1
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Zhou W, Yadav GP, Yang X, Qin F, Li C, Jiang QX. Cryo-EM structure-based selection of computed ligand poses enables design of MTA-synergic PRMT5 inhibitors of better potency. Commun Biol 2022; 5:1054. [PMID: 36192627 DOI: 10.1038/s42003-022-03991-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 09/13/2022] [Indexed: 12/31/2022] Open
Abstract
Projected potential of 2.5-4.0 Å cryo-EM structures for structure-based drug design is not well realized yet. Here we show that a 3.1 Å structure of PRMT5 is suitable for selecting computed poses of a chemical inhibitor and its analogs for enhanced potency. PRMT5, an oncogenic target for various cancer types, has many inhibitors manifesting little cooperativity with MTA, a co-factor analog accumulated in MTAP-/- cells. To achieve MTA-synergic inhibition, a pharmacophore from virtual screen leads to a specific inhibitor (11-2 F). Cryo-EM structures of 11-2 F / MTA-bound human PRMT5/MEP50 complex and its apo form resolved at 3.1 and 3.2 Å respectively show that 11-2 F in the catalytic pocket shifts the cofactor-binding pocket away by ~2.0 Å, contributing to positive cooperativity. Computational analysis predicts subtype specificity of 11-2 F among PRMTs. Structural analysis of ligands in the binding pockets is performed to compare poses of 11-2 F and its redesigned analogs and identifies three new analogs predicted to have significantly better potency. One of them, after synthesis, is ~4 fold more efficient in inhibiting PRMT5 catalysis than 11-2 F, with strong MTA-synergy. These data suggest the feasibility of employing near-atomic resolution cryo-EM structures and computational analysis of ligand poses for small molecule therapeutics.
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2
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Kawamura S, Palte RL, Kim HY, Saurí J, Sondey C, Mansueto MS, Altman MD, Machacek MR. Design and synthesis of unprecedented 9- and 10-membered cyclonucleosides with PRMT5 inhibitory activity. Bioorg Med Chem 2022; 66:116820. [PMID: 35594650 DOI: 10.1016/j.bmc.2022.116820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 11/16/2022]
Abstract
Synthesis of medium-sized rings is known to be challenging due to high transannular strain especially for 9- and 10-membered rings. Herein we report design and synthesis of unprecedented 9- and 10-membered purine 8,5'-cyclonucleosides as the first cyclonucleoside PRMT5 inhibitors. The cocrystal structure of PRMT5:MEP50 in complex with the synthesized 9-membered cyclonucleoside 1 revealed its binding mode in the SAM binding pocket of PRMT5.
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Affiliation(s)
- Shuhei Kawamura
- Discovery Chemistry, Merck & Co., Inc., Boston, MA 02115, United States.
| | - Rachel L Palte
- Computational and Structural Chemistry, Merck & Co., Inc., Boston, MA 02115, United States
| | - Hai-Young Kim
- NMR Structure Elucidation, Process and Analytical Chemistry, Merck & Co., Inc., Boston, MA 02115, United States
| | - Josep Saurí
- NMR Structure Elucidation, Process and Analytical Chemistry, Merck & Co., Inc., Boston, MA 02115, United States
| | - Christopher Sondey
- Quantitative Biosciences, Merck & Co., Inc., Boston, MA 02115, United States
| | - My S Mansueto
- Quantitative Biosciences, Merck & Co., Inc., Boston, MA 02115, United States
| | - Michael D Altman
- Computational and Structural Chemistry, Merck & Co., Inc., Boston, MA 02115, United States
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3
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Usher ET, Namitz KEW, Cosgrove MS, Showalter SA. Probing multiple enzymatic methylation events in real time with NMR spectroscopy. Biophys J 2021; 120:4710-4721. [PMID: 34592262 PMCID: PMC8595733 DOI: 10.1016/j.bpj.2021.09.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 11/25/2022] Open
Abstract
Post-translational modification (PTM) of proteins is of critical importance to the regulation of many cellular processes in eukaryotic organisms. One of the most well-studied protein PTMs is methylation, wherein an enzyme catalyzes the transfer of a methyl group from a cofactor to a lysine or arginine side chain. Lysine methylation is especially abundant in the histone tails and is an important marker for denoting active or repressed genes. Given their relevance to transcriptional regulation, the study of methyltransferase function through in vitro experiments is an important stepping stone toward understanding the complex mechanisms of regulated gene expression. To date, most methyltransferase characterization strategies rely on the use of radioactive cofactors, detection of a methyl transfer byproduct, or discontinuous-type assays. Although such methods are suitable for some applications, information about multiple methylation events and kinetic intermediates is often lost. Herein, we describe the use of two-dimensional NMR to monitor mono-, di-, and trimethylation in a single reaction tube. To do so, we incorporated 13C into the donor methyl group of the enzyme cofactor S-adenosyl methionine. In this way, we may study enzymatic methylation by monitoring the appearance of distinct resonances corresponding to mono-, di-, or trimethyl lysine without the need to isotopically enrich the substrate. To demonstrate the capabilities of this method, we evaluated the activity of three lysine methyltransferases, Set7, MWRAD2 (MLL1 complex), and PRDM9, toward the histone H3 tail. We monitored mono- or multimethylation of histone H3 tail at lysine 4 through sequential short two-dimensional heteronuclear single quantum coherence experiments and fit the resulting progress curves to first-order kinetic models. In summary, NMR detection of PTMs in one-pot, real-time reaction using facile cofactor isotopic enrichment shows promise as a method toward understanding the intricate mechanisms of methyltransferases and other enzymes.
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Affiliation(s)
- Emery T Usher
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology
| | - Kevin E W Namitz
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania
| | - Michael S Cosgrove
- SUNY Upstate Medical University, Department of Biochemistry and Molecular Biology, Syracuse, New York
| | - Scott A Showalter
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology; Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania.
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4
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Nibona E, Niyonkuru C, Liang X, Yao Q, Zhao H. Essential Roles of PRMT5-MEP50 Complex Formation and Cancer Therapy. Russ J Dev Biol 2021. [DOI: 10.1134/s1062360421050064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Maron MI, Lehman SM, Gayatri S, DeAngelo JD, Hegde S, Lorton BM, Sun Y, Bai DL, Sidoli S, Gupta V, Marunde MR, Bone JR, Sun ZW, Bedford MT, Shabanowitz J, Chen H, Hunt DF, Shechter D. Independent transcriptomic and proteomic regulation by type I and II protein arginine methyltransferases. iScience 2021; 24:102971. [PMID: 34505004 PMCID: PMC8417332 DOI: 10.1016/j.isci.2021.102971] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 06/21/2021] [Accepted: 08/09/2021] [Indexed: 12/22/2022] Open
Abstract
Protein arginine methyltransferases (PRMTs) catalyze the post-translational monomethylation (Rme1), asymmetric (Rme2a), or symmetric (Rme2s) dimethylation of arginine. To determine the cellular consequences of type I (Rme2a) and II (Rme2s) PRMTs, we developed and integrated multiple approaches. First, we determined total cellular dimethylarginine levels, revealing that Rme2s was ∼3% of total Rme2 and that this percentage was dependent upon cell type and PRMT inhibition status. Second, we quantitatively characterized in vitro substrates of the major enzymes and expanded upon PRMT substrate recognition motifs. We also compiled our data with publicly available methylarginine-modified residues into a comprehensive database. Third, we inhibited type I and II PRMTs and performed proteomic and transcriptomic analyses to reveal their phenotypic consequences. These experiments revealed both overlapping and independent PRMT substrates and cellular functions. Overall, this study expands upon PRMT substrate diversity, the arginine methylome, and the complex interplay of type I and II PRMTs.
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Affiliation(s)
- Maxim I. Maron
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Stephanie M. Lehman
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Sitaram Gayatri
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
- Graduate Program in Genetics and Epigenetics, The University of Texas MD Anderson UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Joseph D. DeAngelo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Subray Hegde
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Benjamin M. Lorton
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Yan Sun
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Dina L. Bai
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Varun Gupta
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - James R. Bone
- EpiCypher, Inc., Research Triangle Park, NC 27709, USA
| | - Zu-Wen Sun
- EpiCypher, Inc., Research Triangle Park, NC 27709, USA
| | - Mark T. Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
- Graduate Program in Genetics and Epigenetics, The University of Texas MD Anderson UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Hongshan Chen
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Donald F. Hunt
- Departments of Chemistry and Pathology, University of Virginia, Charlottesville, VA 22904, USA
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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6
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Fulton MD, Cao M, Ho MC, Zhao X, Zheng YG. The macromolecular complexes of histones affect protein arginine methyltransferase activities. J Biol Chem 2021; 297:101123. [PMID: 34492270 PMCID: PMC8511957 DOI: 10.1016/j.jbc.2021.101123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/14/2021] [Accepted: 08/24/2021] [Indexed: 11/29/2022] Open
Abstract
Histone arginine methylation is a key post-translational modification that mediates epigenetic events that activate or repress gene transcription. Protein arginine methyltransferases (PRMTs) are the driving force for the process of arginine methylation, and the core histone proteins have been shown to be substrates for most PRMT family members. However, previous reports of the enzymatic activities of PRMTs on histones in the context of nucleosomes seem contradictory. Moreover, what governs nucleosomal substrate recognition of different PRMT members is not understood. We sought to address this key biological question by examining how different macromolecular contexts where the core histones reside may regulate arginine methylation catalyzed by individual PRMT members (i.e., PRMT1, PRMT3, PRMT4, PRMT5, PRMT6, PRMT7, and PRMT8). Our results demonstrated that the substrate context exhibits a huge impact on the histone arginine methylation activity of PRMTs. Although all the tested PRMTs methylate multiple free histones individually, they show a preference for one particular histone substrate in the context of the histone octamer. We found that PRMT1, PRMT3, PRMT5, PRMT6, PRMT7, and PRMT8 preferentially methylate histone H4, whereas PRMT4/coactivator-associated arginine methyltransferase 1 prefers histone H3. Importantly, neither reconstituted nor cell-extracted mononucleosomes could be methylated by any PRMTs tested. Structural analysis suggested that the electrostatic interaction may play a mechanistic role in priming the substrates for methylation by PRMT enzymes. Taken together, this work expands our knowledge on the molecular mechanisms of PRMT substrate recognition and has important implications for understanding cellular dynamics and kinetics of histone arginine methylation in regulating gene transcription and other chromatin-templated processes.
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Affiliation(s)
- Melody D Fulton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, Georgia, USA
| | - Mengtong Cao
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, Georgia, USA
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei, Taiwan
| | - Xinyang Zhao
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, Georgia, USA.
