251
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Burgos ES, Wilczek C, Onikubo T, Bonanno JB, Jansong J, Reimer U, Shechter D. Histone H2A and H4 N-terminal tails are positioned by the MEP50 WD repeat protein for efficient methylation by the PRMT5 arginine methyltransferase. J Biol Chem 2015; 290:9674-89. [PMID: 25713080 DOI: 10.1074/jbc.m115.636894] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Indexed: 11/06/2022] Open
Abstract
The protein arginine methyltransferase PRMT5 is complexed with the WD repeat protein MEP50 (also known as Wdr77 or androgen coactivator p44) in vertebrates in a tetramer of heterodimers. MEP50 is hypothesized to be required for protein substrate recruitment to the catalytic domain of PRMT5. Here we demonstrate that the cross-dimer MEP50 is paired with its cognate PRMT5 molecule to promote histone methylation. We employed qualitative methylation assays and a novel ultrasensitive continuous assay to measure enzyme kinetics. We demonstrate that neither full-length human PRMT5 nor the Xenopus laevis PRMT5 catalytic domain has appreciable protein methyltransferase activity. We show that histones H4 and H3 bind PRMT5-MEP50 more efficiently compared with histone H2A(1-20) and H4(1-20) peptides. Histone binding is mediated through histone fold interactions as determined by competition experiments and by high density histone peptide array interaction studies. Nucleosomes are not a substrate for PRMT5-MEP50, consistent with the primary mode of interaction via the histone fold of H3-H4, obscured by DNA in the nucleosome. Mutation of a conserved arginine (Arg-42) on the MEP50 insertion loop impaired the PRMT5-MEP50 enzymatic efficiency by increasing its histone substrate Km, comparable with that of Caenorhabditis elegans PRMT5. We show that PRMT5-MEP50 prefers unmethylated substrates, consistent with a distributive model for dimethylation and suggesting discrete biological roles for mono- and dimethylarginine-modified proteins. We propose a model in which MEP50 and PRMT5 simultaneously engage the protein substrate, orienting its targeted arginine to the catalytic site.
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Affiliation(s)
- Emmanuel S Burgos
- From the Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461 and
| | - Carola Wilczek
- From the Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461 and
| | - Takashi Onikubo
- From the Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461 and
| | - Jeffrey B Bonanno
- From the Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461 and
| | - Janina Jansong
- JPT Peptide Technologies GmbH, Volmerstrasse 5, 12489 Berlin, Germany
| | - Ulf Reimer
- JPT Peptide Technologies GmbH, Volmerstrasse 5, 12489 Berlin, Germany
| | - David Shechter
- From the Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461 and
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252
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Chemical “Diversity” of Chromatin Through Histone Variants and Histone Modifications. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s40610-015-0005-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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253
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Hu H, Owens EA, Su H, Yan L, Levitz A, Zhao X, Henary M, Zheng YG. Exploration of cyanine compounds as selective inhibitors of protein arginine methyltransferases: synthesis and biological evaluation. J Med Chem 2015; 58:1228-43. [PMID: 25559100 PMCID: PMC4610307 DOI: 10.1021/jm501452j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
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Protein arginine methyltransferase
1 (PRMT1) is involved in many biological activities, such as gene
transcription, signal transduction, and RNA processing. Overexpression
of PRMT1 is related to cardiovascular diseases, kidney diseases, and
cancers; therefore, selective PRMT1 inhibitors serve as chemical probes
to investigate the biological function of PRMT1 and drug candidates
for disease treatment. Our previous work found trimethine cyanine
compounds that effectively inhibit PRMT1 activity. In our present
study, we systematically investigated the structure–activity
relationship of cyanine structures. A pentamethine compound, E-84
(compound 50), showed inhibition on PRMT1 at the micromolar
level and 6- to 25-fold selectivity over CARM1, PRMT5, and PRMT8.
The cellular activity suggests that compound 50 permeated
the cellular membrane, inhibited cellular PRMT1 activity, and blocked
leukemia cell proliferation. Additionally, our molecular docking study
suggested compound 50 might act by occupying the cofactor
binding site, which provided a roadmap to guide further optimization
of this lead compound.
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Affiliation(s)
- Hao Hu
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia , Athens, Georgia 30602, United States
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254
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Chu Y, Guo H. QM/MM MD and free energy simulation study of methyl transfer processes catalyzed by PKMTs and PRMTs. Interdiscip Sci 2015. [PMID: 25595588 DOI: 10.1007/s12539-014-0228-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/19/2014] [Accepted: 10/17/2014] [Indexed: 09/29/2022]
Abstract
Methyl transfer processes catalyzed by protein lysine methyltransferases (PKMTs) and protein arginine methyltransferases (PRMTs) control important biological events including transcriptional regulation and cell signaling. One important property of these enzymes is that different PKMTs and PRMTs catalyze the formation of different methylated product (product specificity). These different methylation states lead to different biological outcomes. Here we review the results of quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) and free energy simulations that have been performed to study the reaction mechanism of PKMTs and PRMTs and the mechanism underlying the product specificity of the methyl transfer processes.
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Affiliation(s)
- Yuzhuo Chu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China,
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255
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Abstract
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Growing
evidence suggests that histone methyltransferases (HMTs,
also known as protein methyltransferases (PMTs)) play an important
role in diverse biological processes and human diseases by regulating
gene expression and the chromatin state. Therefore, HMTs have been
increasingly recognized by the biomedical community as a class of
potential therapeutic targets. High quality chemical probes of HMTs,
as tools for deciphering their physiological functions and roles in
human diseases and testing therapeutic hypotheses, are critical for
advancing this promising field. In this review, we focus on the discovery,
characterization, and biological applications of chemical probes for
HMTs.
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Affiliation(s)
- H. Ümit Kaniskan
- Department of Structural and Chemical Biology, ‡Department of Oncological Sciences, §Department of Pharmacology
and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, New York 10029, United States
| | - Jian Jin
- Department of Structural and Chemical Biology, ‡Department of Oncological Sciences, §Department of Pharmacology
and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, New York 10029, United States
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256
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Kim DI, Park MJ, Lim SK, Park JI, Yoon KC, Han HJ, Gustafsson JÅ, Lim JH, Park SH. PRMT3 regulates hepatic lipogenesis through direct interaction with LXRα. Diabetes 2015; 64:60-71. [PMID: 25187371 DOI: 10.2337/db13-1394] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Arginine methylation is responsible for diverse biological functions and is mediated by protein arginine methyltransferases (PRMTs). Nonalcoholic fatty liver disease (NAFLD) is accompanied by excessive hepatic lipogenesis via liver X receptor α (LXRα). Thus we examined the pathophysiological role of PRMTs in NAFLD and their relationship with LXRα. In this study, palmitic acid (PA) treatment increased PRMT3, which is correlated with the elevation of hepatic lipogenic proteins. The expression of lipogenic proteins was increased by PRMT3 overexpression, but decreased by PRMT3 silencing and use of the PRMT3 knockout (KO) mouse embryonic fibroblast cell line. PRMT3 also increased the transcriptional activity of LXRα by directly binding with LXRα in a methylation-independent manner. In addition, PA treatment translocated PRMT3 to the nucleus. In animal models, a high-fat diet increased the LXRα and PRMT3 expressions and binding, which was not observed in LXRα KO mice. Furthermore, increased PRMT3 expression and its binding with LXRα were observed in NAFLD patients. Taken together, LXRα and PRMT3 expression was increased in cellular and mouse models of NAFLD and human patients, and PRMT3 translocated into the nucleus bound with LXRα as a transcriptional cofactor, which induced lipogenesis. In conclusion, PRMT3 translocation by PA is coupled to the binding of LXRα, which is responsible for the onset of fatty liver.
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Affiliation(s)
- Dong-il Kim
- College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Min-jung Park
- College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Seul-ki Lim
- Metabolism and Functionality Research Group, R&D Division, World Institute of Kimchi, Gwangju, Republic of Korea
| | - Jae-il Park
- Korea Basic Science Institute, Gwangju Center at Chonnam National University, Gwangju, Republic of Korea
| | - Kyung-chul Yoon
- Department of Ophthalmology, Chonnam National University Medical School and Hospital, Gwangju, Republic of Korea
| | - Ho-jae Han
- Department of Verterinary Physiology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jan-åke Gustafsson
- Molecular Nutrition Unit, Department of Bioscience and Nutrition, Karolinska Institutet, Stockholm, Sweden Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX
| | - Jae-hyang Lim
- Department of Microbiology, Ewha Womans University School of Medicine, Seoul, Republic of Korea
| | - Soo-hyun Park
- College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
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257
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Sadakierska-Chudy A, Filip M. A comprehensive view of the epigenetic landscape. Part II: Histone post-translational modification, nucleosome level, and chromatin regulation by ncRNAs. Neurotox Res 2014; 27:172-97. [PMID: 25516120 PMCID: PMC4300421 DOI: 10.1007/s12640-014-9508-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 12/02/2014] [Accepted: 12/03/2014] [Indexed: 12/31/2022]
Abstract
The complexity of the genome is regulated by epigenetic mechanisms, which act on the level of DNA, histones, and nucleosomes. Epigenetic machinery is involved in various biological processes, including embryonic development, cell differentiation, neurogenesis, and adult cell renewal. In the last few years, it has become clear that the number of players identified in the regulation of chromatin structure and function is still increasing. In addition to well-known phenomena, including DNA methylation and histone modification, new, important elements, including nucleosome mobility, histone tail clipping, and regulatory ncRNA molecules, are being discovered. The present paper provides the current state of knowledge about the role of 16 different histone post-translational modifications, nucleosome positioning, and histone tail clipping in the structure and function of chromatin. We also emphasize the significance of cross-talk among chromatin marks and ncRNAs in epigenetic control.
