyltransferase gene undergoes many distinct chromosomal rearrangements to yield poor-prognosis leukemia. The remaining wild-type allele is most commonly, but not always, retained. To what extent the wild-type allele contributes to leukemogenesis is unclear. Here we show, using rigorous, independent animal models, that endogenous MLL1 is dispensable for MLL-rearranged leukemia. Potential redundancy was addressed by co-deleting the closest paralog, Mll2. Surprisingly, Mll2 deletion alone had a significant impact on survival of MLL-AF9-transformed cells, and additional Mll1 loss further reduced viability and proliferation. We show that MLL1/MLL2 collaboration is not through redundancy, but regulation of distinct pathways. These findings highlight the relevance of MLL2 as a drug target in MLL-rearranged leukemia and suggest its broader significance in AML.
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Affiliation(s)
- Yufei Chen
- Department of Pediatrics, Section of Hematology/Oncology/BMT, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Konstantinos Anastassiadis
- Genomics and Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovations Zentrum, Tatzberg 47, Dresden 01307, Germany
| | - Andrea Kranz
- Genomics and Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovations Zentrum, Tatzberg 47, Dresden 01307, Germany
| | - A Francis Stewart
- Genomics and Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovations Zentrum, Tatzberg 47, Dresden 01307, Germany
| | - Kathrin Arndt
- Regeneration in Hematopoiesis and Animal Models in Hematopoiesis, Institute for Immunology, Medical Faculty, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Claudia Waskow
- Regeneration in Hematopoiesis and Animal Models in Hematopoiesis, Institute for Immunology, Medical Faculty, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Mizukami 246-2, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Kenneth Jones
- Department of Pediatrics, Section of Hematology/Oncology/BMT, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Tobias Neff
- Department of Pediatrics, Section of Hematology/Oncology/BMT, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Yoo Lee
- Department of Pediatrics, Section of Hematology/Oncology/BMT, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Patricia Ernst
- Department of Pediatrics, Section of Hematology/Oncology/BMT, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA.
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150
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Bennett RL, Swaroop A, Troche C, Licht JD. The Role of Nuclear Receptor-Binding SET Domain Family Histone Lysine Methyltransferases in Cancer. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026708. [PMID: 28193767 DOI: 10.1101/cshperspect.a026708] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The nuclear receptor-binding SET Domain (NSD) family of histone H3 lysine 36 methyltransferases is comprised of NSD1, NSD2 (MMSET/WHSC1), and NSD3 (WHSC1L1). These enzymes recognize and catalyze methylation of histone lysine marks to regulate chromatin integrity and gene expression. The growing number of reports demonstrating that alterations or translocations of these genes fundamentally affect cell growth and differentiation leading to developmental defects illustrates the importance of this family. In addition, overexpression, gain of function somatic mutations, and translocations of NSDs are associated with human cancer and can trigger cellular transformation in model systems. Here we review the functions of NSD family members and the accumulating evidence that these proteins play key roles in tumorigenesis. Because epigenetic therapy is an important emerging anticancer strategy, understanding the function of NSD family members may lead to the development of novel therapies.
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Affiliation(s)
- Richard L Bennett
- Departments of Medicine, Biochemistry and Molecular Biology and University of Florida Health Cancer Center, The University of Florida, Gainesville, Florida 32610
| | - Alok Swaroop
- Departments of Medicine, Biochemistry and Molecular Biology and University of Florida Health Cancer Center, The University of Florida, Gainesville, Florida 32610
| | - Catalina Troche
- Departments of Medicine, Biochemistry and Molecular Biology and University of Florida Health Cancer Center, The University of Florida, Gainesville, Florida 32610
| | - Jonathan D Licht
- Departments of Medicine, Biochemistry and Molecular Biology and University of Florida Health Cancer Center, The University of Florida, Gainesville, Florida 32610
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