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7
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Mulvaney KM, Blomquist C, Acharya N, Li R, Ranaghan MJ, O'Keefe M, Rodriguez DJ, Young MJ, Kesar D, Pal D, Stokes M, Nelson AJ, Jain SS, Yang A, Mullin-Bernstein Z, Columbus J, Bozal FK, Skepner A, Raymond D, LaRussa S, McKinney DC, Freyzon Y, Baidi Y, Porter D, Aguirre AJ, Ianari A, McMillan B, Sellers WR. Molecular basis for substrate recruitment to the PRMT5 methylosome. Mol Cell 2021; 81:3481-3495.e7. [PMID: 34358446 DOI: 10.1016/j.molcel.2021.07.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/07/2021] [Accepted: 07/14/2021] [Indexed: 12/15/2022]
Abstract
PRMT5 is an essential arginine methyltransferase and a therapeutic target in MTAP-null cancers. PRMT5 uses adaptor proteins for substrate recruitment through a previously undefined mechanism. Here, we identify an evolutionarily conserved peptide sequence shared among the three known substrate adaptors (CLNS1A, RIOK1, and COPR5) and show that it is necessary and sufficient for interaction with PRMT5. We demonstrate that PRMT5 uses modular adaptor proteins containing a common binding motif for substrate recruitment, comparable with other enzyme classes such as kinases and E3 ligases. We structurally resolve the interface with PRMT5 and show via genetic perturbation that it is required for methylation of adaptor-recruited substrates including the spliceosome, histones, and ribosomal complexes. Furthermore, disruption of this site affects Sm spliceosome activity, leading to intron retention. Genetic disruption of the PRMT5-substrate adaptor interface impairs growth of MTAP-null tumor cells and is thus a site for development of therapeutic inhibitors of PRMT5.
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Affiliation(s)
| | | | | | | | - Matthew J Ranaghan
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - Meghan O'Keefe
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Adam Skepner
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - Donald Raymond
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - Salvatore LaRussa
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - David C McKinney
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | | | | | - Dale Porter
- Broad Institute, Cambridge, MA, USA; Cedilla Therapeutics, Cambridge, MA, USA
| | - Andrew J Aguirre
- Broad Institute, Cambridge, MA, USA; Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | | | - Brian McMillan
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA; Tango Therapeutics, Cambridge, MA, USA
| | - William R Sellers
- Broad Institute, Cambridge, MA, USA; Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
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8
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Zappacosta F, Wagner CD, Della Pietra A, Gerhart SV, Keenan K, Korenchuck S, Quinn CJ, Barbash O, McCabe MT, Annan RS. A Chemical Acetylation-Based Mass Spectrometry Platform for Histone Methylation Profiling. Mol Cell Proteomics 2021; 20:100067. [PMID: 33775892 PMCID: PMC8138768 DOI: 10.1016/j.mcpro.2021.100067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/11/2021] [Accepted: 02/18/2021] [Indexed: 12/18/2022] Open
Abstract
Histones are highly posttranslationally modified proteins that regulate gene expression by modulating chromatin structure and function. Acetylation and methylation are the most abundant histone modifications, with methylation occurring on lysine (mono-, di-, and trimethylation) and arginine (mono- and dimethylation) predominately on histones H3 and H4. In addition, arginine dimethylation can occur either symmetrically (SDMA) or asymmetrically (ADMA) conferring different biological functions. Despite the importance of histone methylation on gene regulation, characterization and quantitation of this modification have proven to be quite challenging. Great advances have been made in the analysis of histone modification using both bottom-up and top-down mass spectrometry (MS). However, MS-based analysis of histone posttranslational modifications (PTMs) is still problematic, due both to the basic nature of the histone N-terminal tails and to the combinatorial complexity of the histone PTMs. In this report, we describe a simplified MS-based platform for histone methylation analysis. The strategy uses chemical acetylation with d0-acetic anhydride to collapse all the differently acetylated histone forms into one form, greatly reducing the complexity of the peptide mixture and improving sensitivity for the detection of methylation via summation of all the differently acetylated forms. We have used this strategy for the robust identification and relative quantitation of H4R3 methylation, for which stoichiometry and symmetry status were determined, providing an antibody-independent evidence that H4R3 is a substrate for both Type I and Type II PRMTs. Additionally, this approach permitted the robust detection of H4K5 monomethylation, a very low stoichiometry methylation event (0.02% methylation). In an independent example, we developed an in vitro assay to profile H3K27 methylation and applied it to an EZH2 mutant xenograft model following small-molecule inhibition of the EZH2 methyltransferase. These specific examples highlight the utility of this simplified MS-based approach to quantify histone methylation profiles. Simplification of histone complexity for analysis of lysine and arginine methylation. Improved sensitivity for the analysis of dimethylarginine symmetry. Accurate ratio of symmetric and asymmetric H4R3 dimethylarginine in cancer cells. Catalog of accessible histone methyl marks to facilitate assay development.
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Affiliation(s)
- Francesca Zappacosta
- Discovery Analytical, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Craig D Wagner
- Discovery Analytical, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - Sarah V Gerhart
- Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Kathryn Keenan
- Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - Chad J Quinn
- Discovery Analytical, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Olena Barbash
- Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - Roland S Annan
- Discovery Analytical, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, USA.
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9
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Abstract
Arginine methylation is an essential post-translational modification (PTM) deposited by protein arginine methyltransferases (PRMTs) and recognized by Tudor domain-containing proteins. Of the nine mammalian PRMTs, PRMT5 is the primary enzyme responsible for the deposition of symmetric arginine methylation marks in cells. The staphylococcal nuclease and Tudor domain-containing 1 (SND1) effector protein is a key reader of the marks deposited by PRMT5. Both PRMT5 and SND1 are broadly expressed and their deregulation is reported to be associated with a range of disease phenotypes, including cancer. Hepatocellular carcinoma (HCC) is an example of a cancer type that often displays elevated PRMT5 and SND1 levels, and there is evidence that hyperactivation of this axis is oncogenic. Importantly, this pathway can be tempered with small-molecule inhibitors that target PRMT5, offering a therapeutic node for cancer, such as HCC, that display high PRMT5–SND1 axis activity. Here we summarize the known activities of this writer–reader pair, with a focus on their biological roles in HCC. This will help establish a foundation for treating HCC with PRMT5 inhibitors and also identify potential biomarkers that could predict sensitivity to this type of therapy.
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Affiliation(s)
- Tanner Wright
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; (T.W.); (Y.W.)
- Graduate Program in Genetics & Epigenetics, UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yalong Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; (T.W.); (Y.W.)
| | - Mark T. Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; (T.W.); (Y.W.)
- Correspondence:
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10
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Abstract
Histone arginine methylation is a prevalent posttranslational modification (PTM) in eukaryotic cells and contributes to the histone codes for epigenetic regulation of gene transcription. In this study, we determined how local changes on adjacent residues in the histone H4 substrate regulate arginine asymmetric dimethylation and symmetric dimethylation catalysed by the major protein arginine methyltransferase (PRMT) enzymes PRMT1 and PRMT5, respectively. We found that phosphorylation at histone H4 Ser-1 site (H4S1) was inhibitory to activities of PRMT1 and PRMT5 in both monomethylating and dimethylating H4R3. Also, a positively charged H4K5 was important for PRMT1 catalysis because acetylation of H4K5 or the loss of the H4K5 ε-amine had a similar effect in reducing the catalytic efficiency of asymmetric dimethylation of H4R3. An opposite effect was observed in that acetylation of H4K5 or the loss of the H4K5 ε-amine enhanced PRMT5-mediated symmetric dimethylation of H4R3. Furthermore, we observed that N-terminal acetylation of H4 modestly decreased asymmetric dimethylation of H4R3 by PRMT1 and symmetric dimethylation of H4R3 by PRMT5. This work highlights the significance of local chemical changes in the substrate to regulating PRMT activity and unravels the pattern complexities and subtleties of histone codes.
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Affiliation(s)
- Melody D Fulton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia,USA
| | - Tran Dang
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia,USA
| | - Tyler Brown
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia,USA
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia,USA
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11
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Owens JL, Beketova E, Liu S, Tinsley SL, Asberry AM, Deng X, Huang J, Li C, Wan J, Hu CD. PRMT5 Cooperates with pICln to Function as a Master Epigenetic Activator of DNA Double-Strand Break Repair Genes. iScience 2019; 23:100750. [PMID: 31884170 PMCID: PMC6941881 DOI: 10.1016/j.isci.2019.100750] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 11/06/2019] [Accepted: 11/22/2019] [Indexed: 01/21/2023] Open
Abstract
DNA double-strand break (DSB) repair is critical for cell survival and genome integrity. Upon recognition of DSBs, repair proteins are transiently upregulated to facilitate repair through homologous recombination (HR) or non-homologous end joining (NHEJ). We present evidence that PRMT5 cooperates with pICln to function as a master epigenetic activator of DNA damage response (DDR) genes involved in HR, NHEJ, and G2 arrest (including RAD51, BRCA1, and BRCA2) to upregulate gene expression upon DNA damage. Contrary to the predominant role of PRMT5 as an epigenetic repressor, our results demonstrate that PRMT5 and pICln can activate gene expression, potentially independent of PRMT5's obligate cofactor MEP50. Targeting PRMT5 or pICln hinders repair of DSBs in multiple cancer cell lines, and both PRMT5 and pICln expression positively correlates with DDR genes across 32 clinical cancer datasets. Thus, targeting PRMT5 or pICln may be explored in combination with radiation or chemotherapy for cancer treatment. PRMT5 activates transcription of DSB repair genes upon DNA damage pICln cooperates with PRMT5 to activate transcription of DSB repair genes Targeting PRMT5 is effective to sensitize multiple cancer types to radiation PRMT5 expression positively correlates with DSB repair genes in cancer tissues
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Affiliation(s)
- Jake L Owens
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Elena Beketova
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; Purdue University Interdisciplinary Life Sciences Graduate Program, Purdue University, West Lafayette, IN 47907, USA
| | - Sheng Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; The Indiana University Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN 46202, USA
| | - Samantha L Tinsley
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; Purdue University Interdisciplinary Life Sciences Graduate Program, Purdue University, West Lafayette, IN 47907, USA
| | - Andrew M Asberry
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; Purdue University Interdisciplinary Life Sciences Graduate Program, Purdue University, West Lafayette, IN 47907, USA
| | - Xuehong Deng
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Chenglong Li
- Department of Medicinal Chemistry, University of Florida College of Pharmacy, Gainesville, FL 32610, USA
| | - Jun Wan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; The Indiana University Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN 46202, USA; The Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indiana University - Purdue University Indianapolis, Indianapolis, IN 46202, USA.
| | - Chang-Deng Hu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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12
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Lu W, Kim JD, Tabara S, Kwon C, Mizukami H, Kimura K, Fukamizu A. The N-terminal sequence of murine PRMT5 variant 2 is required for Hsp70 interaction and CHIP ligase-mediated degradation. Biochem Biophys Res Commun 2019; 514:1185-1191. [PMID: 31103260 DOI: 10.1016/j.bbrc.2019.05.077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 05/10/2019] [Indexed: 10/26/2022]
Abstract
Protein arginine methyltransferase PRMT5 synthesizes the symmetric dimethylarginine in nuclear and cytoplasmic proteins such as histone H2A, H4 and several non-histone proteins that are required for a variety of biological processes. Currently, two splice variants (v1 and v2) of murine PRMT5 have been deposited in the NCBI sequence database, in which PRMT5-v1 and -v2 contain different 33 and 16 amino acids at the N-terminal sequences, respectively. Here we showed that murine PRMT5-v1 is stable, but PRMT5-v2 is constantly degraded through both the ubiquitin proteasome system (UPS) and the autophagic-lysosomal pathway (ALP) in an N-terminal sequence-dependent manner. Furthermore, inhibition of UPS and ALP elevated the stability of PRMT5-v2 that made it localized in the nucleus and the cytoplasm. In addition, PRMT5-v2 exhibited the enzyme activity to catalyze histone H2A and H4 methylation. Notably, we found that the heat shock protein (Hsp) 70 specially recognizes the N-terminal sequence of PRMT5-v2 and the carboxyl terminus of Hsp70-interacting protein (CHIP) is required for poly-ubiquitination and the degradation of PRMT5-v2. These results suggest that Hsp70/CHIP chaperone-mediated protein degradation system is crucial in the regulation of PRMT5-v2 turnover, which has the potential to balance the symmetrical arginine dimethylation in cells.