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Affiliation(s)
- Anna Sadakierska-Chudy
- Laboratory of Drug Addiction Pharmacology, Institute of Pharmacology Polish Academy of Sciences, Smetna 12, 31-343, Kraków, Poland,
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258
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Abstract
Mounting evidence suggests that protein methyltransferases (PMTs), which catalyze methylation of histone and nonhistone proteins, play a crucial role in diverse biological processes and human diseases. In particular, PMTs have been recognized as major players in regulating gene expression and chromatin state. PMTs are divided into two categories: protein lysine methyltransferases (PKMTs) and protein arginine methyltransferases (PRMTs). There has been a steadily growing interest in these enzymes as potential therapeutic targets and therefore discovery of PMT inhibitors has also been pursued increasingly over the past decade. Here, we present a perspective on selective, small-molecule inhibitors of PMTs with an emphasis on their discovery, characterization, and applicability as chemical tools for deciphering the target PMTs' physiological functions and involvement in human diseases. We highlight the current state of PMT inhibitors and discuss future directions and opportunities for PMT inhibitor discovery.
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Affiliation(s)
- H Ümit Kaniskan
- Department of Structural and Chemical Biology, ‡Department of Oncological Sciences, §Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai , 1425 Madison Avenue, New York, New York 10029, United States
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259
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Le JM, Squarize CH, Castilho RM. Histone modifications: Targeting head and neck cancer stem cells. World J Stem Cells 2014; 6:511-525. [PMID: 25426249 PMCID: PMC4178252 DOI: 10.4252/wjsc.v6.i5.511] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 09/10/2014] [Accepted: 09/17/2014] [Indexed: 02/06/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide, and is responsible for a quarter of a million deaths annually. The survival rate for HNSCC patients is poor, showing only minor improvement in the last three decades. Despite new surgical techniques and chemotherapy protocols, tumor resistance to chemotherapy remains a significant challenge for HNSCC patients. Numerous mechanisms underlie chemoresistance, including genetic and epigenetic alterations in cancer cells that may be acquired during treatment and activation of mitogenic signaling pathways, such as nuclear factor kappa-light-chain-enhancer-of activated B cell, that cause reduced apoptosis. In addition to dysfunctional molecular signaling, emerging evidence reveals involvement of cancer stem cells (CSCs) in tumor development and in tumor resistance to chemotherapy and radiotherapy. These observations have sparked interest in understanding the mechanisms involved in the control of CSC function and fate. Post-translational modifications of histones dynamically influence gene expression independent of alterations to the DNA sequence. Recent findings from our group have shown that pharmacological induction of post-translational modifications of tumor histones dynamically modulates CSC plasticity. These findings suggest that a better understanding of the biology of CSCs in response to epigenetic switches and pharmacological inhibitors of histone function may directly translate to the development of a mechanism-based strategy to disrupt CSCs. In this review, we present and discuss current knowledge on epigenetic modifications of HNSCC and CSC response to DNA methylation and histone modifications. In addition, we discuss chromatin modifications and their role in tumor resistance to therapy.
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260
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Tough DF, Lewis HD, Rioja I, Lindon MJ, Prinjha RK. Epigenetic pathway targets for the treatment of disease: accelerating progress in the development of pharmacological tools: IUPHAR Review 11. Br J Pharmacol 2014; 171:4981-5010. [PMID: 25060293 PMCID: PMC4253452 DOI: 10.1111/bph.12848] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 05/22/2014] [Accepted: 06/13/2014] [Indexed: 02/06/2023] Open
Abstract
The properties of a cell are determined both genetically by the DNA sequence of its genes and epigenetically through processes that regulate the pattern, timing and magnitude of expression of its genes. While the genetic basis of disease has been a topic of intense study for decades, recent years have seen a dramatic increase in the understanding of epigenetic regulatory mechanisms and a growing appreciation that epigenetic misregulation makes a significant contribution to human disease. Several large protein families have been identified that act in different ways to control the expression of genes through epigenetic mechanisms. Many of these protein families are finally proving tractable for the development of small molecules that modulate their function and represent new target classes for drug discovery. Here, we provide an overview of some of the key epigenetic regulatory proteins and discuss progress towards the development of pharmacological tools for use in research and therapy.
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Affiliation(s)
- David F Tough
- Immuno-Inflammation Therapy Area, GlaxoSmithKline R&D, Medicines Research Centre, Epinova DPU, Stevenage, UK
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261
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Kebede AF, Schneider R, Daujat S. Novel types and sites of histone modifications emerge as players in the transcriptional regulation contest. FEBS J 2014; 282:1658-74. [DOI: 10.1111/febs.13047] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 09/03/2014] [Accepted: 09/09/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Adam F. Kebede
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; CNRS UMR 7104 - Inserm U964; Université de Strasbourg; Illkirch France
| | - Robert Schneider
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; CNRS UMR 7104 - Inserm U964; Université de Strasbourg; Illkirch France
| | - Sylvain Daujat
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; CNRS UMR 7104 - Inserm U964; Université de Strasbourg; Illkirch France
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262
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Abstract
Diffuse high-grade gliomas (HGGs) of childhood are a devastating spectrum of disease with no effective cures. The two-year survival for paediatric HGG ranges from 30%, for tumours arising in the cerebral cortex, to less than 10% for diffuse intrinsic pontine gliomas (DIPGs), which arise in the brainstem. Recent genome-wide studies provided abundant evidence that unique selective pressures drive HGG in children compared to adults, identifying novel oncogenic mutations connecting tumorigenesis and chromatin regulation, as well as developmental signalling pathways. These new genetic findings give insights into disease pathogenesis and the challenges and opportunities for improving patient survival in these mostly incurable childhood brain tumours.
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263
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Brown Z, Müller MM, Jain S, Allis CD, Lewis PW, Muir TW. Strategy for "detoxification" of a cancer-derived histone mutant based on mapping its interaction with the methyltransferase PRC2. J Am Chem Soc 2014; 136:13498-501. [PMID: 25180930 PMCID: PMC4183613 DOI: 10.1021/ja5060934] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Indexed: 01/17/2023]
Abstract
The histone methyltransferase PRC2 plays a central role in genomic stability and cellular development. Consequently, its misregulation has been implicated in several cancers. Recent work has shown that a histone H3 mutant, where the PRC2 substrate residue Lys27 is replaced by methionine, is also associated with cancer phenotypes and functions as an inhibitor of PRC2. Here we investigate the mechanism of this PRC2 inhibition through kinetic studies and photo-cross-linking. Efficient inhibition is dependent on (1) hydrophobic lysine isosteres blocking the active site, (2) proximal residues, and (3) the H3 tail forming extensive contacts with the EZH2 subunit of PRC2. We further show that naturally occurring post-translational modifications of the same H3 tail, both proximal and distal to K27M, can greatly diminish the inhibition of PRC2. These results suggest that this potent gain of function mutation may be "detoxified" by modulating alternate chromatin modification pathways.
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Affiliation(s)
- Zachary
Z. Brown
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Manuel M. Müller
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Siddhant
U. Jain
- Epigenetics
Theme, Wisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53715, United States
| | - C. David Allis
- Laboratory
of Chromatin Biology & Epigenetics, The Rockefeller University, New
York, New York 10065, United States
| | - Peter W. Lewis
- Epigenetics
Theme, Wisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53715, United States
| | - Tom W. Muir
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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264
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Tibshirani M, Tradewell ML, Mattina KR, Minotti S, Yang W, Zhou H, Strong MJ, Hayward LJ, Durham HD. Cytoplasmic sequestration of FUS/TLS associated with ALS alters histone marks through loss of nuclear protein arginine methyltransferase 1. Hum Mol Genet 2014; 24:773-86. [PMID: 25274782 DOI: 10.1093/hmg/ddu494] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mutations in the RNA-binding protein FUS/TLS (FUS) have been linked to the neurodegenerative disease amyotrophic lateral sclerosis (ALS). Although predominantly nuclear, this heterogenous nuclear ribonuclear protein (hnRNP) has multiple functions in RNA processing including intracellular trafficking. In ALS, mutant or wild-type (WT) FUS can form neuronal cytoplasmic inclusions. Asymmetric arginine methylation of FUS by the class 1 arginine methyltransferase, protein arginine methyltransferase 1 (PRMT1), regulates nucleocytoplasmic shuttling of FUS. In motor neurons of primary spinal cord cultures, redistribution of endogenous mouse and that of ectopically expressed WT or mutant human FUS to the cytoplasm led to nuclear depletion of PRMT1, abrogating methylation of its nuclear substrates. Specifically, hypomethylation of arginine 3 of histone 4 resulted in decreased acetylation of lysine 9/14 of histone 3 and transcriptional repression. Distribution of neuronal PRMT1 coincident with FUS also was detected in vivo in the spinal cord of FUS(R495X) transgenic mice. However, nuclear PRMT1 was not stable postmortem obviating meaningful evaluation of ALS autopsy cases. This study provides evidence for loss of PRMT1 function as a consequence of cytoplasmic accumulation of FUS in the pathogenesis of ALS, including changes in the histone code regulating gene transcription.
