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Beyer JN, Raniszewski NR, Burslem GM. Advances and Opportunities in Epigenetic Chemical Biology. Chembiochem 2020; 22:17-42. [PMID: 32786101 DOI: 10.1002/cbic.202000459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/10/2020] [Indexed: 12/13/2022]
Abstract
The study of epigenetics has greatly benefited from the development and application of various chemical biology approaches. In this review, we highlight the key targets for modulation and recent methods developed to enact such modulation. We discuss various chemical biology techniques to study DNA methylation and the post-translational modification of histones as well as their effect on gene expression. Additionally, we address the wealth of protein synthesis approaches to yield histones and nucleosomes bearing epigenetic modifications. Throughout, we highlight targets that present opportunities for the chemical biology community, as well as exciting new approaches that will provide additional insight into the roles of epigenetic marks.
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Affiliation(s)
- Jenna N Beyer
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - Nicole R Raniszewski
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - George M Burslem
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA.,Department of Cancer Biology and Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
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2
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Jbara M, Maity SK, Brik A. Examining Several Strategies for the Chemical Synthesis of Phosphorylated Histone H3 Reveals the Effectiveness of the Convergent Approach. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900257] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Muhammad Jbara
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; 3200008 Haifa Israel
| | - Suman Kumar Maity
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; 3200008 Haifa Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; 3200008 Haifa Israel
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3
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Guidotti N, Lechner CC, Bachmann AL, Fierz B. A Modular Ligation Strategy for Asymmetric Bivalent Nucleosomes Trimethylated at K36 and K27. Chembiochem 2019; 20:1124-1128. [PMID: 30615245 DOI: 10.1002/cbic.201800744] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 12/19/2022]
Abstract
In nature, individual histones in the same nucleosome can carry identical (symmetric) or different (asymmetric) post-translational modification (PTM) patterns, increasing the combinatorial complexity. Embryonic stem cells exhibit "bivalent" nucleosomes, some of which are marked by an asymmetric arrangement of H3K36me3 (an activating PTM) and H3K27me3 (a repressive PTM). Here we describe a modular synthetic method to access such asymmetrically modified nucleosomes and show that H3K36me3 inhibits the activity of the methyltransferase PRC2 locally while still prolonging its chromatin binding time.
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Affiliation(s)
- Nora Guidotti
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 6, CH B3 485, 1015, Lausanne, Switzerland
| | - Carolin C Lechner
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 6, CH B3 485, 1015, Lausanne, Switzerland.,Present address: Bachem AG, Hauptstrasse 144, 4416, Bubendorf, Switzerland
| | - Andreas L Bachmann
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 6, CH B3 485, 1015, Lausanne, Switzerland
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 6, CH B3 485, 1015, Lausanne, Switzerland
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4
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Lang K. Building Peptide Bonds in Haifa: The Seventh Chemical Protein Synthesis (CPS) Meeting. Chembiochem 2018; 19:115-120. [PMID: 29251813 DOI: 10.1002/cbic.201700606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Indexed: 01/24/2023]
Abstract
The power of CPS, live! More than 90 attendees from around the world came together in Haifa to present and hear about cutting-edge science in protein chemistry, from advances in synthetic methods to applications in biology and medicine. The meeting was a powerful demonstration that chemical protein synthesis can provide otherwise unattainable insights into protein structure and function.
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Affiliation(s)
- Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstrasse 4, 85748, Garching, Germany
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5
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Probst D, Heitz M, Poirier M, Gan BH, Delalande C, Reymond JL. Frontiers in Medicinal Chemistry 2017 in Bern, Switzerland. ChemMedChem 2017; 12:1645-1651. [PMID: 28941184 DOI: 10.1002/cmdc.201700306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Indexed: 11/06/2022]
Abstract
Sharing capital ideas: The 2017 Frontiers in Medicinal Chemistry (FiMC) conference, organized jointly by the German Chemical Society, the German Pharmaceutical Society, and the Swiss Chemical Society, was held at the Department of Chemistry and Biochemistry of the University of Bern in February 2017. Herein we summarize the many conference highlights, and look forward to the next FiMC meeting, to be held in Jena (Germany) in March 2018.