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Affiliation(s)
- Weizhe Lu
- Ph.D. Program in Human Biology, School of Integrative Global Majors (SIGMA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, Japan
| | - Jun-Dal Kim
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, Japan
| | - Saori Tabara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, Japan
| | - Chulwon Kwon
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, Japan
| | - Hayase Mizukami
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, Japan
| | - Keiji Kimura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, Japan
| | - Akiyoshi Fukamizu
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, Japan; International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, Japan.
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13
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Tewary SK, Zheng YG, Ho MC. Protein arginine methyltransferases: insights into the enzyme structure and mechanism at the atomic level. Cell Mol Life Sci 2019; 76:2917-2932. [PMID: 31123777 DOI: 10.1007/s00018-019-03145-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 02/06/2023]
Abstract
Protein arginine methyltransferases (PRMTs) catalyze the methyl transfer to the arginine residues of protein substrates and are classified into three major types based on the final form of the methylated arginine. Recent studies have shown a strong correlation between PRMT expression level and the prognosis of cancer patients. Currently, crystal structures of eight PRMT members have been determined. Kinetic and structural studies have shown that all PRMTs share similar, but unique catalytic and substrate recognition mechanism. In this review, we discuss the structural similarities and differences of different PRMT members, focusing on their overall structure, S-adenosyl-L-methionine-binding pocket, substrate arginine recognition and catalytic mechanisms. Since PRMTs are valuable targets for drug discovery, we also rationally classify the known PRMT inhibitors into five classes and discuss their mechanisms of action at the atomic level.
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Affiliation(s)
| | - Y George Zheng
- College of Pharmacy, University of Georgia, Athens, GA, 30602, USA
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan. .,Institute of Biochemical Sciences, National Taiwan University, Taipei, 106, Taiwan.
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14
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Christou-Kent M, Kherraf ZE, Amiri-Yekta A, Le Blévec E, Karaouzène T, Conne B, Escoffier J, Assou S, Guttin A, Lambert E, Martinez G, Boguenet M, Fourati Ben Mustapha S, Cedrin Durnerin I, Halouani L, Marrakchi O, Makni M, Latrous H, Kharouf M, Coutton C, Thierry-Mieg N, Nef S, Bottari SP, Zouari R, Issartel JP, Ray PF, Arnoult C. PATL2 is a key actor of oocyte maturation whose invalidation causes infertility in women and mice. EMBO Mol Med 2019; 10:emmm.201708515. [PMID: 29661911 PMCID: PMC5938616 DOI: 10.15252/emmm.201708515] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The genetic causes of oocyte meiotic deficiency (OMD), a form of primary infertility characterised by the production of immature oocytes, remain largely unexplored. Using whole exome sequencing, we found that 26% of a cohort of 23 subjects with OMD harboured the same homozygous nonsense pathogenic mutation in PATL2, a gene encoding a putative RNA‐binding protein. Using Patl2 knockout mice, we confirmed that PATL2 deficiency disturbs oocyte maturation, since oocytes and zygotes exhibit morphological and developmental defects, respectively. PATL2's amphibian orthologue is involved in the regulation of oocyte mRNA as a partner of CPEB. However, Patl2's expression profile throughout oocyte development in mice, alongside colocalisation experiments with Cpeb1, Msy2 and Ddx6 (three oocyte RNA regulators) suggest an original role for Patl2 in mammals. Accordingly, transcriptomic analysis of oocytes from WT and Patl2−/− animals demonstrated that in the absence of Patl2, expression levels of a select number of highly relevant genes involved in oocyte maturation and early embryonic development are deregulated. In conclusion, PATL2 is a novel actor of mammalian oocyte maturation whose invalidation causes OMD in humans.
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Affiliation(s)
- Marie Christou-Kent
- Genetics, Epigenetics and Therapies of Infertility, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble, France
| | - Zine-Eddine Kherraf
- Genetics, Epigenetics and Therapies of Infertility, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble, France
| | - Amir Amiri-Yekta
- Genetics, Epigenetics and Therapies of Infertility, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble, France.,UM GI-DPI, CHU de Grenoble, Grenoble, France.,Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Emilie Le Blévec
- Genetics, Epigenetics and Therapies of Infertility, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble, France
| | - Thomas Karaouzène
- Genetics, Epigenetics and Therapies of Infertility, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble, France
| | - Béatrice Conne
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Jessica Escoffier
- Genetics, Epigenetics and Therapies of Infertility, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble, France
| | - Said Assou
- IRMB, INSERM U1183, CHRU Montpellier, Université Montpellier, Montpellier, France
| | - Audrey Guttin
- Grenoble Neuroscience Institute, INSERM 1216, Université Grenoble Alpes, Grenoble, France
| | - Emeline Lambert
- Genetics, Epigenetics and Therapies of Infertility, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble, France
| | - Guillaume Martinez
- Genetics, Epigenetics and Therapies of Infertility, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble, France.,UM GI-DPI, CHU de Grenoble, Grenoble, France.,UM de Génétique Chromosomique, CHU de Grenoble, Grenoble, France
| | - Magalie Boguenet
- Genetics, Epigenetics and Therapies of Infertility, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble, France
| | | | - Isabelle Cedrin Durnerin
- Service de Médecine de la Reproduction, Centre Hospitalier Universitaire Jean Verdier, Assistance Publique - Hôpitaux de Paris, Bondy, France
| | - Lazhar Halouani
- Polyclinique les Jasmins, Centre d'Aide Médicale à la Procréation, Centre Urbain Nord, Tunis, Tunisia
| | - Ouafi Marrakchi
- Polyclinique les Jasmins, Centre d'Aide Médicale à la Procréation, Centre Urbain Nord, Tunis, Tunisia
| | - Mounir Makni
- Polyclinique les Jasmins, Centre d'Aide Médicale à la Procréation, Centre Urbain Nord, Tunis, Tunisia
| | - Habib Latrous
- Polyclinique les Jasmins, Centre d'Aide Médicale à la Procréation, Centre Urbain Nord, Tunis, Tunisia
| | - Mahmoud Kharouf
- Polyclinique les Jasmins, Centre d'Aide Médicale à la Procréation, Centre Urbain Nord, Tunis, Tunisia
| | - Charles Coutton
- Genetics, Epigenetics and Therapies of Infertility, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble, France.,UM GI-DPI, CHU de Grenoble, Grenoble, France.,UM de Génétique Chromosomique, CHU de Grenoble, Grenoble, France
| | | | - Serge Nef
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Serge P Bottari
- Genetics, Epigenetics and Therapies of Infertility, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble, France
| | - Raoudha Zouari
- Polyclinique les Jasmins, Centre d'Aide Médicale à la Procréation, Centre Urbain Nord, Tunis, Tunisia
| | - Jean Paul Issartel
- Grenoble Neuroscience Institute, INSERM 1216, Université Grenoble Alpes, Grenoble, France
| | - Pierre F Ray
- Genetics, Epigenetics and Therapies of Infertility, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble, France.,UM GI-DPI, CHU de Grenoble, Grenoble, France
| | - Christophe Arnoult
- Genetics, Epigenetics and Therapies of Infertility, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble, France
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15
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Abstract
Xenopus laevis development is marked by accelerated cell division solely supported by the proteins maternally deposited in the egg. Oocytes mature to eggs with concomitant transcriptional silencing. The unique maternal chromatin state contributing to this silencing and subsequent zygotic activation is likely established by histone posttranslational modifications and histone variants. Therefore, tools for understanding the nature and function of maternal and embryonic histones are essential to deciphering mechanisms of regulation of development, chromatin assembly, and transcription. Here we describe protocols for isolating pronuclear sperm chromatin from Xenopus egg extracts and hydroxyapatite-based histone purification from this chromatin. The histones purified through this method can be directly assembled into chromatin through in vitro assembly reactions, providing a unique opportunity to biochemically dissect the effect of histone variants, histone modifications, and other factors in chromatin replication and assembly. We also describe how to isolate chromatin from staged embryos and analyze the proteins to reveal dynamic developmental histone modifications. Finally, we present protocols to measure chromatin assembly in extracts, including supercoiling and micrococcal nuclease assays. Using these approaches, analysis of maternal and zygotic histone posttranslational modifications concomitant with cell-cycle and developmental transitions can be tested.
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Affiliation(s)
- Wei-Lin Wang
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Takashi Onikubo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
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16
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Banasavadi-Siddegowda YK, Welker AM, An M, Yang X, Zhou W, Shi G, Imitola J, Li C, Hsu S, Wang J, Phelps M, Zhang J, Beattie CE, Baiocchi R, Kaur B. PRMT5 as a druggable target for glioblastoma therapy. Neuro Oncol 2019; 20:753-763. [PMID: 29106602 DOI: 10.1093/neuonc/nox206] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background In spite of standard multimodal therapy consisting of surgical resection followed by radiation and concurrent chemotherapy, prognosis for glioblastoma (GBM) patients remains poor. The identification of both differentiated and undifferentiated "stem cell like" populations in the tumor highlights the significance of finding novel targets that affect the heterogeneous tumor cell population. Protein arginine methyltransferase 5 (PRMT5) is one such candidate gene whose nuclear expression correlates with poor survival and has been reported to be required for survival of differentiated GBM cells and self-renewal of undifferentiated GBM cells. In the current study we screened the specificity and efficacy of 4 novel PRMT5 inhibitors in the treatment of GBM. Methods Efficacies of these inhibitors were screened using an in vitro GBM neurosphere model and an in vivo intracranial zebrafish model of glioma. Standard molecular biology methods were employed to investigate changes in cell cycle, growth, and senescence. Results In vitro and in vivo studies revealed that among the 4 PRMT5 inhibitors, treatment of GBM cells with compound 5 (CMP5) mirrored the effects of PRMT5 knockdown wherein it led to apoptosis of differentiated GBM cells and drove undifferentiated primary patient derived GBM cells into a nonreplicative senescent state. Conclusion In vivo antitumor efficacy combined with the specificity of CMP5 underscores the importance of developing it for translation.