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Affiliation(s)
- Michael Tibshirani
- Montreal Neurological Institute and Department of Neurology/Neurosurgery, McGill University, Montreal, Quebec, Canada H3A 2B4
| | - Miranda L Tradewell
- Montreal Neurological Institute and Department of Neurology/Neurosurgery, McGill University, Montreal, Quebec, Canada H3A 2B4
| | - Katie R Mattina
- Montreal Neurological Institute and Department of Neurology/Neurosurgery, McGill University, Montreal, Quebec, Canada H3A 2B4
| | - Sandra Minotti
- Montreal Neurological Institute and Department of Neurology/Neurosurgery, McGill University, Montreal, Quebec, Canada H3A 2B4
| | - Wencheng Yang
- Robarts Research Institute, Western University, London, Ontario, Canada N6A 5C1 and
| | - Hongru Zhou
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Michael J Strong
- Robarts Research Institute, Western University, London, Ontario, Canada N6A 5C1 and
| | - Lawrence J Hayward
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Heather D Durham
- Montreal Neurological Institute and Department of Neurology/Neurosurgery, McGill University, Montreal, Quebec, Canada H3A 2B4
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265
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Jahan S, Davie JR. Protein arginine methyltransferases (PRMTs): role in chromatin organization. Adv Biol Regul 2014; 57:173-84. [PMID: 25263650 DOI: 10.1016/j.jbior.2014.09.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 09/06/2014] [Indexed: 01/19/2023]
Abstract
The mammalian genome encodes eleven protein arginine methyltransferases (PRMTs) that are involved in the transfer of a methyl group from S-adenosylmethionine (AdoMet) to the guanidino nitrogen of arginine. The substrates for these enzymes range from histones to several nuclear and cytoplasmic proteins. Methylation of histones by PRMTs can block the docking site for other reader/effector molecules and thus this modification can interfere with histone code orchestration. Several members of the PRMTs have roles in chromatin organization and function. Although PRMT aberrant expression is correlated with several diseases including cancer, the underlying mechanisms are still obscure in most cases.
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Affiliation(s)
- Sanzida Jahan
- Manitoba Institute of Child Health, University of Manitoba, Winnipeg, Manitoba R3E 3P4 Canada
| | - James R Davie
- Manitoba Institute of Child Health, University of Manitoba, Winnipeg, Manitoba R3E 3P4 Canada.
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266
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Schapira M, Ferreira de Freitas R. Structural biology and chemistry of protein arginine methyltransferases. MEDCHEMCOMM 2014; 5:1779-1788. [PMID: 26693001 PMCID: PMC4655611 DOI: 10.1039/c4md00269e] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 08/20/2014] [Indexed: 12/21/2022]
Abstract
PRMT inhibitors can compete with cofactor, substrate, or bind at allosteric sites found in the active or inactive states.
Protein arginine methyltransferases (PRMTs), an emerging target class in drug discovery, can methylate histones and other substrates, and can be divided into three subgroups, based on the methylation pattern of the reaction product (monomethylation, symmetrical or asymmetrical dimethylation). Here, we review the growing body of structural information characterizing this protein family, including structures in complex with substrate-competitive and allosteric inhibitors. We outline structural differences between type I, II and III enzymes and propose a model underlying class-specificity. We analyze the structural plasticity and diversity of the substrate, cofactor and allosteric binding sites, and propose that the conformational dynamics of PRMTs can be exploited towards the discovery of allosteric inhibitors that would antagonize conformationally active states.
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Affiliation(s)
- Matthieu Schapira
- Structural Genomics Consortium , University of Toronto , Toronto , ON M5G 1L7 , Canada . ; Tel: +1-416-978-3092 ; The Department of Pharmacology and Toxicology , University of Toronto , Toronto , ON M5S 1A8 , Canada
| | - Renato Ferreira de Freitas
- Structural Genomics Consortium , University of Toronto , Toronto , ON M5G 1L7 , Canada . ; Tel: +1-416-978-3092
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267
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Yang JH, Chiou YY, Fu SL, Shih IY, Weng TH, Lin WJ, Lin CH. Arginine methylation of hnRNPK negatively modulates apoptosis upon DNA damage through local regulation of phosphorylation. Nucleic Acids Res 2014; 42:9908-24. [PMID: 25104022 PMCID: PMC4150800 DOI: 10.1093/nar/gku705] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Heterogeneous nuclear ribonucleoprotein K (hnRNPK) is an RNA/DNA-binding protein involved in chromatin remodeling, RNA processing and the DNA damage response. In addition, increased hnRNPK expression has been associated with tumor development and progression. A variety of post-translational modifications of hnRNPK have been identified and shown to regulate hnRNPK function, including phosphorylation, ubiquitination, sumoylation and methylation. However, the functional significance of hnRNPK arginine methylation remains unclear. In the present study, we demonstrated that the methylation of two essential arginines, Arg296 and Arg299, on hnRNPK inhibited a nearby Ser302 phosphorylation that was mediated through the pro-apoptotic kinase PKCδ. Notably, the engineered U2OS cells carrying an Arg296/Arg299 methylation-defective hnRNPK mutant exhibited increased apoptosis upon DNA damage. While such elevated apoptosis can be diminished through addition with wild-type hnRNPK, we further demonstrated that this increased apoptosis occurred through both intrinsic and extrinsic pathways and was p53 independent, at least in part. Here, we provide the first evidence that the arginine methylation of hnRNPK negatively regulates cell apoptosis through PKCδ-mediated signaling during DNA damage, which is essential for the anti-apoptotic role of hnRNPK in apoptosis and the evasion of apoptosis in cancer cells.
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Affiliation(s)
- Jen-Hao Yang
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming University, Taipei 11221, Taiwan
| | - Yi-Ying Chiou
- Institute of Biopharmaceutical Sciences, National Yang Ming University, Taipei 11221, Taiwan
| | - Shu-Ling Fu
- Institute of Traditional Medicine, National Yang-Ming University, Taipei 11221, Taiwan
| | - I-Yun Shih
- Institute of Biopharmaceutical Sciences, National Yang Ming University, Taipei 11221, Taiwan
| | - Tsai-Hsuan Weng
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming University, Taipei 11221, Taiwan
| | - Wey-Jinq Lin
- Institute of Biopharmaceutical Sciences, National Yang Ming University, Taipei 11221, Taiwan
| | - Chao-Hsiung Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming University, Taipei 11221, Taiwan Institute of Biopharmaceutical Sciences, National Yang Ming University, Taipei 11221, Taiwan Proteomics Research Center, National Yang Ming University, Taipei 11221, Taiwan
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268
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Gayatri S, Bedford MT. Readers of histone methylarginine marks. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1839:702-10. [PMID: 24583552 PMCID: PMC4099268 DOI: 10.1016/j.bbagrm.2014.02.015] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 01/31/2014] [Accepted: 02/14/2014] [Indexed: 11/15/2022]
Abstract
Arginine methylation is a common posttranslational modification (PTM) that alters roughly 0.5% of all arginine residues in the cells. There are three types of arginine methylation: monomethylarginine (MMA), asymmetric dimethylarginine (ADMA), and symmetric dimethylarginine (SDMA). These three PTMs are enriched on RNA-binding proteins and on histones, and also impact signal transduction cascades. To date, over thirty arginine methylation sites have been cataloged on the different core histones. These modifications alter protein structure, impact interactions with DNA, and also generate docking sites for effector molecules. The primary "readers" of methylarginine marks are Tudor domain-containing proteins. The complete family of thirty-six Tudor domain-containing proteins has yet to be fully characterized, but at least ten bind methyllysine motifs and eight bind methylarginine motifs. In this review, we will highlight the biological roles of the Tudor domains that interact with arginine methylated motifs, and also address other types of interactions that are regulated by these particular PTMs. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
- Sitaram Gayatri
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Mark T Bedford
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.
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269
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Lott K, Zhu L, Fisk JC, Tomasello DL, Read LK. Functional interplay between protein arginine methyltransferases in Trypanosoma brucei. Microbiologyopen 2014; 3:595-609. [PMID: 25044453 PMCID: PMC4234254 DOI: 10.1002/mbo3.191] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/05/2014] [Accepted: 05/23/2014] [Indexed: 12/21/2022] Open
Abstract
Arginine methylation is a common posttranslational modification that has far-reaching cellular effects. Trypanosoma brucei is an early-branching eukaryote with four characterized protein arginine methyltransferases (PRMTs), one additional putative PRMT, and over 800 arginine methylated proteins, suggesting that arginine methylation has widespread impacts in this organism. While much is known about the activities of individual T. brucei PRMTs (TbPRMTs), little is known regarding how TbPRMTs function together in vivo. In this study, we analyzed single and selected double TbPRMT knockdowns for the impact on expression of TbPRMTs and global methylation status. Repression of TbPRMT1 caused a decrease in asymmetric dimethylarginine and a marked increase in monomethylarginine that was catalyzed by TbPRMT7, suggesting that TbPRMT1 and TbPRMT7 can compete for the same substrate. We also observed an unexpected and strong interdependence between TbPRMT1 and TbPRMT3 protein levels. This finding, together with the observation of similar methyl landscape profiles in TbPRMT1 and TbPRMT3 repressed cells, strongly suggests that these two enzymes form a functional complex. We show that corepression of TbPRMT6/7 synergistically impacts growth of procyclic-form T. brucei. Our findings also implicate the actions of noncanonical, and as yet unidentified, PRMTs in T. brucei. Together, our studies indicate that TbPRMTs display a functional interplay at multiple levels.