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Affiliation(s)
- Daniel Probst
- Universität Bern, Departement für Chemie und Biochemie, Freiestrasse 3, Bern, 3012, Switzerland
| | - Marc Heitz
- Universität Bern, Departement für Chemie und Biochemie, Freiestrasse 3, Bern, 3012, Switzerland
| | - Marion Poirier
- Universität Bern, Departement für Chemie und Biochemie, Freiestrasse 3, Bern, 3012, Switzerland
| | - Bee Ha Gan
- Universität Bern, Departement für Chemie und Biochemie, Freiestrasse 3, Bern, 3012, Switzerland
| | - Clémence Delalande
- Universität Bern, Departement für Chemie und Biochemie, Freiestrasse 3, Bern, 3012, Switzerland
| | - Jean-Louis Reymond
- Universität Bern, Departement für Chemie und Biochemie, Freiestrasse 3, Bern, 3012, Switzerland
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6
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Jbara M, Maity SK, Brik A. Palladium in der chemischen Synthese und Modifizierung von Proteinen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702370] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Muhammad Jbara
- Schulich Faculty of Chemie; Technion - Israel Institute of Technology; Haifa 3200008 Israel
| | - Suman Kumar Maity
- Schulich Faculty of Chemie; Technion - Israel Institute of Technology; Haifa 3200008 Israel
| | - Ashraf Brik
- Schulich Faculty of Chemie; Technion - Israel Institute of Technology; Haifa 3200008 Israel
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7
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Jbara M, Maity SK, Brik A. Palladium in the Chemical Synthesis and Modification of Proteins. Angew Chem Int Ed Engl 2017; 56:10644-10655. [DOI: 10.1002/anie.201702370] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Indexed: 01/24/2023]
Affiliation(s)
- Muhammad Jbara
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
| | - Suman Kumar Maity
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
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8
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Virdee S. 2016 EMBO Chemical Biology Conference. Chembiochem 2016; 18:66-71. [PMID: 27862792 DOI: 10.1002/cbic.201600597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Indexed: 11/07/2022]
Abstract
The full breadth of the field: The 2016 EMBO Chemical Biology Conference, covering topics from tool development to biological applications and from computational drug design to synthetic chemistry, took place in Heidelberg from 31st August to 3rd September.
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Affiliation(s)
- Satpal Virdee
- University of Dundee, MRC Protein Phosphorylation and Ubiquitylation Unit, Dow Street, Dundee, DD1 5EH, UK
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9
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Liokatis S, Klingberg R, Tan S, Schwarzer D. Differentially Isotope-Labeled Nucleosomes To Study Asymmetric Histone Modification Crosstalk by Time-Resolved NMR Spectroscopy. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Stamatios Liokatis
- Department of Structural Biology; Leibniz-Institut für Molekulare Pharmakologie; Robert-Rössle-Strasse 10 13125 Berlin Germany
| | - Rebecca Klingberg
- Department of Chemical Biology; Leibniz-Institut für Molekulare Pharmakologie; Robert-Rössle-Strasse 10 13125 Berlin Germany
| | - Song Tan
- Department of Biochemistry and Molecular Biology; The Pennsylvania State University; University Park PA 16802-1014 USA
| | - Dirk Schwarzer
- Department of Chemical Biology; Leibniz-Institut für Molekulare Pharmakologie; Robert-Rössle-Strasse 10 13125 Berlin Germany
- Chemische Biologie, Interfakultäres Institut für Biochemie; Universität Tübingen; Hoppe-Seyler-Strasse 4 72076 Tübingen Germany
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10
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Liokatis S, Klingberg R, Tan S, Schwarzer D. Differentially Isotope-Labeled Nucleosomes To Study Asymmetric Histone Modification Crosstalk by Time-Resolved NMR Spectroscopy. Angew Chem Int Ed Engl 2016; 55:8262-5. [PMID: 27219518 DOI: 10.1002/anie.201601938] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Indexed: 01/09/2023]
Abstract
Post-translational modifications (PTMs) of histones regulate chromatin structure and function. Because nucleosomes contain two copies each of the four core histones, the establishment of different PTMs on individual "sister" histones in the same nucleosomal context, that is, asymmetric histone PTMs, are difficult to analyze. Here, we generated differentially isotope-labeled nucleosomes to study asymmetric histone modification crosstalk by time-resolved NMR spectroscopy. Specifically, we present mechanistic insights into nucleosomal histone H3 modification reactions in cis and in trans, that is, within individual H3 copies or between them. We validated our approach by using the H3S10phK14ac crosstalk mechanism, which is mediated by the Gcn5 acetyltransferase. Moreover, phosphorylation assays on methylated substrates showed that, under certain conditions, Haspin kinase is able to produce nucleosomes decorated asymmetrically with two distinct types of PTMs.
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Affiliation(s)
- Stamatios Liokatis
- Department of Structural Biology, Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125, Berlin, Germany.
| | - Rebecca Klingberg
- Department of Chemical Biology, Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Song Tan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802-1014, USA
| | - Dirk Schwarzer
- Department of Chemical Biology, Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125, Berlin, Germany.,Chemische Biologie, Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Strasse 4, 72076, Tübingen, Germany
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