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Affiliation(s)
- Yeshavanth Kumar Banasavadi-Siddegowda
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas.,Department of Neurological Surgery, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Alessandra M Welker
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio.,Department of Pathology, Center of Cancer Research, Massachusetts General Hospital, Boston, Massachusetts.,Harvard Stem Cell Institute, Boston, Massachusetts
| | - Min An
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Xiaozhi Yang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida
| | - Wei Zhou
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida
| | - Guqin Shi
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Jaime Imitola
- Laboratory for Neural Stem Cells and Functional Neurogenetics, Division of Neuroimmunology and Multiple Sclerosis, Departments of Neurology and Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Chenglong Li
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida.,Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida.,Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Sigmund Hsu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
| | - Jiang Wang
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Mitch Phelps
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Jianying Zhang
- Center for Biostatistics, Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
| | - Christine E Beattie
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Robert Baiocchi
- College of Medicine, Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | - Balveen Kaur
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas.,Department of Neurological Surgery, College of Medicine, The Ohio State University, Columbus, Ohio
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17
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Yang CY, Chiu LL, Chang CC, Chuang HC, Tan TH. Induction of DUSP14 ubiquitination by PRMT5-mediated arginine methylation. FASEB J 2018; 32:fj201800244RR. [PMID: 29920217 PMCID: PMC6219832 DOI: 10.1096/fj.201800244rr] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 06/04/2018] [Indexed: 12/24/2022]
Abstract
Dual-specificity phosphatase (DUSP)14 (also known as MAP-kinase phosphatase 6) inhibits T-cell receptor (TCR) signaling and T-cell-mediated immune responses by inactivation of the TGF-β activated kinase 1 binding protein (TAB1)-TGF-β activated kinase 1 (TAK1) complex and ERK. DUSP14 phosphatase activity is induced by the E3 ligase TNF receptor associated factor (TRAF)2-mediated Lys63-linked ubiquitination. Here we report an interaction between DUSP14 and protein arginine methyltransferase (PRMT)5 by proximity ligation assay; similarly, DUSP14 directly interacted with TAB1 but not TAK1. DUSP14 is methylated by PRMT5 at arginine 17, 38, and 45 residues. The DUSP14 triple-methylation mutant was impaired in PRMT5-mediated arginine methylation, TRAF2-mediated lysine ubiquitination, and DUSP14 phosphatase activity. Consistently, DUSP14 methylation, TRAF2 binding, and DUSP14 ubiquitination were attenuated by PRMT5 short hairpin RNA knockdown. Furthermore, DUSP14 was inducibly interacted with PRMT5 and was methylated during TCR signaling in T cells. Together, these findings reveal a novel regulatory mechanism of DUSP14 by which PRMT5-mediated arginine methylation may sequentially stimulate TRAF2-mediated DUSP14 ubiquitination and phosphatase activity, leading to inhibition of TCR signaling.-Yang, C.-Y., Chiu, L.-L., Chang, C.-C., Chuang, H.-C., Tan, T.-H. Induction of DUSP14 ubiquitination by PRMT5-mediated arginine methylation.
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Affiliation(s)
- Chia-Yu Yang
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Li-Li Chiu
- Department of Medical Education and Research, Taichung Veterans General Hospital, Taichung, Taiwan; and
| | - Chih-Chi Chang
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Huai-Chia Chuang
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Tse-Hua Tan
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
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18
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Abstract
INTRODUCTION Exploration in the field of epigenetics has revealed the diverse roles of the protein arginine methyltransferase (PRMT) family of proteins in multiple disease states. These findings have led to the development of specific inhibitors and discovery of several new classes of drugs with potential to treat both benign and malignant conditions. Areas covered: We provide an overview on the role of PRMT enzymes in healthy and malignant cells, highlighting the role of arginine methylation in specific pathways relevant to cancer pathogenesis. Additionally, we describe structure and catalytic activity of PRMT and discuss the mechanisms of action of novel small molecule inhibitors of specific members of the arginine methyltransferase family. Expert opinion: As the field of PRMT biology advances, it's becoming clear that this class of enzymes is highly relevant to maintaining normal physiologic processes as well and disease pathogenesis. We discuss the potential impact of PRMT inhibitors as a broad class of drugs, including the pleiotropic effects, off target effects the need for more detailed PRMT-centric interactomes, and finally, the potential for targeting this class of enzymes in clinical development of experimental therapeutics for cancer.
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Affiliation(s)
- Emily Smith
- The Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Wei Zhou
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Polina Shindiapina
- The Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Said Sif
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Chenglong Li
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Robert A. Baiocchi
- The Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
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19
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Abstract
Chromatin, primarily a complex of DNA and histone proteins, is the physiological form of the genome. Chromatin is generally repressive for transcription and other information transactions that occur on DNA. A wealth of post-translational modifications on canonical histones and histone variants encode regulatory information to recruit or repel effector proteins on chromatin, promoting and further repressing transcription and thereby form the basis of epigenetic information. During metazoan oogenesis, large quantities of histone proteins are synthesized and stored in preparation for the rapid early cell cycles of development and to elicit maternal control of chromatin assembly pathways. Oocyte and egg cell-free extracts of the frog Xenopus laevis are a compelling model system for the study of chromatin assembly and transcription, precisely because they exist in an extreme state primed for rapid chromatin assembly or for transcriptional activity. We show that chromatin assembly rates are slower in the X. laevis oocyte than in egg extracts, while conversely, only oocyte extracts transcribe template plasmids. We demonstrate that rapid chromatin assembly in egg extracts represses RNA Polymerase II dependent transcription, while pre-binding of TATA-Binding Protein (TBP) to a template plasmid promotes transcription. Our experimental evidence presented here supports a model in which chromatin assembly and transcription are in competition and that the onset of zygotic genomic activation may be in part due to stable transcriptional complex assembly.
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Affiliation(s)
- Wei-Lin Wang
- Department of Biochemistry. Albert Einstein College of Medicine, Bronx, NY, USA
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20
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Abstract
Chromatin is the complex of DNA and histone proteins that is the physiological form of the eukaryotic genome. Chromatin is generally repressive for transcription, especially so during early metazoan development when maternal factors are explicitly in control of new zygotic gene expression. In the important model organism Xenopus laevis, maturing oocytes are transcriptionally active with reduced rates of chromatin assembly, while laid eggs and fertilized embryos have robust rates of chromatin assembly and are transcriptionally repressed. As the DNA-to-cytoplasmic ratio decreases approaching the mid-blastula transition (MBT) and the onset of zygotic genome activation (ZGA), the chromatin assembly process changes with the concomitant reduction in maternal chromatin components. Chromatin assembly is mediated in part by histone chaperones that store maternal histones and release them into new zygotic chromatin. Here, we review literature on chromatin and transcription in frog embryos and cell-free extracts and highlight key insights demonstrating the roles of maternal and zygotic histone deposition and their relationship with transcriptional regulation. We explore the central historical and recent literature on the use of Xenopus embryos and the key contributions provided by experiments in cell-free oocyte and egg extracts for the interplay between histone chaperones, chromatin assembly, and transcriptional regulation. Ongoing and future studies in Xenopus cell free extracts will likely contribute essential new insights into the interplay between chromatin assembly and transcriptional regulation.
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Affiliation(s)
- Takashi Onikubo
- Department of Biochemistry. Albert Einstein College of Medicine, Bronx, NY, USA
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21
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Rengasamy M, Zhang F, Vashisht A, Song WM, Aguilo F, Sun Y, Li S, Zhang W, Zhang B, Wohlschlegel JA, Walsh MJ. The PRMT5/WDR77 complex regulates alternative splicing through ZNF326 in breast cancer. Nucleic Acids Res 2017; 45:11106-11120. [PMID: 28977470 PMCID: PMC5737218 DOI: 10.1093/nar/gkx727] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 08/11/2017] [Indexed: 12/22/2022] Open
Abstract
We observed overexpression and increased intra-nuclear accumulation of the PRMT5/WDR77 in breast cancer cell lines relative to immortalized breast epithelial cells. Utilizing mass spectrometry and biochemistry approaches we identified the Zn-finger protein ZNF326, as a novel interaction partner and substrate of the nuclear PRMT5/WDR77 complex. ZNF326 is symmetrically dimethylated at arginine 175 (R175) and this modification is lost in a PRMT5 and WDR77-dependent manner. Loss of PRMT5 or WDR77 in MDA-MB-231 cells leads to defects in alternative splicing, including inclusion of A-T rich exons in target genes, a phenomenon that has previously been observed upon loss of ZNF326. We observed that the alternatively spliced transcripts of a subset of these genes, involved in proliferation and tumor cell migration like REPIN1/AP4, ST3GAL6, TRNAU1AP and PFKM are degraded upon loss of PRMT5. In summary, we have identified a novel mechanism through which the PRMT5/WDR77 complex maintains the balance between splicing and mRNA stability through methylation of ZNF326.
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Affiliation(s)
- Madhumitha Rengasamy
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Fan Zhang
- Department of Medicine, Division of Nephrology, Bioinformatics Laboratory, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Center for Life Sciences, School of Life Sciences and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Ajay Vashisht
- Departmentof Biological Chemistry and the Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Won-Min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Francesca Aguilo
- Wallenberg Centre for Molecular Medicine, Department of Medical Biosciences, University of Umeå, Försörjningsvägen 19073, Umeå, Sweden
| | - Yifei Sun
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Mount Sinai Center for RNA Biology and Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - SiDe Li
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Mount Sinai Center for RNA Biology and Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weijia Zhang
- Department of Medicine, Division of Nephrology, Bioinformatics Laboratory, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James A Wohlschlegel
- Departmentof Biological Chemistry and the Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Martin J Walsh
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Mount Sinai Center for RNA Biology and Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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22
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Burgos ES, Walters RO, Huffman DM, Shechter D. A simplified characterization of S-adenosyl-l-methionine-consuming enzymes with 1-Step EZ-MTase: a universal and straightforward coupled-assay for in vitro and in vivo setting. Chem Sci 2017; 8:6601-6612. [PMID: 29449933 PMCID: PMC5676521 DOI: 10.1039/c7sc02830j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/25/2017] [Indexed: 01/02/2023] Open
Abstract
Methyltransferases use S-adenosyl-l-methionine (SAM) to deposit methyl marks. Many of these epigenetic 'writers' are associated with gene regulation. As cancer etiology is highly correlated with misregulated methylation patterns, methyltransferases are emerging therapeutic targets. Successful assignment of methyltransferases' roles within intricate biological networks relies on (1) the access to enzyme mechanistic insights and (2) the efficient screening of chemical probes against these targets. To characterize methyltransferases in vitro and in vivo, we report a highly-sensitive one-step deaminase-linked continuous assay where the S-adenosyl-l-homocysteine (SAH) enzyme-product is rapidly and quantitatively catabolized to S-inosyl-l-homocysteine (SIH). To highlight the broad capabilities of this assay, we established enzymatic characteristics of two protein arginine methyltransferases (PRMT5 and PRMT7), a histone-lysine N-methyltransferase (DIM-5) and a sarcosine/dimethylglycine N-methyltransferase (SDMT). Since the coupling deaminase TM0936 displays robust activity over a broad pH-range we determined the pH dependence of SDMT reaction rates. TM0936 reactions are monitored at 263 nm, so a drawback may arise when methyl acceptor substrates absorb within this UV-range. To overcome this limitation, we used an isosteric fluorescent SAM-analog: S-8-aza-adenosyl-l-methionine. Most enzymes tolerated this probe and sustained methyltransfers were efficiently monitored through loss of fluorescence at 360 nm. Unlike discontinuous radioactive- and antibody-based assays, our assay provides a simple, versatile and affordable approach towards the characterization of methyltransferases. Supported by three logs of linear dynamic range, the 1-Step EZ-MTase can detect methylation rates as low as 2 μM h-1, thus making it possible to quantify low nanomolar concentrations of glycine N-methyltransferase within crude biological samples. With Z'-factors above 0.75, this assay is well suited to high-throughput screening and may promote the identification of novel therapeutics.