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Affiliation(s)
- Kaylen Lott
- Department of Microbiology and Immunology, University at Buffalo School of Medicine, Buffalo, New York, 14214
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270
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Lin S, Wein S, Gonzales-Cope M, Otte GL, Yuan ZF, Afjehi-Sadat L, Maile T, Berger SL, Rush J, Lill JR, Arnott D, Garcia BA. Stable-isotope-labeled histone peptide library for histone post-translational modification and variant quantification by mass spectrometry. Mol Cell Proteomics 2014; 13:2450-66. [PMID: 25000943 DOI: 10.1074/mcp.o113.036459] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
To facilitate accurate histone variant and post-translational modification (PTM) quantification via mass spectrometry, we present a library of 93 synthetic peptides using Protein-Aqua™ technology. The library contains 55 peptides representing different modified forms from histone H3 peptides, 23 peptides representing H4 peptides, 5 peptides representing canonical H2A peptides, 8 peptides representing H2A.Z peptides, and peptides for both macroH2A and H2A.X. The PTMs on these peptides include lysine mono- (me1), di- (me2), and tri-methylation (me3); lysine acetylation; arginine me1; serine/threonine phosphorylation; and N-terminal acetylation. The library was subjected to chemical derivatization with propionic anhydride, a widely employed protocol for histone peptide quantification. Subsequently, the detection efficiencies were quantified using mass spectrometry extracted ion chromatograms. The library yields a wide spectrum of detection efficiencies, with more than 1700-fold difference between the peptides with the lowest and highest efficiencies. In this paper, we describe the impact of different modifications on peptide detection efficiencies and provide a resource to correct for detection biases among the 93 histone peptides. In brief, there is no correlation between detection efficiency and molecular weight, hydrophobicity, basicity, or modification type. The same types of modifications may have very different effects on detection efficiencies depending on their positions within a peptide. We also observed antagonistic effects between modifications. In a study of mouse trophoblast stem cells, we utilized the detection efficiencies of the peptide library to correct for histone PTM/variant quantification. For most histone peptides examined, the corrected data did not change the biological conclusions but did alter the relative abundance of these peptides. For a low-abundant histone H2A variant, macroH2A, the corrected data led to a different conclusion than the uncorrected data. The peptide library and detection efficiencies presented here may serve as a resource to facilitate studies in the epigenetics and proteomics fields.
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Affiliation(s)
- Shu Lin
- From the ‡Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Samuel Wein
- From the ‡Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Michelle Gonzales-Cope
- From the ‡Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104; §Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
| | - Gabriel L Otte
- ¶Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Zuo-Fei Yuan
- From the ‡Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Leila Afjehi-Sadat
- From the ‡Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Tobias Maile
- ‖Department of Protein Chemistry, Genentech Inc., South San Francisco, California 94080
| | - Shelley L Berger
- ¶Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - John Rush
- **Cell Signaling Technology Inc., Danvers, Massachusetts 01923
| | - Jennie R Lill
- ‖Department of Protein Chemistry, Genentech Inc., South San Francisco, California 94080
| | - David Arnott
- ‖Department of Protein Chemistry, Genentech Inc., South San Francisco, California 94080
| | - Benjamin A Garcia
- From the ‡Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
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271
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Macadangdang BR, Oberai A, Spektor T, Campos OA, Sheng F, Carey MF, Vogelauer M, Kurdistani SK. Evolution of histone 2A for chromatin compaction in eukaryotes. eLife 2014; 3:e02792. [PMID: 24939988 PMCID: PMC4098067 DOI: 10.7554/elife.02792] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 06/16/2014] [Indexed: 12/16/2022] Open
Abstract
During eukaryotic evolution, genome size has increased disproportionately to nuclear volume, necessitating greater degrees of chromatin compaction in higher eukaryotes, which have evolved several mechanisms for genome compaction. However, it is unknown whether histones themselves have evolved to regulate chromatin compaction. Analysis of histone sequences from 160 eukaryotes revealed that the H2A N-terminus has systematically acquired arginines as genomes expanded. Insertion of arginines into their evolutionarily conserved position in H2A of a small-genome organism increased linear compaction by as much as 40%, while their absence markedly diminished compaction in cells with large genomes. This effect was recapitulated in vitro with nucleosomal arrays using unmodified histones, indicating that the H2A N-terminus directly modulates the chromatin fiber likely through intra- and inter-nucleosomal arginine-DNA contacts to enable tighter nucleosomal packing. Our findings reveal a novel evolutionary mechanism for regulation of chromatin compaction and may explain the frequent mutations of the H2A N-terminus in cancer.
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Affiliation(s)
- Benjamin R Macadangdang
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, United States
| | - Amit Oberai
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
| | - Tanya Spektor
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
| | - Oscar A Campos
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, United States
| | - Fang Sheng
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
| | - Michael F Carey
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, United States
| | - Maria Vogelauer
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
| | - Siavash K Kurdistani
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, United States
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States
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272
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Di Lorenzo A, Yang Y, Macaluso M, Bedford MT. A gain-of-function mouse model identifies PRMT6 as a NF-κB coactivator. Nucleic Acids Res 2014; 42:8297-309. [PMID: 24939901 PMCID: PMC4117762 DOI: 10.1093/nar/gku530] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Protein arginine methyltransferase 6 (PRMT6) is a nuclear enzyme that modifies histone tails. To help elucidate the biological function of PRMT6 in vivo, we generated transgenic mice that ubiquitously express PRMT6 fused to the hormone-binding portion of the estrogen receptor (ER*). The ER*-PRMT6 fusion is unstable and cytoplasmic, but upon systemic treatment with tamoxifen, it becomes stabilized and translocates into the nucleus. As a result, a dramatic increase in the H3R2me2a histone mark is observed. We found that one consequence of induced ER*-PRMT6 activation is increased IL-6 levels. IL-6 expression is regulated by the nuclear factor-kappa B (NF-κB) transcription factor, and PRMT6 functions as a coactivator of this pathway. We show that PRMT6 directly interacts with RelA, and that its overexpression enhances the transcriptional activity of an ectopic NF-κB reporter and endogenously regulates NF-κB target genes. PRMT6 is recruited, by RelA, to selective NF-κB target promoters upon TNF-α stimulation. Moreover, ER*-PRMT6 activation causes RelA accumulation in the nucleus. In summary, we observe that PRMT6 is recruited to chromatin at selective NF-κB target promoters, where it likely impacts the histone code and/or methylates other chromatin-associated proteins to facilitate transcription.
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Affiliation(s)
- Alessandra Di Lorenzo
- The University of Texas MD Anderson Cancer Center, Science Park, P.O. Box 389, Smithville, TX 78957, USA
| | - Yanzhong Yang
- The University of Texas MD Anderson Cancer Center, Science Park, P.O. Box 389, Smithville, TX 78957, USA
| | - Marc Macaluso
- The University of Texas MD Anderson Cancer Center, Science Park, P.O. Box 389, Smithville, TX 78957, USA
| | - Mark T Bedford
- The University of Texas MD Anderson Cancer Center, Science Park, P.O. Box 389, Smithville, TX 78957, USA
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273
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Kang C, Song JJ, Lee J, Kim MY. Epigenetics: An emerging player in gastric cancer. World J Gastroenterol 2014; 20:6433-6447. [PMID: 24914365 PMCID: PMC4047329 DOI: 10.3748/wjg.v20.i21.6433] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 01/21/2014] [Accepted: 02/20/2014] [Indexed: 02/06/2023] Open
Abstract
Cancers, like other diseases, arise from gene mutations and/or altered gene expression, which eventually cause dysregulation of numerous proteins and noncoding RNAs. Changes in gene expression, i.e., upregulation of oncogenes and/or downregulation of tumor suppressor genes, can be generated not only by genetic and environmental factors but also by epigenetic factors, which are inheritable but nongenetic modifications of cellular chromosome components. Identification of the factors that contribute to individual cancers is a prerequisite to a full understanding of cancer mechanisms and the development of customized cancer therapies. The search for genetic and environmental factors has a long history in cancer research, but epigenetic factors only recently began to be associated with cancer formation, progression, and metastasis. Epigenetic alterations of chromatin include DNA methylation and histone modifications, which can affect gene-expression profiles. Recent studies have revealed diverse mechanisms by which chromatin modifiers, including writers, erasers and readers of the aforementioned modifications, contribute to the formation and progression of cancer. Furthermore, functional RNAs, such as microRNAs and long noncoding RNAs, have also been identified as key players in these processes. This review highlights recent findings concerning the epigenetic alterations associated with cancers, especially gastric cancer.
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274
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Hong W, Li J, Laughton CA, Yap LF, Paterson IC, Wang H. Investigating the binding preferences of small molecule inhibitors of human protein arginine methyltransferase 1 using molecular modelling. J Mol Graph Model 2014; 51:193-202. [PMID: 24937176 DOI: 10.1016/j.jmgm.2014.05.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 01/12/2023]
Abstract
Protein arginine methyltransferases (PRMTs) catalyse the methylation of arginine residues of target proteins. PRMTs utilise S-adenosyl methionine (SAM) as the methyl group donor, leading to S-adenosyl homocysteine (SAH) and monomethylarginine (mMA). A combination of homology modelling, molecular docking, Active Site Pressurisation, molecular dynamic simulations and MM-PBSA free energy calculations is used to investigate the binding poses of three PRMT1 inhibitors (ligands 1-3), which target both SAM and substrate arginine binding sites by containing a guanidine group joined by short linkers with the SAM derivative. It was assumed initially that the adenine moieties of the inhibitors would bind in sub-site 1 (PHE44, GLU137, VAL136 and GLU108), the guanidine side chain would occupy sub-site 2 (GLU 161, TYR160, TYR156 and TRP302), with the amino acid side chain occupying sub-site 3 (GLU152, ARG62, GLY86 and ASP84; pose 1). However, the SAH homocysteine moiety does not fully occupy sub-site 3, suggesting another binding pose may exist (pose 2), whereby the adenine moiety binds in sub-site 1, the guanidine side chain occupies sub-site 3, and the amino acid side chain occupies sub-site 2. Our results indicate that ligand 1 (pose 1 or 2), ligand 2 (pose 2) and ligand 3 (pose 1) are the predominant binding poses and we demonstrate for the first time that sub-site 3 contains a large space that could be exploited in the future to develop novel inhibitors with higher binding affinities.
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Affiliation(s)
- Wei Hong
- School of Chemistry and Chemical Engineering, Beifang University of Nationalities, Yinchuan, PR China; Department of Oral Biology and Biomedical Sciences, and Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Jingyang Li
- School of Pharmacy, Ningxia Medical University, Yinchuan, PR China
| | - Charles A Laughton
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Lee Fah Yap
- Department of Oral Biology and Biomedical Sciences, and Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Ian C Paterson
- Department of Oral Biology and Biomedical Sciences, and Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Hao Wang
- School of Pharmacy, Ningxia Medical University, Yinchuan, PR China.
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275
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Structural basis for histone mimicry and hijacking of host proteins by influenza virus protein NS1. Nat Commun 2014; 5:3952. [PMID: 24853335 DOI: 10.1038/ncomms4952] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 04/25/2014] [Indexed: 11/08/2022] Open
Abstract
Pathogens can interfere with vital biological processes of their host by mimicking host proteins. The NS1 protein of the influenza A H3N2 subtype possesses a histone H3K4-like sequence at its carboxyl terminus and has been reported to use this mimic to hijack host proteins. However, this mimic lacks a free N-terminus that is essential for binding to many known H3K4 readers. Here we show that the double chromodomains of CHD1 adopt an 'open pocket' to interact with the free N-terminal amine of H3K4, and the open pocket permits the NS1 mimic to bind in a distinct conformation. We also explored the possibility that NS1 hijacks other cellular proteins and found that the NS1 mimic has access to only a subset of chromatin-associated factors, such as WDR5. Moreover, methylation of the NS1 mimic can not be reversed by the H3K4 demethylase LSD1. Overall, we thus conclude that the NS1 mimic is an imperfect histone mimic.
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276
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Emerging technologies to map the protein methylome. J Mol Biol 2014; 426:3350-62. [PMID: 24805349 DOI: 10.1016/j.jmb.2014.04.024] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 01/26/2023]
Abstract
Protein methylation plays an integral role in cellular signaling, most notably by modulating proteins bound at chromatin and increasingly through regulation of non-histone proteins. One central challenge in understanding how methylation acts in signaling is identifying and measuring protein methylation. This includes locus-specific modification of histones, on individual non-histone proteins, and globally across the proteome. Protein methylation has been studied traditionally using candidate approaches such as methylation-specific antibodies, mapping of post-translational modifications by mass spectrometry, and radioactive labeling to characterize methylation on target proteins. Recent developments have provided new approaches to identify methylated proteins, measure methylation levels, identify substrates of methyltransferase enzymes, and match methylated proteins to methyl-specific reader domains. Methyl-binding protein domains and improved antibodies with broad specificity for methylated proteins are being used to characterize the "protein methylome". They also have the potential to be used in high-throughput assays for inhibitor screens and drug development. These tools are often coupled to improvements in mass spectrometry to quickly identify methylated residues, as well as to protein microarrays, where they can be used to screen for methylated proteins. Finally, new chemical biology strategies are being used to probe the function of methyltransferases, demethylases, and methyl-binding "reader" domains. These tools create a "system-level" understanding of protein methylation and integrate protein methylation into broader signaling processes.
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277
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Structural determinants for the strict monomethylation activity by trypanosoma brucei protein arginine methyltransferase 7. Structure 2014; 22:756-68. [PMID: 24726341 DOI: 10.1016/j.str.2014.03.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 03/02/2014] [Accepted: 03/03/2014] [Indexed: 12/15/2022]
Abstract
Trypanosoma brucei protein arginine methyltransferase 7 (TbPRMT7) exclusively generates monomethylarginine (MMA), which directs biological consequences distinct from that of symmetric dimethylarginine (SDMA) and asymmetric dimethylarginine (ADMA). However, determinants controlling the strict monomethylation activity are unknown. We present the crystal structure of the TbPRMT7 active core in complex with S-adenosyl-L-homocysteine (AdoHcy) and a histone H4 peptide substrate. In the active site, residues E172, E181, and Q329 hydrogen bond the guanidino group of the target arginine and align the terminal guanidino nitrogen in a position suitable for nucleophilic attack on the methyl group of S-adenosyl-L-methionine (AdoMet). Structural comparisons and isothermal titration calorimetry data suggest that the TbPRMT7 active site is narrower than those of protein arginine dimethyltransferases, making it unsuitable to bind MMA in a manner that would support a second turnover, thus abolishing the production of SDMA and ADMA. Our results present the structural interpretations for the monomethylation activity of TbPRMT7.
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278
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Liu Y, Liu K, Qin S, Xu C, Min J. Epigenetic targets and drug discovery: part 1: histone methylation. Pharmacol Ther 2014; 143:275-94. [PMID: 24704322 DOI: 10.1016/j.pharmthera.2014.03.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 03/24/2014] [Indexed: 01/10/2023]
Abstract
Dynamic chromatin structure is modulated by post-translational modifications on histones, such as acetylation, phosphorylation and methylation. Research on histone methylation has become the most flourishing area of epigenetics in the past fourteen years, and a large amount of data has been accumulated regarding its biology and disease implications. Correspondingly, a lot of efforts have been made to develop small molecule compounds that can specifically modulate histone methyltransferases and methylation reader proteins, aiming for potential therapeutic drugs. Here, we summarize recent progress in chemical probe and drug discovery of histone methyltransferases and methylation reader proteins. For each target, we will review their biological/biochemical functions first, and then focus on their disease implications and drug discovery. We can also see that structure-based compound design and optimization plays a critical role in facilitating the development of highly potent and selective chemical probes and inhibitors for these targets.
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Affiliation(s)
- Yanli Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Su Qin
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Chao Xu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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279
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Su X, Zhu G, Ding X, Lee SY, Dou Y, Zhu B, Wu W, Li H. Molecular basis underlying histone H3 lysine-arginine methylation pattern readout by Spin/Ssty repeats of Spindlin1. Genes Dev 2014; 28:622-36. [PMID: 24589551 PMCID: PMC3967050 DOI: 10.1101/gad.233239.113] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 01/30/2014] [Indexed: 01/22/2023]
Abstract
Histone modification patterns and their combinatorial readout have emerged as a fundamental mechanism for epigenetic regulation. Here we characterized Spindlin1 as a histone effector that senses a cis-tail histone H3 methylation pattern involving trimethyllysine 4 (H3K4me3) and asymmetric dimethylarginine 8 (H3R8me2a) marks. Spindlin1 consists of triple tudor-like Spin/Ssty repeats. Cocrystal structure determination established concurrent recognition of H3K4me3 and H3R8me2a by Spin/Ssty repeats 2 and 1, respectively. Both H3K4me3 and H3R8me2a are recognized using an "insertion cavity" recognition mode, contributing to a methylation state-specific layer of regulation. In vivo functional studies suggest that Spindlin1 activates Wnt/β-catenin signaling downstream from protein arginine methyltransferase 2 (PRMT2) and the MLL complex, which together are capable of generating a specific H3 "K4me3-R8me2a" pattern. Mutagenesis of Spindlin1 reader pockets impairs activation of Wnt target genes. Taken together, our work connects a histone "lysine-arginine" methylation pattern readout by Spindlin1-to-Wnt signaling at the transcriptional level.
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Affiliation(s)
- Xiaonan Su
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Guixin Zhu
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiaozhe Ding
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Shirley Y. Lee
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Bing Zhu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Wei Wu
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haitao Li
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
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280
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Yan L, Yan C, Qian K, Su H, Kofsky-Wofford SA, Lee WC, Zhao X, Ho MC, Ivanov I, Zheng YG. Diamidine compounds for selective inhibition of protein arginine methyltransferase 1. J Med Chem 2014; 57:2611-22. [PMID: 24564570 PMCID: PMC3983339 DOI: 10.1021/jm401884z] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein arginine methylation is a posttranslational modification critical for a variety of biological processes. Misregulation of protein arginine methyltransferases (PRMTs) has been linked to many pathological conditions. Most current PRMT inhibitors display limited specificity and selectivity, indiscriminately targeting many methyltransferase enzymes that use S-adenosyl-l-methionine as a cofactor. Here we report diamidine compounds for specific inhibition of PRMT1, the primary type I enzyme. Docking, molecular dynamics, and MM/PBSA analysis together with biochemical assays were conducted to understand the binding modes of these inhibitors and the molecular basis of selective inhibition for PRMT1. Our data suggest that 2,5-bis(4-amidinophenyl)furan (1, furamidine, DB75), one leading inhibitor, targets the enzyme active site and is primarily competitive with the substrate and noncompetitive toward the cofactor. Furthermore, cellular studies revealed that 1 is cell membrane permeable and effectively inhibits intracellular PRMT1 activity and blocks cell proliferation in leukemia cell lines with different genetic lesions.
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Affiliation(s)
- Leilei Yan
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia , Athens, Georgia 30602, United States
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281
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Wang C, Zhu Y, Chen J, Li X, Peng J, Chen J, Zou Y, Zhang Z, Jin H, Yang P, Wu J, Niu L, Gong Q, Teng M, Shi Y. Crystal structure of arginine methyltransferase 6 from Trypanosoma brucei. PLoS One 2014; 9:e87267. [PMID: 24498306 PMCID: PMC3911951 DOI: 10.1371/journal.pone.0087267] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 12/26/2013] [Indexed: 11/21/2022] Open
Abstract
Arginine methylation plays vital roles in the cellular functions of the protozoan Trypanosoma brucei. The T. brucei arginine methyltransferase 6 (TbPRMT6) is a type I arginine methyltransferase homologous to human PRMT6. In this study, we report the crystal structures of apo-TbPRMT6 and its complex with the reaction product S-adenosyl-homocysteine (SAH). The structure of apo-TbPRMT6 displays several features that are different from those of type I PRMTs that were structurally characterized previously, including four stretches of insertion, the absence of strand β15, and a distinct dimerization arm. The comparison of the apo-TbPRMT6 and SAH-TbPRMT6 structures revealed the fine rearrangements in the active site upon SAH binding. The isothermal titration calorimetry results demonstrated that SAH binding greatly increases the affinity of TbPRMT6 to a substrate peptide derived from bovine histone H4. The western blotting and mass spectrometry results revealed that TbPRMT6 methylates bovine histone H4 tail at arginine 3 but cannot methylate several T. brucei histone tails. In summary, our results highlight the structural differences between TbPRMT6 and other type I PRMTs and reveal that the active site rearrangement upon SAH binding is important for the substrate binding of TbPRMT6.