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Affiliation(s)
- Emmanuel S Burgos
- Department of Biochemistry , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , USA . ; ; ; Tel: +1-718-430-4120 ; Tel: +1-718-430-4128
| | - Ryan O Walters
- Department of Molecular Pharmacology , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , USA.,Department of Medicine , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , USA.,Department of Institute for Aging Research , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , USA
| | - Derek M Huffman
- Department of Molecular Pharmacology , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , USA.,Department of Medicine , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , USA.,Department of Institute for Aging Research , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , USA
| | - David Shechter
- Department of Biochemistry , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , USA . ; ; ; Tel: +1-718-430-4120 ; Tel: +1-718-430-4128
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23
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Fulton MD, Zhang J, He M, Ho MC, Zheng YG. Intricate Effects of α-Amino and Lysine Modifications on Arginine Methylation of the N-Terminal Tail of Histone H4. Biochemistry 2017. [PMID: 28644004 DOI: 10.1021/acs.biochem.7b00450] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chemical modifications of the DNA and nucleosomal histones tightly control the gene transcription program in eukaryotic cells. The "histone code" hypothesis proposes that the frequency, combination, and location of post-translational modifications (PTMs) of the core histones compose a complex network of epigenetic regulation. Currently, there are at least 23 different types and >450 histone PTMs that have been discovered, and the PTMs of lysine and arginine residues account for a crucial part of the histone code. Although significant progress has been achieved in recent years, the molecular basis for the histone code is far from being fully understood. In this study, we investigated how naturally occurring N-terminal acetylation and PTMs of histone H4 lysine-5 (H4K5) affect arginine-3 methylation catalyzed by both type I and type II PRMTs at the biochemical level. Our studies found that acylations of H4K5 resulted in decreased levels of arginine methylation by PRMT1, PRMT3, and PRMT8. In contrast, PRMT5 exhibits an increased rate of arginine methylation upon H4K5 acetylation, propionylation, and crotonylation, but not upon H4K5 methylation, butyrylation, or 2-hydroxyisobutyrylation. Methylation of H4K5 did not affect arginine methylation by PRMT1 or PRMT5. There was a small increase in the rate of arginine methylation by PRMT8. Strikingly, a marked increase in the rate of arginine methylation was observed for PRMT3. Finally, N-terminal acetylation reduced the rate of arginine methylation by PRMT3 but had little influence on PRMT1, -5, and -8 activity. These results together highlight the underlying mechanistic differences in substrate recognition among different PRMTs and pave the way for the elucidation of the complex interplay of histone modifications.
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Affiliation(s)
- Melody D Fulton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia , Athens, Georgia 30602, United States
| | - Jing Zhang
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia , Athens, Georgia 30602, United States
| | - Maomao He
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia , Athens, Georgia 30602, United States
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia , Athens, Georgia 30602, United States
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24
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Hanley ML, Yoo TY, Sonnett M, Needleman DJ, Mitchison TJ. Chromosomal passenger complex hydrodynamics suggests chaperoning of the inactive state by nucleoplasmin/nucleophosmin. Mol Biol Cell 2017; 28:1444-1456. [PMID: 28404751 PMCID: PMC5449145 DOI: 10.1091/mbc.e16-12-0860] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/27/2017] [Accepted: 04/04/2017] [Indexed: 01/30/2023] Open
Abstract
The chromosomal passenger complex (CPC) is a conserved, essential regulator of cell division. As such, significant anti-cancer drug development efforts have been focused on targeting it, most notably by inhibiting its AURKB kinase subunit. The CPC is activated by AURKB-catalyzed autophosphorylation on multiple subunits, but how this regulates CPC interactions with other mitotic proteins remains unclear. We investigated the hydrodynamic behavior of the CPC in Xenopus laevis egg cytosol using sucrose gradient sedimentation and in HeLa cells using fluorescence correlation spectroscopy. We found that autophosphorylation of the CPC decreases its sedimentation coefficient in egg cytosol and increases its diffusion coefficient in live cells, indicating a decrease in mass. Using immunoprecipitation coupled with mass spectrometry and immunoblots, we discovered that inactive, unphosphorylated CPC interacts with nucleophosmin/nucleoplasmin proteins, which are known to oligomerize into pentamers and decamers. Autophosphorylation of the CPC causes it to dissociate from nucleophosmin/nucleoplasmin. We propose that nucleophosmin/nucleoplasmin complexes serve as chaperones that negatively regulate the CPC and/or stabilize its inactive form, preventing CPC autophosphorylation and recruitment to chromatin and microtubules in mitosis.
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Affiliation(s)
- Mariah L Hanley
- Department of Systems Biology, Harvard Medical School, Boston, MA 02114-5701.,Department of Chemistry, Harvard University, Cambridge, MA 02138-2902
| | - Tae Yeon Yoo
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138-2902
| | - Matthew Sonnett
- Department of Systems Biology, Harvard Medical School, Boston, MA 02114-5701
| | - Daniel J Needleman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138-2902.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138-2902
| | - Timothy J Mitchison
- Department of Systems Biology, Harvard Medical School, Boston, MA 02114-5701
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25
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Abstract
Brain-derived neurotrophic factor (BDNF) is required for the development of the nervous system, proper cognitive function and memory formation. While aberrant expression of BDNF has been implicated in neurological disorders, the transcriptional regulation of BDNF remains to be elucidated. In response to different stimuli, BDNF expression can be initiated from different promoters. Several studies have suggested that the expression of BDNF is regulated by promoter methylation. An emerging theme points to the possibility that histone modifications at the BDNF promoters may link to the neurological pathology. Thus, understanding the epigenetic regulation at the BDNF promoters will shed light on future therapies for neurological disorders. The present review summarizes the current knowledge of histone modifications of the BDNF gene in neuronal diseases, as well as the developmental regulation of the BDNF gene based on data from the Encyclopedia of DNA Elements (ENCODE).
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Affiliation(s)
- Kuan-Wei Chen
- Institute of Molecular Medicine and Department of Medical Science, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan.
| | - Linyi Chen
- Institute of Molecular Medicine and Department of Medical Science, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan.
- Department of Medical Science, National Tsing Hua University, Hsinchu 30013, Taiwan.
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26
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Sun J, Zhao Y, McGreal R, Cohen-Tayar Y, Rockowitz S, Wilczek C, Ashery-Padan R, Shechter D, Zheng D, Cvekl A. Pax6 associates with H3K4-specific histone methyltransferases Mll1, Mll2, and Set1a and regulates H3K4 methylation at promoters and enhancers. Epigenetics Chromatin 2016; 9:37. [PMID: 27617035 PMCID: PMC5018195 DOI: 10.1186/s13072-016-0087-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 08/31/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Pax6 is a key regulator of the entire cascade of ocular lens formation through specific binding to promoters and enhancers of batteries of target genes. The promoters and enhancers communicate with each other through DNA looping mediated by multiple protein-DNA and protein-protein interactions and are marked by specific combinations of histone posttranslational modifications (PTMs). Enhancers are distinguished from bulk chromatin by specific modifications of core histone H3, including H3K4me1 and H3K27ac, while promoters show increased H3K4me3 PTM. Previous studies have shown the presence of Pax6 in as much as 1/8 of lens-specific enhancers but a much smaller fraction of tissue-specific promoters. Although Pax6 is known to interact with EP300/p300 histone acetyltransferase responsible for generation of H3K27ac, a potential link between Pax6 and histone H3K4 methylation remains to be established. RESULTS Here we show that Pax6 co-purifies with H3K4 methyltransferase activity in lens cell nuclear extracts. Proteomic studies show that Pax6 immunoprecipitates with Set1a, Mll1, and Mll2 enzymes, and their associated proteins, i.e., Wdr5, Rbbp5, Ash2l, and Dpy30. ChIP-seq studies using chromatin prepared from mouse lens and cultured lens cells demonstrate that Pax6-bound regions are mostly enriched with H3K4me2 and H3K4me1 in enhancers and promoters, though H3K4me3 marks only Pax6-containing promoters. The shRNA-mediated knockdown of Pax6 revealed down-regulation of a set of direct target genes, including Cap2, Farp1, Pax6, Plekha1, Prox1, Tshz2, and Zfp536. Pax6 knockdown was accompanied by reduced H3K4me1 at enhancers and H3K4me3 at promoters, with little or no changes of the H3K4me2 modifications. These changes were prominent in Plekha1, a gene regulated by Pax6 in both lens and retinal pigmented epithelium. CONCLUSIONS Our study supports a general model of Pax6-mediated recruitment of histone methyltransferases Mll1 and Mll2 to lens chromatin, especially at distal enhancers. Genome-wide data in lens show that Pax6 binding correlates with H3K4me2, consistent with the idea that H3K4me2 PTMs correlate with the binding of transcription factors. Importantly, partial reduction of Pax6 induces prominent changes in local H3K4me1 and H3K4me3 modification. Together, these data open the field to mechanistic studies of Pax6, Mll1, Mll2, and H3K4me1/2/3 dynamics at distal enhancers and promoters of developmentally controlled genes.