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Affiliation(s)
- Chongyuan Wang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui, China
| | - Yuwei Zhu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui, China
| | - Jiajia Chen
- Department of Chemistry and Institute of Biomedical Science, Fudan University, Shanghai, China
| | - Xu Li
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui, China
| | - Junhui Peng
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui, China
| | - Jiajing Chen
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui, China
| | - Yang Zou
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui, China
| | - Zhiyong Zhang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui, China
| | - Hong Jin
- Department of Chemistry and Institute of Biomedical Science, Fudan University, Shanghai, China
| | - Pengyuan Yang
- Department of Chemistry and Institute of Biomedical Science, Fudan University, Shanghai, China
| | - Jihui Wu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui, China
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui, China
| | - Qingguo Gong
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui, China
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui, China
| | - Yunyu Shi
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui, China
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282
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Slade DJ, Subramanian V, Fuhrmann J, Thompson PR. Chemical and biological methods to detect post-translational modifications of arginine. Biopolymers 2014; 101:133-43. [PMID: 23576281 PMCID: PMC3900596 DOI: 10.1002/bip.22256] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 04/01/2013] [Indexed: 12/11/2022]
Abstract
Post-translational modifications (PTMs) of protein embedded arginines are increasingly being recognized as playing an important role in both prokaryotic and eukaryotic biology, and it is now clear that these PTMs modulate a number of cellular processes including DNA binding, gene transcription, protein-protein interactions, immune system activation, and proteolysis. There are currently four known enzymatic PTMs of arginine (i.e., citrullination, methylation, phosphorylation, and ADP-ribosylation), and two non-enzymatic PTMs [i.e., carbonylation, advanced glycation end-products (AGEs)]. Enzymatic modification of arginine is tightly controlled during normal cellular function, and can be drastically altered in response to various second messengers and in different disease states. Non-enzymatic arginine modifications are associated with a loss of metabolite regulation during normal human aging. This abnormally large number of modifications to a single amino acid creates a diverse set of structural perturbations that can lead to altered biological responses. While the biological role of methylation has been the most extensively characterized of the arginine PTMs, recent advances have shown that the once obscure modification known as citrullination is involved in the onset and progression of inflammatory diseases and cancer. This review will highlight the reported arginine PTMs and their methods of detection, with a focus on new chemical methods to detect protein citrullination.
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Affiliation(s)
- Daniel J. Slade
- Department of Chemistry, The Kellogg School of Graduate Studies, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Venkataraman Subramanian
- Department of Chemistry, The Kellogg School of Graduate Studies, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Jakob Fuhrmann
- Department of Chemistry, The Kellogg School of Graduate Studies, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Paul R. Thompson
- Department of Chemistry, The Kellogg School of Graduate Studies, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
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283
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Abstract
In humans, genomic DNA is organized in 23 chromosome pairs coding for roughly 25,000 genes. Not all of them are active at all times. During development, a broad range of different cell types needs to be generated in a highly ordered and reproducible manner, requiring selective gene expression programs. Epigenetics can be regarded as the information management system that is able to index or bookmark distinct regions in our genome to regulate the readout of DNA. It further comprises the molecular memory of any given cell, allowing it to store information of previously experienced external (e.g., environmental) or internal (e.g., developmental) stimuli, to learn from this experience and to respond. The underlying epigenetic mechanisms can be synergistic, antagonistic, or mutually exclusive and their large variety combined with the variability and interdependence is thought to provide the molecular basis for any phenotypic variation in physiological and pathological conditions. Thus, widespread reconfiguration of the epigenome is not only a key feature of neurodevelopment, brain maturation, and adult brain function but also disease.
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Affiliation(s)
- Katja Kobow
- Department of Neuropathology, University Hospital Erlangen, Schwabachanlage, Erlangen, Germany
| | - Ingmar Blümcke
- Department of Neuropathology, University Hospital Erlangen, Schwabachanlage, Erlangen, Germany.
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284
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Lau HT, Lewis KA, Ong SE. Quantifying in vivo, site-specific changes in protein methylation with SILAC. Methods Mol Biol 2014; 1188:161-175. [PMID: 25059611 DOI: 10.1007/978-1-4939-1142-4_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Interest in protein methylation has grown rapidly in recent years. Mass spectrometry-based proteomics is ideally suited to characterize protein modifications, but the multiplicity of methylated residues and the lack of efficient methods to enrich methylated proteins have limited the proteomic identification of protein methylation sites. In this protocol, we compare two metabolic labeling approaches, stable isotope labeling by amino acids in cell culture (SILAC) and its variant heavy methyl SILAC, for studying protein methylation. Instead of heavy lysine and arginine in the typical SILAC experiment, heavy methyl SILAC uses (13)C, (2)H methionine as the labeling amino acid. As cells convert methionine to S-adenosylmethionine, heavy methyl SILAC encodes a 4 Da mass tag for each methyl group, distinguishing between degrees of methylation is possible from mass difference alone. We provide a protocol for SILAC-based analyses of protein methylation and highlight the strengths and weaknesses of each method for targeted and proteomic analyses.
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Affiliation(s)
- Ho-Tak Lau
- Department of Pharmacology, University of Washington, 1959 NE Pacific Street, 357280, Seattle, WA, 98195, USA
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285
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Hu YJ, Sif S, Imbalzano AN. Prmt7 is dispensable in tissue culture models for adipogenic differentiation. F1000Res 2013; 2:279. [PMID: 24715966 PMCID: PMC3962006 DOI: 10.12688/f1000research.2-279.v1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/16/2013] [Indexed: 12/11/2022] Open
Abstract
Protein arginine methylation is a common posttranslational modification that has been implicated in numerous biological processes including gene expression. The mammalian genome encodes nine protein arginine methyltransferases (Prmts) that catalyze monomethylation, asymmetric dimethylation, and symmetric dimethylation on arginine residues. Protein arginine methyltransferase 7 (Prmt7) is categorized as a type II and type III enzyme that produces symmetric dimethylated arginine and monomethylated arginine, respectively. However, the biological role of Prmt7 is not well characterized. We previously showed that Prmt5, a type II Prmt that associates with Brg1-based SWI/SNF chromatin remodeling complex, is required for adipocyte differentiation. Since Prmt7 also associates with Brg1-based SWI/SNF complex and modifies core histones, we hypothesized that Prmt7 might play a role in transcriptional regulation of adipogenesis. In the present study, we determined that the expression of Prmt7 did not change throughout adipogenic differentiation of C3H10T1/2 mesenchymal cells. Knockdown or over-expression of Prmt7 had no effect on lipid accumulation or adipogenic gene expression in differentiating C3H10T1/2 cells or in C/EBPα-reprogrammed NIH3T3 fibroblasts. Based on these results, we conclude that Prmt7, unlike Prmt5, is dispensable for adipogenic differentiation in tissue culture models.
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Affiliation(s)
- Yu-Jie Hu
- Department of Cell & Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Saïd Sif
- Department of Molecular and Cellular Biochemistry, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Anthony N Imbalzano
- Department of Cell & Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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286
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Targeting protein arginine N-methyltransferases with peptide-based inhibitors: opportunities and challenges. Future Med Chem 2013; 5:2199-206. [DOI: 10.4155/fmc.13.184] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Recently peptide-based inhibitors have been used to selectively inhibit a family of epigenetic enzymes called protein arginine N-methyltransferases (PRMTs), which has been implicated in different physiological processes and human diseases, such as heart disease and cancer. The diverse efforts to tease out subtle structural differences among PRMT enzymes in order to generate selective inhibitors as well as existing challenges in the field will be examined. The acquisition of PRMT substrate sequence preferences and structural information obtained from small-molecule inhibitors have helped in developing different peptide-based inhibitors that show great promise not only as inhibitors, but also as molecular probes to characterize PRMTs.
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287
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Epigenetics of estrogen receptor signaling: role in hormonal cancer progression and therapy. Cancers (Basel) 2013; 3:1691-707. [PMID: 21814622 PMCID: PMC3147309 DOI: 10.3390/cancers3021691] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Estrogen receptor (ERα) signaling plays a key role in hormonal cancer progression. ERα is a ligand-dependent transcription factor that modulates gene transcription via recruitment to the target gene chromatin. Emerging evidence suggests that ERα signaling has the potential to contribute to epigenetic changes. Estrogen stimulation is shown to induce several histone modifications at the ERα target gene promoters including acetylation, phosphorylation and methylation via dynamic interactions with histone modifying enzymes. Deregulation of enzymes involved in the ERα-mediated epigenetic pathway could play a vital role in ERα driven neoplastic processes. Unlike genetic alterations, epigenetic changes are reversible, and hence offer novel therapeutic opportunities to reverse ERα driven epigenetic changes. In this review, we summarize current knowledge on mechanisms by which ERα signaling potentiates epigenetic changes in cancer cells via histone modifications.
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288
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Girardot M, Hirasawa R, Kacem S, Fritsch L, Pontis J, Kota SK, Filipponi D, Fabbrizio E, Sardet C, Lohmann F, Kadam S, Ait-Si-Ali S, Feil R. PRMT5-mediated histone H4 arginine-3 symmetrical dimethylation marks chromatin at G + C-rich regions of the mouse genome. Nucleic Acids Res 2013; 42:235-48. [PMID: 24097435 PMCID: PMC3874197 DOI: 10.1093/nar/gkt884] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Symmetrical dimethylation on arginine-3 of histone H4 (H4R3me2s) has been reported to occur at several repressed genes, but its specific regulation and genomic distribution remained unclear. Here, we show that the type-II protein arginine methyltransferase PRMT5 controls H4R3me2s in mouse embryonic fibroblasts (MEFs). In these differentiated cells, we find that the genome-wide pattern of H4R3me2s is highly similar to that in embryonic stem cells. In both the cell types, H4R3me2s peaks are detected predominantly at G + C-rich regions. Promoters are consistently marked by H4R3me2s, independently of transcriptional activity. Remarkably, H4R3me2s is mono-allelic at imprinting control regions (ICRs), at which it marks the same parental allele as H3K9me3, H4K20me3 and DNA methylation. These repressive chromatin modifications are regulated independently, however, since PRMT5-depletion in MEFs resulted in loss of H4R3me2s, without affecting H3K9me3, H4K20me3 or DNA methylation. Conversely, depletion of ESET (KMT1E) or SUV420H1/H2 (KMT5B/C) affected H3K9me3 and H4K20me3, respectively, without altering H4R3me2s at ICRs. Combined, our data indicate that PRMT5-mediated H4R3me2s uniquely marks the mammalian genome, mostly at G + C-rich regions, and independently from transcriptional activity or chromatin repression. Furthermore, comparative bioinformatics analyses suggest a putative role of PRMT5-mediated H4R3me2s in chromatin configuration in the nucleus.
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Affiliation(s)
- Michael Girardot
- Institute of Molecular Genetics (IGMM), CNRS UMR 5535, University of Montpellier, 1919 route de Mende, 34293 Montpellier, Laboratoire Epigénétique et Destin Cellulaire, UMR7216, CNRS, Université Paris Diderot, 35 rue Hélène Brion, 75013 Paris, France and Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
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289
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Cellot S, Hope KJ, Chagraoui J, Sauvageau M, Deneault É, MacRae T, Mayotte N, Wilhelm BT, Landry JR, Ting SB, Krosl J, Humphries K, Thompson A, Sauvageau G. RNAi screen identifies Jarid1b as a major regulator of mouse HSC activity. Blood 2013; 122:1545-55. [PMID: 23777767 PMCID: PMC5289888 DOI: 10.1182/blood-2013-04-496281] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Histone methylation is a dynamic and reversible process proposed to directly impact on stem cell fate. The Jumonji (JmjC) domain-containing family of demethylases comprises 27 members that target mono-, di-, and trimethylated lysine residues of histone (or nonhistone) proteins. To evaluate their role in regulation of hematopoietic stem cell (HSC) behavior, we performed an in vivo RNAi-based functional screen and demonstrated that Jarid1b and Jhdm1f play opposing roles in regulation of HSC activity. Decrease in Jarid1b levels correlated with an in vitro expansion of HSCs with preserved long-term in vivo lymphomyeloid differentiation potential. Through RNA sequencing analysis, Jarid1b knockdown was associated with increased expression levels of several HSC regulators (Hoxa7, Hoxa9, Hoxa10, Hes1, Gata2) and reduced levels of differentiation-associated genes. shRNA against Jhdmlf, in contrast, impaired hematopoietic reconstitution of bone marrow cells. Together, our studies identified Jarid1b as a negative regulator of HSC activity and Jhdmlf as a positive regulator of HSC activity.
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Affiliation(s)
- Sonia Cellot
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Division of Hematology, Ste-Justine Hospital, Montréal, QC, Canada
| | - Kristin J. Hope
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Jalila Chagraoui
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Martin Sauvageau
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Éric Deneault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Tara MacRae
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Nadine Mayotte
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Brian T. Wilhelm
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Josette R. Landry
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Stephen B. Ting
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Monash University, Melbourne, Australia
| | - Jana Krosl
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Keith Humphries
- Terry Fox Laboratory, British Columbia Cancer Agency, and Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Alexander Thompson
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Northern Ireland
| | - Guy Sauvageau
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Division of Hematology, Maisonneuve-Rosemont Hospital, Montréal, QC, Canada
- Leukemia Cell Bank of Quebec, Maisonneuve-Rosemont Hospital, Montréal, QC, Canada
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290
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Loss of the major Type I arginine methyltransferase PRMT1 causes substrate scavenging by other PRMTs. Sci Rep 2013; 3:1311. [PMID: 23419748 PMCID: PMC3575585 DOI: 10.1038/srep01311] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 01/31/2013] [Indexed: 12/28/2022] Open
Abstract
Arginine methylation is a common posttranslational modification that is found on both histone and non-histone proteins. Three types of arginine methylation exist in mammalian cells: monomethylarginine (MMA), asymmetric dimethylarginine (ADMA) and symmetric dimethylarginine (SDMA). PRMT1 is the primary methyltransferase that deposits the ADMA mark, and it accounts for over 90% of this type of methylation. Here, we show that with the loss of PRMT1 activity, there are major increases in global MMA and SDMA levels, as detected by type-specific antibodies. Amino acid analysis confirms that MMA and SDMA levels accumulate when ADMA levels are reduced. These findings reveal the dynamic interplay between different arginine methylation types in the cells, and that the pre-existence of the dominant ADMA mark can block the occurrence of SDMA and MMA marks on the same substrate. This study provides clear evidence of competition for different arginine methylation types on the same substrates.
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291
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Giordani L, Puri PL. Epigenetic control of skeletal muscle regeneration: Integrating genetic determinants and environmental changes. FEBS J 2013; 280:4014-25. [PMID: 23745685 DOI: 10.1111/febs.12383] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 06/04/2013] [Accepted: 06/06/2013] [Indexed: 12/13/2022]
Abstract
During embryonic development, pluripotent cells are genetically committed to specific lineages by the expression of cell-type-specific transcriptional activators that direct the formation of specialized tissues and organs in response to developmental cues. Chromatin-modifying proteins are emerging as essential components of the epigenetic machinery, which establishes the nuclear landscape that ultimately determines the final identity and functional specialization of adult cells. Recent evidence has revealed that discrete populations of adult cells can retain the ability to adopt alternative cell fates in response to environmental cues. These cells include conventional adult stem cells and a still poorly defined collection of cell types endowed with facultative phenotype and functional plasticity. Under physiological conditions or adaptive states, these cells cooperate to support tissue and organ homeostasis, and to promote growth or compensatory regeneration. However, during chronic diseases and aging these cells can adopt a pathological phenotype and mediate maladaptive responses, such as the formation of fibrotic scars and fat deposition that progressively replaces structural and functional units of tissues and organs. The molecular determinants of these phenotypic transitions are only emerging from recent studies that reveal how dynamic chromatin states can generate flexible epigenetic landscapes, which confer on cells the ability to retain partial pluripotency and adapt to environmental changes. This review summarizes our current knowledge on the role of the epigenetic machinery as a 'filter' between genetic commitment and environmental signals in cell types that can alternatively promote skeletal muscle regeneration or fibro-adipogenic degeneration.
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Affiliation(s)
- Lorenzo Giordani
- Sanford-Burnham Medical Research Institute, Sanford Children's Health Research Center, La Jolla, CA, USA
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292
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Chu Y, Li G, Guo H. QM/MM MD and free energy simulations of the methylation reactions catalyzed by protein arginine methyltransferase PRMT3. CAN J CHEM 2013. [DOI: 10.1139/cjc-2012-0483] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Protein arginine N-methyltransferases (PRMTs) catalyze the transfer of methyl group(s) from S-adenosyl-l-methionine (AdoMet) to the guanidine group of arginine residue in abundant eukaryotic proteins. Two major types of PRMTs have been identified in mammalian cells. Type I PRMTs catalyze the formation of asymmetric ω-NG, NG-dimethylarginine (ADMA), while Type II PRMTs catalyze the formation of symmetric ω-NG, N′G-dimethylarginine (SDMA). The two different methylation products (ADMA or SDMA) of the substrate could lead to different biological consequences. Although PRMTs have been the subject of extensive experimental investigations, the origin of the product specificity remains unclear. In this study, quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) and free energy simulations are performed to study the reaction mechanism for one of Type I PRMTs, PRMT3, and to gain insights into the energetic origin of its product specificity (ADMA). Our simulations have identified some important interactions and proton transfers involving the active site residues. These interactions and proton transfers seem to be responsible, at least in part, in making the Nη2 atom of the substrate arginine the target of the both 1st and 2nd methylations, leading to the asymmetric dimethylation product. The simulations also suggest that the methyl transfer and proton transfer appear to be somehow concerted processes and that Glu326 is likely to function as the general base during the catalysis.
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Affiliation(s)
- Yuzhuo Chu
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, TN 37996, USA
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Hong Guo
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
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293
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Tsutsui T, Fukasawa R, Shinmyouzu K, Nakagawa R, Tobe K, Tanaka A, Ohkuma Y. Mediator complex recruits epigenetic regulators via its two cyclin-dependent kinase subunits to repress transcription of immune response genes. J Biol Chem 2013; 288:20955-20965. [PMID: 23749998 DOI: 10.1074/jbc.m113.486746] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The Mediator complex (Mediator) plays pivotal roles in activating transcription by RNA polymerase II, but relatively little is known about its roles in repression. Here, we identified the histone arginine methyltransferase PRMT5 and WD repeat protein 77/methylosome protein 50 (WDR77/MEP50) as Mediator cyclin-dependent kinase (CDK)-interacting proteins and studied the roles of PRMT5 in the transcriptional regulation of CCAAT enhancer-binding protein (C/EBP) β target genes. First, we purified CDK8- and CDK19-containing complexes from HeLa nuclear extracts and subjected these purified complexes to mass spectrometric analyses. These experiments revealed that two Mediator CDKs, CDK8 and CDK19, individually interact with PRMT5 and WDR77, and their interactions with PRMT5 cause transcriptional repression of C/EBPβ target genes by regulating symmetric dimethylation of histone H4 arginine 3 (H4R3me2s) in the promoter regions of those genes. Furthermore, the recruitment of the DNA methyltransferase DNMT3A correlated with H4R3 dimethylation potentially leading to DNA methylation at the promoter proximal region and tight inhibition of preinitiation complex formation. In vertebrates, C/EBPβ regulates many genes involved in immune responses and cell differentiation. These findings shed light on the molecular mechanisms of the repressive roles of Mediator CDKs in transcription of C/EBPβ target genes and might provide clues that enable future studies of the functional associations between Mediators and epigenetic regulation.