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Affiliation(s)
- Jian Sun
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Yilin Zhao
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Rebecca McGreal
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA ; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Yamit Cohen-Tayar
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Sagol school of Neuroscience, Tel-Aviv University, Tel Aviv, 69978 Israel
| | - Shira Rockowitz
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Carola Wilczek
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Ruth Ashery-Padan
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Sagol school of Neuroscience, Tel-Aviv University, Tel Aviv, 69978 Israel
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA ; Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461 USA ; Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Ales Cvekl
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA ; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461 USA
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27
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Bunkar N, Pathak N, Lohiya NK, Mishra PK. Epigenetics: A key paradigm in reproductive health. Clin Exp Reprod Med 2016; 43:59-81. [PMID: 27358824 PMCID: PMC4925870 DOI: 10.5653/cerm.2016.43.2.59] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 02/06/2016] [Accepted: 03/16/2016] [Indexed: 12/17/2022] Open
Abstract
It is well established that there is a heritable element of susceptibility to chronic human ailments, yet there is compelling evidence that some components of such heritability are transmitted through non-genetic factors. Due to the complexity of reproductive processes, identifying the inheritance patterns of these factors is not easy. But little doubt exists that besides the genomic backbone, a range of epigenetic cues affect our genetic programme. The inter-generational transmission of epigenetic marks is believed to operate via four principal means that dramatically differ in their information content: DNA methylation, histone modifications, microRNAs and nucleosome positioning. These epigenetic signatures influence the cellular machinery through positive and negative feedback mechanisms either alone or interactively. Understanding how these mechanisms work to activate or deactivate parts of our genetic programme not only on a day-to-day basis but also over generations is an important area of reproductive health research.
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Affiliation(s)
- Neha Bunkar
- Translational Research Laboratory, School of Biological Sciences, Dr. Hari Singh Central University, Sagar, India
| | - Neelam Pathak
- Translational Research Laboratory, School of Biological Sciences, Dr. Hari Singh Central University, Sagar, India.; Reproductive Physiology Laboratory, Centre for Advanced Studies, University of Rajasthan, Jaipur, India
| | - Nirmal Kumar Lohiya
- Reproductive Physiology Laboratory, Centre for Advanced Studies, University of Rajasthan, Jaipur, India
| | - Pradyumna Kumar Mishra
- Translational Research Laboratory, School of Biological Sciences, Dr. Hari Singh Central University, Sagar, India.; Department of Molecular Biology, National Institute for Research in Environmental Health (ICMR), Bhopal, India
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28
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Chen H, Lorton B, Gupta V, Shechter D. A TGFβ-PRMT5-MEP50 axis regulates cancer cell invasion through histone H3 and H4 arginine methylation coupled transcriptional activation and repression. Oncogene 2017; 36:373-86. [PMID: 27270440 DOI: 10.1038/onc.2016.205] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 04/13/2016] [Accepted: 04/29/2016] [Indexed: 12/22/2022]
Abstract
Protein arginine methyltransferase 5 (PRMT5) complexed with MEP50/WDR77 catalyzes arginine methylation on histones and other proteins. PRMT5-MEP50 activity is elevated in cancer cells and its expression is highly correlated with poor prognosis in many human tumors. We demonstrate that PRMT5-MEP50 is essential for transcriptional regulation promoting cancer cell invasive phenotypes in lung adenocarcinoma, lung squamous cell carcinoma and breast carcinoma cancer cells. RNA-Seq transcriptome analysis demonstrated that PRMT5 and MEP50 are required to maintain expression of metastasis and Epithelial-to-mesenchymal transition (EMT) markers and to potentiate an epigenetic mechanism of the TGFβ response. We show that PRMT5-MEP50 activity both positively and negatively regulates expression of a wide range of genes. Exogenous TGFβ promotes EMT in a unique pathway of PRMT5-MEP50 catalyzed histone mono- and dimethylation of chromatin at key metastasis suppressor and EMT genes, defining a new mechanism regulating cancer invasivity. PRMT5 methylation of histone H3R2me1 induced transcriptional activation by recruitment of WDR5 and concomitant H3K4 methylation at targeted genes. In parallel, PRMT5 methylation of histone H4R3me2s suppressed transcription at distinct genomic loci. Our decoding of histone methylarginine at key genes supports a critical role for complementary PRMT5-MEP50 transcriptional activation and repression in cancer invasion pathways and in response to TGFβ stimulation and therefore and orients future chemotherapeutic opportunities.
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29
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Li G, Gao Y, Cui L, Wu L, Yang X, Chen J. Anguilla japonicalectin 1 delivery through adenovirus vector induces apoptotic cancer cell death through interaction with PRMT5. J Gene Med 2016; 18:65-74. [DOI: 10.1002/jgm.2878] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 02/20/2016] [Accepted: 03/07/2016] [Indexed: 12/22/2022] Open
Affiliation(s)
- Gongchu Li
- College of Life Sciences; Zhejiang Sci-Tech University; Hangzhou Zhejiang China
| | - Yajun Gao
- College of Life Sciences; Zhejiang Sci-Tech University; Hangzhou Zhejiang China
| | - Lianzhen Cui
- College of Life Sciences; Zhejiang Sci-Tech University; Hangzhou Zhejiang China
| | - Liqin Wu
- College of Life Sciences; Zhejiang Sci-Tech University; Hangzhou Zhejiang China
| | - Xinyan Yang
- College of Life Sciences; Zhejiang Sci-Tech University; Hangzhou Zhejiang China
| | - Jing Chen
- Institute of Life Sciences, College of Life and Environmental Sciences; Hangzhou Normal University; Hangzhou Zhejiang China
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30
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Marjon K, Cameron MJ, Quang P, Clasquin MF, Mandley E, Kunii K, McVay M, Choe S, Kernytsky A, Gross S, Konteatis Z, Murtie J, Blake ML, Travins J, Dorsch M, Biller SA, Marks KM. MTAP Deletions in Cancer Create Vulnerability to Targeting of the MAT2A/PRMT5/RIOK1 Axis. Cell Rep 2016; 15:574-587. [PMID: 27068473 DOI: 10.1016/j.celrep.2016.03.043] [Citation(s) in RCA: 233] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/08/2016] [Accepted: 03/10/2016] [Indexed: 12/31/2022] Open
Abstract
Homozygous deletions of p16/CDKN2A are prevalent in cancer, and these mutations commonly involve co-deletion of adjacent genes, including methylthioadenosine phosphorylase (MTAP). Here, we used shRNA screening and identified the metabolic enzyme, methionine adenosyltransferase II alpha (MAT2A), and the arginine methyltransferase, PRMT5, as vulnerable enzymes in cells with MTAP deletion. Metabolomic and biochemical studies revealed a mechanistic basis for this synthetic lethality. The MTAP substrate methylthioadenosine (MTA) accumulates upon MTAP loss. Biochemical profiling of a methyltransferase enzyme panel revealed that MTA is a potent and selective inhibitor of PRMT5. MTAP-deleted cells have reduced PRMT5 methylation activity and increased sensitivity to PRMT5 depletion. MAT2A produces the PRMT5 substrate S-adenosylmethionine (SAM), and MAT2A depletion reduces growth and PRMT5 methylation activity selectively in MTAP-deleted cells. Furthermore, this vulnerability extends to PRMT5 co-complex proteins such as RIOK1. Thus, the unique biochemical features of PRMT5 create an axis of targets vulnerable in CDKN2A/MTAP-deleted cancers.
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Affiliation(s)
- Katya Marjon
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | | | - Phong Quang
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | | | - Everton Mandley
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | - Kaiko Kunii
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | - Michael McVay
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | - Sung Choe
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | - Andrew Kernytsky
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | - Stefan Gross
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | - Zenon Konteatis
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | - Joshua Murtie
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | - Michelle L Blake
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | - Jeremy Travins
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | - Marion Dorsch
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | - Scott A Biller
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | - Kevin M Marks
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA.
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31
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Ratovitski T, Arbez N, Stewart JC, Chighladze E, Ross CA. PRMT5- mediated symmetric arginine dimethylation is attenuated by mutant huntingtin and is impaired in Huntington's disease (HD). Cell Cycle 2016; 14:1716-29. [PMID: 25927346 DOI: 10.1080/15384101.2015.1033595] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Abnormal protein interactions of mutant huntingtin (Htt) triggered by polyglutamine expansion are thought to mediate Huntington's disease (HD) pathogenesis. Here, we explored a functional interaction of Htt with protein arginine methyltransferase 5 (PRMT5), an enzyme mediating symmetrical dimethylation of arginine (sDMA) of key cellular proteins, including histones, and spliceosomal Sm proteins. Gene transcription and RNA splicing are impaired in HD. We demonstrated PRMT5 and Htt interaction and their co-localization in transfected neurons and in HD brain. As a result of this interaction, normal (but to a lesser extend mutant) Htt stimulated PRMT5 activity in vitro. SDMA of histones H2A and H4 was reduced in the presence of mutant Htt in primary cultured neurons and in HD brain, consistent with a demonstrated reduction in R3Me2s occupancy at the transcriptionally repressed promoters in HD brain. SDMA of another PRMT5 substrate, Cajal body marker coilin, was also reduced in the HD mouse model and in human HD brain. Finally, compensation of PRMT5 deficiency by ectopic expression of PRMT5/MEP50 complexes, or by the knock-down of H4R3Me2 demethylase JMJD6, reversed the toxic effects of mutant Htt in primary cortical neurons, suggesting that PRMT5 deficiency may mediate, at least in part, HD pathogenesis. These studies revealed a potential new mechanism for disruption of gene expression and RNA processing in HD, involving a loss of normal function of Htt in facilitation of PRMT5, supporting the idea that epigenetic regulation of gene transcription may be involved in HD and highlighting symmetric dimethylation of arginine as potential new therapeutic target.
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Key Words
- BDNF, brain-derived neurotrophic factor
- CB, Cajal body
- ChIP, the chromatin immunoprecipitation
- DMEM, Dulbecco's modified Eagle's medium
- FBS, fetal bovine serum
- HD, Huntington's disease
- HEK, human embryonic kidney
- Htt, huntingtin
- Huntington's disease mechanism
- IP, immunoprecipitation
- IgG, immunoglobulin
- PIC, protease inhibitors cocktail
- PRMT5, protein arginine methyltransferase
- RNA processing
- SMN, survival of motor neurons
- Sm proteins, spleceosomal small nuclear ribonucleoproteins
- gene transcription
- huntingtin
- neurodegeneration
- polyQ, polyglutamine
- protein interactions
- protein methylation
- sDMA, symmetrical arginine dimethylation
- snRNPs, small nuclear ribonucleoprotein particles
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Affiliation(s)
- Tamara Ratovitski
- a Division of Neurobiology; Department of Psychiatry; Johns Hopkins University School of Medicine ; CMSC 8-121; Baltimore , MD , USA
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32
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Harris DP, Chandrasekharan UM, Bandyopadhyay S, Willard B, DiCorleto PE. PRMT5-Mediated Methylation of NF-κB p65 at Arg174 Is Required for Endothelial CXCL11 Gene Induction in Response to TNF-α and IFN-γ Costimulation. PLoS One 2016; 11:e0148905. [PMID: 26901772 PMCID: PMC4768879 DOI: 10.1371/journal.pone.0148905] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 01/24/2016] [Indexed: 12/24/2022] Open
Abstract
Inflammatory agonists differentially activate gene expression of the chemokine family of proteins in endothelial cells (EC). TNF is a weak inducer of the chemokine CXCL11, while TNF and IFN-γ costimulation results in potent CXCL11 induction. The molecular mechanisms underlying TNF plus IFN-γ-mediated CXCL11 induction are not fully understood. We have previously reported that the protein arginine methyltransferase PRMT5 catalyzes symmetrical dimethylation of the NF-κB subunit p65 in EC at multiple arginine residues. Methylation of Arg30 and Arg35 on p65 is critical for TNF induction of CXCL10 in EC. Here we show that PRMT5-mediated methylation of p65 at Arg174 is required for induction of CXCL11 when EC are costimulated with TNF and IFN-γ. Knockdown of PRMT5 by RNAi reduced CXCL11 mRNA and protein levels in costimulated cells. Reconstitution of p65 Arg174Ala or Arg174Lys mutants into EC that were depleted of endogenous p65 blunted TNF plus IFN-γ-mediated CXCL11 induction. Mass spectrometric analyses showed that p65 Arg174 arginine methylation is enhanced by TNF plus IFN-γ costimulation, and is catalyzed by PRMT5. Chromatin immunoprecipitation assays (ChIP) demonstrated that PRMT5 is necessary for p65 association with the CXCL11 promoter in response to TNF plus IFN-γ. Further, reconstitution of p65 Arg174Lys mutant in EC abrogated this p65 association with the CXCL11 promoter. Finally, ChIP and Re-ChIP assays revealed that symmetrical dimethylarginine-containing proteins complexed with the CXCL11 promoter were diminished in p65 Arg174Lys-reconstituted EC stimulated with TNF and IFN-γ. In total, these results indicate that PRMT5-mediated p65 methylation at Arg174 is essential for TNF plus IFN-γ-mediated CXCL11 gene induction. We therefore suggest that the use of recently developed small molecule inhibitors of PRMT5 may present a therapeutic approach to moderating chronic inflammatory pathologies.
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Affiliation(s)
- Daniel P. Harris
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute and Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Unnikrishnan M. Chandrasekharan
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute and Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Smarajit Bandyopadhyay
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute and Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Belinda Willard
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute and Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Paul E. DiCorleto
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute and Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail:
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Sidoli S, Yuan ZF, Lin S, Karch K, Wang X, Bhanu N, Arnaudo AM, Britton LM, Cao XJ, Gonzales-Cope M, Han Y, Liu S, Molden RC, Wein S, Afjehi-Sadat L, Garcia BA. Drawbacks in the use of unconventional hydrophobic anhydrides for histone derivatization in bottom-up proteomics PTM analysis. Proteomics 2016; 15:1459-69. [PMID: 25641854 DOI: 10.1002/pmic.201400483] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/09/2015] [Indexed: 11/09/2022]
Abstract
MS-based proteomics has become the most utilized tool to characterize histone PTMs. Since histones are highly enriched in lysine and arginine residues, lysine derivatization has been developed to prevent the generation of short peptides (<6 residues) during trypsin digestion. One of the most adopted protocols applies propionic anhydride for derivatization. However, the propionyl group is not sufficiently hydrophobic to fully retain the shortest histone peptides in RP LC, and such procedure also hampers the discovery of natural propionylation events. In this work we tested 12 commercially available anhydrides, selected based on their safety and hydrophobicity. Performance was evaluated in terms of yield of the reaction, MS/MS fragmentation efficiency, and drift in retention time using the following samples: (i) a synthetic unmodified histone H3 tail, (ii) synthetic modified histone peptides, and (iii) a histone extract from cell lysate. Results highlighted that seven of the selected anhydrides increased peptide retention time as compared to propionic, and several anhydrides such as benzoic and valeric led to high MS/MS spectra quality. However, propionic anhydride derivatization still resulted, in our opinion, as the best protocol to achieve high MS sensitivity and even ionization efficiency among the analyzed peptides.
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Affiliation(s)
- Simone Sidoli
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
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Morales Y, Cáceres T, May K, Hevel JM. Biochemistry and regulation of the protein arginine methyltransferases (PRMTs). Arch Biochem Biophys 2015; 590:138-152. [PMID: 26612103 DOI: 10.1016/j.abb.2015.11.030] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/14/2015] [Accepted: 11/15/2015] [Indexed: 12/27/2022]
Abstract
Many key cellular processes can be regulated by the seemingly simple addition of one, or two, methyl groups to arginine residues by the nine known mammalian protein arginine methyltransferases (PRMTs). The impact that arginine methylation has on cellular well-being is highlighted by the ever growing evidence linking PRMT dysregulation to disease states, which has marked the PRMTs as prominent pharmacological targets. This review is meant to orient the reader with respect to the structural features of the PRMTs that account for catalytic activity, as well as provide a framework for understanding how these enzymes are regulated. An overview of what we understand about substrate recognition and binding is provided. Control of product specificity and enzyme processivity are introduced as necessary but flexible features of the PRMTs. Precise control of PRMT activity is a critical component to eukaryotic cell health, especially given that an arginine demethylase has not been identified. We therefore conclude the review with a comprehensive discussion of how protein arginine methylation is regulated.
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Affiliation(s)
- Yalemi Morales
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322, United States
| | - Tamar Cáceres
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322, United States
| | - Kyle May
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322, United States
| | - Joan M Hevel
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322, United States.
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Abstract
Organisms must be able to rapidly alter gene expression in response to changes in their nutrient environment. This review summarizes evidence that epigenetic modifications of chromatin depend on particular metabolites of intermediary metabolism, enabling the facile regulation of gene expression in tune with metabolic state. Nutritional or dietary control of chromatin is an often-overlooked, yet fundamental regulatory mechanism directly linked to human physiology. Nutrient-sensitive epigenetic marks are dynamic, suggesting rapid turnover, and may have functions beyond the regulation of gene transcription, including pH regulation and as carbon sources in cancer cells.
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Affiliation(s)
- Zhiguang Huang
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Ling Cai
- Children's Medical Center Research Institute, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Benjamin P Tu
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
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Stopa N, Krebs JE, Shechter D. The PRMT5 arginine methyltransferase: many roles in development, cancer and beyond. Cell Mol Life Sci 2015; 72:2041-59. [PMID: 25662273 PMCID: PMC4430368 DOI: 10.1007/s00018-015-1847-9] [Citation(s) in RCA: 312] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 01/10/2015] [Accepted: 01/29/2015] [Indexed: 10/24/2022]
Abstract
Post-translational arginine methylation is responsible for regulation of many biological processes. The protein arginine methyltransferase 5 (PRMT5, also known as Hsl7, Jbp1, Skb1, Capsuleen, or Dart5) is the major enzyme responsible for mono- and symmetric dimethylation of arginine. An expanding literature demonstrates its critical biological function in a wide range of cellular processes. Histone and other protein methylation by PRMT5 regulate genome organization, transcription, stem cells, primordial germ cells, differentiation, the cell cycle, and spliceosome assembly. Metazoan PRMT5 is found in complex with the WD-repeat protein MEP50 (also known as Wdr77, androgen receptor coactivator p44, or Valois). PRMT5 also directly associates with a range of other protein factors, including pICln, Menin, CoPR5 and RioK1 that may alter its subcellular localization and protein substrate selection. Protein substrate and PRMT5-MEP50 post-translation modifications induce crosstalk to regulate PRMT5 activity. Crystal structures of C. elegans PRMT5 and human and frog PRMT5-MEP50 complexes provide substantial insight into the mechanisms of substrate recognition and procession to dimethylation. Enzymological studies of PRMT5 have uncovered compelling insights essential for future development of specific PRMT5 inhibitors. In addition, newly accumulating evidence implicates PRMT5 and MEP50 expression levels and their methyltransferase activity in cancer tumorigenesis, and, significantly, as markers of poor clinical outcome, marking them as potential oncogenes. Here, we review the substantial new literature on PRMT5 and its partners to highlight the significance of understanding this essential enzyme in health and disease.
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Affiliation(s)
- Nicole Stopa
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA
| | - Jocelyn E. Krebs
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
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Onikubo T, Nicklay JJ, Xing L, Warren C, Anson B, Wang WL, Burgos ES, Ruff SE, Shabanowitz J, Cheng RH, Hunt DF, Shechter D. Developmentally Regulated Post-translational Modification of Nucleoplasmin Controls Histone Sequestration and Deposition. Cell Rep 2015; 10:1735-48. [PMID: 25772360 DOI: 10.1016/j.celrep.2015.02.038] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 01/09/2015] [Accepted: 02/13/2015] [Indexed: 11/23/2022] Open
Abstract
Nucleoplasmin (Npm) is an abundant histone chaperone in vertebrate oocytes and embryos. During embryogenesis, regulation of Npm histone binding is critical for its function in storing and releasing maternal histones to establish and maintain the zygotic epigenome. Here, we demonstrate that Xenopus laevis Npm post-translational modifications (PTMs) specific to the oocyte and egg promote either histone deposition or sequestration, respectively. Mass spectrometry and Npm phosphomimetic mutations used in chromatin assembly assays identified hyperphosphorylation on the N-terminal tail as a critical regulator for sequestration. C-terminal tail phosphorylation and PRMT5-catalyzed arginine methylation enhance nucleosome assembly by promoting histone interaction with the second acidic tract of Npm. Electron microscopy reconstructions of Npm and TTLL4 activity toward the C-terminal tail demonstrate that oocyte- and egg-specific PTMs cause Npm conformational changes. Our results reveal that PTMs regulate Npm chaperoning activity by modulating Npm conformation and Npm-histone interaction, leading to histone sequestration in the egg.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Wei TY, Hsia JY, Chiu SC, Su LJ, Juan CC, Lee YC, Chen JM, Chou HY, Huang JY, Huang HM, Yu CT. Methylosome protein 50 promotes androgen- and estrogen-independent tumorigenesis. Cell Signal 2014; 26:2940-50. [PMID: 25277535 DOI: 10.1016/j.cellsig.2014.09.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/11/2014] [Accepted: 09/23/2014] [Indexed: 11/23/2022]
Abstract
Methylosome protein 50 (MEP50) is a component of methylosome where MEP50 binds protein substrates and activates the oncogenic protein arginine methyl transferase 5 (PRMT5). MEP50 is also a coactivator for androgen receptor (AR) and estrogen receptor (ER), and transforms cells in the presence of androgen or estrogen. To extend the understanding of how MEP50 transforms cells, we investigated whether MEP50 could transform cells independent of AR and ER, and clarified whether PRMT5 could contribute to the MEP50-caused tumor formation. Microarray and Western blot analyses revealed the association of MEP50 with many human cancers including lung cancer. Knockdown of MEP50 retarded cell growth and migration in selected lung cancer cell lines, which expressed very low level of AR and ER and were insensitive to inhibitors of AR and ER. Moreover, overexpression of Myc-MEP50 enhanced cell transforming activities of 293T cells which are known lack of expression of AR and ER. Mechanistic analyses showed that MEP50 controlled G2 progression, upregulated cyclin-dependent kinase 1(CDK1)/cyclin B1, and activated the survival cascade Phosphoinositide 3-kinase (PI3K)/AKT. MEP50 promoted cell migration, and activated the cell migration pathways such as Ras-related C3 botulinum toxin substrate 1 (Rac1)/vasodilator-stimulated phosphoprotein (VASP), and forkhead box protein A2 (FOXA2)/slug/cadherin cascades. Further analyses revealed that MEP50 activated the survival factor PI3K through PRMT5-catalyzed dimethylation of PI3K. Collectively, it is concluded that MEP50 can transform cells independent of AR and ER, and PRMT5 has partial contribution to that process.