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Affiliation(s)
- Taiki Tsutsui
- From the Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, and
| | - Rikiya Fukasawa
- From the Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, and
| | - Kaori Shinmyouzu
- the Mass Spectrometry Analysis Unit, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Reiko Nakagawa
- the Mass Spectrometry Analysis Unit, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Kazuyuki Tobe
- the First Department of Internal Medicine, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan and
| | - Aki Tanaka
- From the Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, and
| | - Yoshiaki Ohkuma
- From the Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, and.
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294
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Liu H, Galka M, Mori E, Liu X, Lin YF, Wei R, Pittock P, Voss C, Dhami G, Li X, Miyaji M, Lajoie G, Chen B, Li SSC. A method for systematic mapping of protein lysine methylation identifies functions for HP1β in DNA damage response. Mol Cell 2013; 50:723-35. [PMID: 23707759 DOI: 10.1016/j.molcel.2013.04.025] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 03/13/2013] [Accepted: 04/12/2013] [Indexed: 11/28/2022]
Abstract
Lysine methylation occurs on both histone and nonhistone proteins. However, our knowledge on the prevalence and function of nonhistone protein methylation is poor. We describe an approach that combines peptide array, bioinformatics, and mass spectrometry to systematically identify lysine methylation sites and map methyllysine-driven protein-protein interactions. Using this approach, we identified a high-confidence and high-resolution interactome of the heterochromatin protein 1β (HP1β) and uncovered, simultaneously, numerous methyllysine sites on nonhistone proteins. We found that HP1β binds to DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and regulates its localization to double-strand breaks (DSBs) during DNA damage response (DDR). Mutation of the methylation sites in DNA-PKcs or depletion of HP1β in cells caused defects in DDR. Furthermore, we showed that the methylation of DNA-PKcs and many other proteins in the HP1β interactome undergoes large changes in response to DNA damage, indicating that Lys methylation is a highly dynamic posttranslational modification.
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Affiliation(s)
- Huadong Liu
- Department of Biochemistry and the Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5C1, Canada
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295
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Huang BW, Ray PD, Iwasaki K, Tsuji Y. Transcriptional regulation of the human ferritin gene by coordinated regulation of Nrf2 and protein arginine methyltransferases PRMT1 and PRMT4. FASEB J 2013; 27:3763-74. [PMID: 23699174 DOI: 10.1096/fj.12-226043] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Antioxidant genes such as ferritin are transcriptionally activated in oxidative stress via the antioxidant responsive element (ARE), to which nuclear factor-E2-related factor 2 (Nrf2) binds and activates transcription. Histone modification plays a cooperative and essential role in transcriptional regulation; however, its role in antioxidant gene transcription remains elusive. Arsenic exposure activated ferritin transcription via the ARE concomitant with increased methylation of histones H4Arg3 (H4R3) and H3Arg17 (H3R17). To test our hypothesis that histone H4R3 and H3R17 methylation regulates ferritin transcription, H4R3 and H3R17 protein arginine (R) methyltransferases 1 and 4 (PRMT1 and PRMT4) were investigated. Arsenic exposure of human HaCaT keratinocytes induced nuclear accumulation of PRMT1 and PRMT4, histone H4R3 and H3R17 methylation proximal to the ARE, but not to the non-ARE regions of ferritin genes. PRMT1 or PRMT4 knockdown did not block Nrf2 nuclear accumulation but inhibited Nrf2 binding to the AREs by ∼40% (P<0.05), thus diminishing ferritin transcription in HaCaT and human primary keratinocytes and fibroblasts, causing enhanced cellular susceptibility to arsenic toxicity as evidenced by 2-fold caspase 3 activation. Focused microarray further characterized several oxidative stress response genes are subject to PRMT1 or PRMT4 regulation. Collectively, PRMT1 and PRMT4 regulate the ARE and cellular antioxidant response to arsenic.
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Affiliation(s)
- Bo-Wen Huang
- Department of Environmental and Molecular Toxicology, North Carolina State University, Campus Box 7633, Raleigh, NC 27695, USA
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296
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Esse R, Florindo C, Imbard A, Rocha MS, de Vriese AS, Smulders YM, Teerlink T, Tavares de Almeida I, Castro R, Blom HJ. Global protein and histone arginine methylation are affected in a tissue-specific manner in a rat model of diet-induced hyperhomocysteinemia. Biochim Biophys Acta Mol Basis Dis 2013; 1832:1708-14. [PMID: 23707560 DOI: 10.1016/j.bbadis.2013.05.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 05/08/2013] [Accepted: 05/13/2013] [Indexed: 10/26/2022]
Abstract
Accumulation of S-adenosylhomocysteine (AdoHcy), the homocysteine (Hcy) precursor and a potent methyltransferase inhibitor, may mediate the neurological and vascular complications associated with elevated Hcy. Protein arginine methylation is a crucial post-translational modification and generates monomethylarginine (MMA) and dimethylarginine (asymmetric, ADMA, and symmetric, SDMA) residues. We aimed at determining whether protein arginine methylation status is disturbed in an animal model of diet-induced hyperhomocysteinemia (HHcy). HHcy was achieved by dietary manipulation of Wistar rats: methionine-enrichment (HM), B vitamins deficiency (LV), or both (HMLV). Total Hcy, S-adenosylmethionine (AdoMet), AdoHcy, MMA, ADMA and SDMA concentrations in plasma or tissues (heart, brain and liver) were determined by adequate high-performance liquid chromatography or liquid chromatography-electrospray ionization-tandem mass spectrometry methods. Moreover, in tissues from the HMLV group, histone arginine asymmetric dimethylation was evaluated by Western blotting, and the histone methylation marks H3R17me2a, H3R8me2a and H4R3me2a were studied. HHcy was induced by all special diets, with elevation of AdoHcy concentrations in liver (LV and HMLV) and heart (HMLV) (all versus control). Plasma ADMA levels were lower in all hyperhomocysteinemic animals. Protein-incorporated ADMA levels were decreased in brain and in heart (both for the LV and HMLV groups). Moreover, in brain of animals exposed to the HMLV diet, the H3R8me2a mark was profoundly decreased. In conclusion, our results show that diet-induced Hcy elevation disturbs global protein arginine methylation in a tissue-specific manner and affects histone arginine methylation in brain. Future research is warranted to disclose the functional implications of the global protein and histone arginine hypomethylation triggered by Hcy elevation.
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Affiliation(s)
- Ruben Esse
- Department of Clinical Chemistry, VU University Medical Center, Amsterdam, The Netherlands
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297
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James LI, Beaver JE, Rice NW, Waters ML. A Synthetic Receptor for Asymmetric Dimethyl Arginine. J Am Chem Soc 2013; 135:6450-5. [DOI: 10.1021/ja307907p] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Lindsey I. James
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North
Carolina 27599, United States
| | - Joshua E. Beaver
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North
Carolina 27599, United States
| | - Natalie W. Rice
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North
Carolina 27599, United States
| | - Marcey L. Waters
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North
Carolina 27599, United States
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298
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299
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Abstract
Clinical neurologists and scientists who study multiple sclerosis face open questions regarding the integration of epidemiological data with genome-wide association studies and clinical management of patients. It is becoming evident that the interplay of environmental influences and individual genetic susceptibility modulates disease presentation and therapeutic responsiveness. The molecular mechanisms through which environmental signals are translated into changes in gene expression include DNA methylation, post-translational modification of nucleosomal histones, and non-coding RNAs. These mechanisms are regulated by families of specialised enzymes that are tissue selective and cell-type specific. A model of multiple sclerosis pathogenesis should integrate underlying risk related to genetic susceptibility with cell-type specific epigenetic changes occurring in the immune system and in the brain in response to ageing and environmental stimuli.
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300
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Liu F, Li F, Ma A, Dobrovetsky E, Dong A, Gao C, Korboukh I, Liu J, Smil D, Brown PJ, Frye SV, Arrowsmith CH, Schapira M, Vedadi M, Jin J. Exploiting an allosteric binding site of PRMT3 yields potent and selective inhibitors. J Med Chem 2013; 56:2110-24. [PMID: 23445220 PMCID: PMC4319713 DOI: 10.1021/jm3018332] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein arginine methyltransferases (PRMTs) play an important role in diverse biological processes. Among the nine known human PRMTs, PRMT3 has been implicated in ribosomal biosynthesis via asymmetric dimethylation of the 40S ribosomal protein S2 and in cancer via interaction with the DAL-1 tumor suppressor protein. However, few selective inhibitors of PRMTs have been discovered. We recently disclosed the first selective PRMT3 inhibitor, which occupies a novel allosteric binding site and is noncompetitive with both the peptide substrate and cofactor. Here we report comprehensive structure-activity relationship studies of this series, which resulted in the discovery of multiple PRMT3 inhibitors with submicromolar potencies. An X-ray crystal structure of compound 14u in complex with PRMT3 confirmed that this inhibitor occupied the same allosteric binding site as our initial lead compound. These studies provide the first experimental evidence that potent and selective inhibitors can be created by exploiting the allosteric binding site of PRMT3.
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Affiliation(s)
- Feng Liu
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Anqi Ma
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Elena Dobrovetsky
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Cen Gao
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Ilia Korboukh
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jing Liu
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - David Smil
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Peter J. Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Stephen V. Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Jian Jin
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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