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Wang WL, Anderson LC, Nicklay JJ, Chen H, Gamble MJ, Shabanowitz J, Hunt DF, Shechter D. Phosphorylation and arginine methylation mark histone H2A prior to deposition during Xenopus laevis development. Epigenetics Chromatin 2014; 7:22. [PMID: 25302076 PMCID: PMC4191874 DOI: 10.1186/1756-8935-7-22] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 08/14/2014] [Indexed: 01/21/2023] Open
Abstract
Background Stored, soluble histones in eggs are essential for early development, in particular during the maternally controlled early cell cycles in the absence of transcription. Histone post-translational modifications (PTMs) direct and regulate chromatin-templated transactions, so understanding the nature and function of pre-deposition maternal histones is essential to deciphering mechanisms of regulation of development, chromatin assembly, and transcription. Little is known about histone H2A pre-deposition modifications nor known about the transitions that occur upon the onset of zygotic control of the cell cycle and transcription at the mid-blastula transition (MBT). Results We isolated histones from staged Xenopus laevis oocytes, eggs, embryos, and assembled pronuclei to identify changes in histone H2A modifications prior to deposition and in chromatin. Soluble and chromatin-bound histones from eggs and embryos demonstrated distinct patterns of maternal and zygotic H2A PTMs, with significant pre-deposition quantities of S1ph and R3me1, and R3me2s. We observed the first functional distinction between H2A and H4 S1 phosphorylation, as we showed that H2A and H2A.X-F (also known as H2A.X.3) serine 1 (S1) is phosphorylated concomitant with germinal vesicle breakdown (GVBD) while H4 serine 1 phosphorylation occurs post-MBT. In egg extract H2A/H4 S1 phosphorylation is independent of the cell cycle, chromatin assembly, and DNA replication. H2AS1ph is highly enriched on blastula chromatin during repression of zygotic gene expression while H4S1ph is correlated with the beginning of maternal gene expression and the lengthening of the cell cycle, consistent with distinct biological roles for H2A and H4 S1 phosphorylation. We isolated soluble H2A and H2A.X-F from the egg and chromatin-bound in pronuclei and analyzed them by mass spectrometry analysis to quantitatively determine abundances of S1ph and R3 methylation. We show that H2A and H4 S1ph, R3me1 and R3me2s are enriched on nucleosomes containing both active and repressive histone PTMs in human A549 cells and Xenopus embryos. Conclusions Significantly, we demonstrated that H2A phosphorylation and H4 arginine methylation form a new class of bona fide pre-deposition modifications in the vertebrate embryo. We show that S1ph and R3me containing chromatin domains are not correlated with H3 regulatory PTMs, suggesting a unique role for phosphorylation and arginine methylation.
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Affiliation(s)
- Wei-Lin Wang
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA
| | - Lissa C Anderson
- Department of Chemistry, Health Sciences Center, University of Virginia, Charlottesville, VA 22904, USA
| | - Joshua J Nicklay
- Department of Chemistry, Health Sciences Center, University of Virginia, Charlottesville, VA 22904, USA
| | - Hongshan Chen
- Department of Molecular Pharmacology, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA
| | - Matthew J Gamble
- Department of Molecular Pharmacology, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, Health Sciences Center, University of Virginia, Charlottesville, VA 22904, USA
| | - Donald F Hunt
- Department of Chemistry, Health Sciences Center, University of Virginia, Charlottesville, VA 22904, USA ; Department of Pathology, Health Sciences Center, University of Virginia, Charlottesville, VA 22904, USA
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Wu L, Yang X, Duan X, Cui L, Li G. Exogenous expression of marine lectins DlFBL and SpRBL induces cancer cell apoptosis possibly through PRMT5-E2F-1 pathway. Sci Rep 2014; 4:4505. [PMID: 24675921 DOI: 10.1038/srep04505] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/04/2014] [Indexed: 02/03/2023] Open
Abstract
Lectins are widely existed in marine bioresources, and some purified marine lectins were found toxic to cancer cells. In this report, genes encoding Dicentrarchus labrax fucose-binding lectin (DlFBL) and Strongylocentrotus purpuratus rhamnose-binding lectin (SpRBL) were inserted into an adenovirus vector to form Ad.FLAG-DlFBL and Ad.FLAG-SpRBL, which elicited significant in vitro suppressive effect on a variety of cancer cells. Anti-apoptosis factors Bcl-2 and XIAP were determined to be downregulated by Ad.FLAG-DlFBL and Ad.FLAG-SpRBL. Subcellular localization studies showed that DlFBL but not SpRBL widely distributed in membrane systems. Both DlFBL and SpRBL were shown associated with protein arginine methyltransferase 5 (PRMT5), and PRMT5-E2F-1 pathway was suggested to be responsible for the DlFBL and SpRBL induced apoptosis. Further investigations revealed that PRMT5 acted as a common binding target for various exogenous lectin and non-lectin proteins, suggesting a role of PRMT5 as a barrier for foreign gene invasion. The cellular response to exogenous lectins may provide insights into a novel way for cancer gene therapy.
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Ramos I, Fernández-Rivero N, Arranz R, Aloria K, Finn R, Arizmendi JM, Ausió J, Valpuesta JM, Muga A, Prado A. The intrinsically disordered distal face of nucleoplasmin recognizes distinct oligomerization states of histones. Nucleic Acids Res 2013; 42:1311-25. [PMID: 24121686 PMCID: PMC3902905 DOI: 10.1093/nar/gkt899] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The role of Nucleoplasmin (NP) as a H2A-H2B histone chaperone has been extensively characterized. To understand its putative interaction with other histone ligands, we have characterized its ability to bind H3-H4 and histone octamers. We find that the chaperone forms distinct complexes with histones, which differ in the number of molecules that build the assembly and in their spatial distribution. When complexed with H3-H4 tetramers or histone octamers, two NP pentamers form an ellipsoidal particle with the histones located at the center of the assembly, in stark contrast with the NP/H2A-H2B complex that contains up to five histone dimers bound to one chaperone pentamer. This particular assembly relies on the ability of H3-H4 to form tetramers either in solution or as part of the octamer, and it is not observed when a variant of H3 (H3C110E), unable to form stable tetramers, is used instead of the wild-type protein. Our data also suggest that the distal face of the chaperone is involved in the interaction with distinct types of histones, as supported by electron microscopy analysis of the different NP/histone complexes. The use of the same structural region to accommodate all type of histones could favor histone exchange and nucleosome dynamics.
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Affiliation(s)
- Isbaal Ramos
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del PaísVasco, P. O. Box 644, 48080 Bilbao, Spain, Unidad de Biofísica (Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea), Barrio Sarriena s/n, 48080 Leioa Spain, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain and Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
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Abstract
Formation of the germline in an embryo marks a fresh round of reproductive potential, yet the developmental stage and location within the embryo where the primordial germ cells (PGCs) form differs wildly among species. In most animals, the germline is formed either by an inherited mechanism, in which maternal provisions within the oocyte drive localized germ-cell fate once acquired in the embryo, or an inductive mechanism that involves signaling between cells that directs germ-cell fate. The inherited mechanism has been widely studied in model organisms such as Drosophila melanogaster, Caenorhabditis elegans, Xenopus laevis, and Danio rerio. Given the rapid generation time and the effective adaptation for laboratory research of these organisms, it is not coincidental that research on these organisms has led the field in elucidating mechanisms for germline specification. The inductive mechanism, however, is less well understood and is studied primarily in the mouse (Mus musculus). In this review, we compare and contrast these two fundamental mechanisms for germline determination, beginning with the key molecular determinants that play a role in the formation of germ cells across all animal taxa. We next explore the current understanding of the inductive mechanism of germ-cell determination in mice, and evaluate the hypotheses for selective pressures on these contrasting mechanisms. We then discuss the hypothesis that the transition between these determination mechanisms, which has happened many times in phylogeny, is more of a continuum than a binary change. Finally, we propose an analogy between germline determination and sex determination in vertebrates-two of the milestones of reproduction and development-in which animals use contrasting strategies to activate similar pathways.
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Affiliation(s)
- Riyad N H Seervai
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, 02192, USA
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Ho MC, Wilczek C, Bonanno JB, Xing L, Seznec J, Matsui T, Carter LG, Onikubo T, Kumar PR, Chan MK, Brenowitz M, Cheng RH, Reimer U, Almo SC, Shechter D. Structure of the arginine methyltransferase PRMT5-MEP50 reveals a mechanism for substrate specificity. PLoS One 2013; 8:e57008. [PMID: 23451136 DOI: 10.1371/journal.pone.0057008] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 01/16/2013] [Indexed: 01/07/2023] Open
Abstract
The arginine methyltransferase PRMT5-MEP50 is required for embryogenesis and is misregulated in many cancers. PRMT5 targets a wide variety of substrates, including histone proteins involved in specifying an epigenetic code. However, the mechanism by which PRMT5 utilizes MEP50 to discriminate substrates and to specifically methylate target arginines is unclear. To test a model in which MEP50 is critical for substrate recognition and orientation, we determined the crystal structure of Xenopus laevis PRMT5-MEP50 complexed with S-adenosylhomocysteine (SAH). PRMT5-MEP50 forms an unusual tetramer of heterodimers with substantial surface negative charge. MEP50 is required for PRMT5-catalyzed histone H2A and H4 methyltransferase activity and binds substrates independently. The PRMT5 catalytic site is oriented towards the cross-dimer paired MEP50. Histone peptide arrays and solution assays demonstrate that PRMT5-MEP50 activity is inhibited by substrate phosphorylation and enhanced by substrate acetylation. Electron microscopy and reconstruction showed substrate centered on MEP50. These data support a mechanism in which MEP50 binds substrate and stimulates PRMT5 activity modulated by substrate post-translational modifications.
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Abstract
Arginine methylation was discovered in the mid-1960s. About 15 years ago, the first protein arginine N-methyltransferase (PRMT) enzyme was described. The PRMT family now stands at nine members, and these enzymes play a key role in regulating a multitude of cellular events. The majority of the PRMTs have been deleted in mice, thus providing genetically tractable systems for in vivo and cell-based studies. These studies have implicated this posttranslational modification in chromatin remodeling, transcriptional regulation, RNA processing, protein/RNA trafficking, signal transduction, and DNA repair. In this chapter, we introduce different approaches that have been developed to assess protein arginine methylation levels and characterize PRMT substrates.
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Affiliation(s)
- Donghang Cheng
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas, USA.
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