51
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Maity SK, Jbara M, Brik A. Chemical and semisynthesis of modified histones. J Pept Sci 2016; 22:252-9. [DOI: 10.1002/psc.2848] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 12/06/2015] [Accepted: 12/07/2015] [Indexed: 01/09/2023]
Affiliation(s)
- Suman Kumar Maity
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
| | - Muhammad Jbara
- 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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52
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Vlaming H, van Leeuwen F. The upstreams and downstreams of H3K79 methylation by DOT1L. Chromosoma 2016; 125:593-605. [PMID: 26728620 DOI: 10.1007/s00412-015-0570-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/16/2015] [Accepted: 12/21/2015] [Indexed: 12/14/2022]
Abstract
Histone modifications regulate key processes of eukaryotic genomes. Misregulation of the enzymes that place these modifications can lead to disease. An example of this is DOT1L, the enzyme that can mono-, di-, and trimethylate the nucleosome core on lysine 79 of histone H3 (H3K79). DOT1L plays a role in development and its misregulation has been implicated in several cancers, most notably leukemias caused by a rearrangement of the MLL gene. A DOT1L inhibitor is in clinical trials for these leukemias and shows promising results, yet we are only beginning to understand DOT1L's function and regulation in the cell. Here, we review what happens upstream and downstream of H3K79 methylation. H3K79 methylation levels are highest in transcribed genes, where H2B ubiquitination can promote DOT1L activity. In addition, DOT1L can be targeted to transcribed regions of the genome by several of its interaction partners. Although methylation levels strongly correlate with transcription, the mechanistic link between the two is unclear and probably context-dependent. Methylation of H3K79 may act through recruiting or repelling effector proteins, but we do not yet know which effectors mediate DOT1L's functions. Understanding DOT1L biology better will help us to understand the effects of DOT1L inhibitors and may allow the development of alternative strategies to target the DOT1L pathway.
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Affiliation(s)
- Hanneke Vlaming
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands.
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53
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Bi X, Yang R, Feng X, Rhodes D, Liu CF. Semisynthetic UbH2A reveals different activities of deubiquitinases and inhibitory effects of H2A K119 ubiquitination on H3K36 methylation in mononucleosomes. Org Biomol Chem 2015; 14:835-9. [PMID: 26615908 DOI: 10.1039/c5ob02323h] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using a genetically incorporated azidonorleucine for ubiquitin installation, we prepared multi-milligram quantities of H2AK119ub (ubH2A). With a native isopeptide linkage, the synthetic ubH2A was used to study the activity of deubiquitinases and crosstalk between H2A ubiquitination and H3K36 methylation in the context of chemically defined mononucleosomes.
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Affiliation(s)
- Xiaobao Bi
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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54
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Howard CJ, Yu RR, Gardner ML, Shimko JC, Ottesen JJ. Chemical and biological tools for the preparation of modified histone proteins. Top Curr Chem (Cham) 2015; 363:193-226. [PMID: 25863817 DOI: 10.1007/128_2015_629] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Eukaryotic chromatin is a complex and dynamic system in which the DNA double helix is organized and protected by interactions with histone proteins. This system is regulated through a large network of dynamic post-translational modifications (PTMs) which ensure proper gene transcription, DNA repair, and other processes involving DNA. Homogenous protein samples with precisely characterized modification sites are necessary to understand better the functions of modified histone proteins. Here, we discuss sets of chemical and biological tools developed for the preparation of modified histones, with a focus on the appropriate choice of tool for a given target. We start with genetic approaches for the creation of modified histones, including the incorporation of genetic mimics of histone modifications, chemical installation of modification analogs, and the use of the expanded genetic code to incorporate modified amino acids. We also cover the chemical ligation techniques which have been invaluable in the generation of complex modified histones indistinguishable from their natural counterparts. We end with a prospectus on future directions.
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Affiliation(s)
- Cecil J Howard
- Department of Chemistry and Biochemistry and The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, 43210, USA
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55
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Identification of a functional hotspot on ubiquitin required for stimulation of methyltransferase activity on chromatin. Proc Natl Acad Sci U S A 2015; 112:10365-70. [PMID: 26240340 DOI: 10.1073/pnas.1504483112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ubiquitylation of histone H2B at lysine 120 (H2B-Ub) plays a critical role in transcriptional elongation, chromatin conformation, as well as the regulation of specific histone H3 methylations. Herein, we report a strategy for the site-specific chemical attachment of ubiquitin to preassembled nucleosomes. This allowed expedited structure-activity studies into how H2B-Ub regulates H3K79 methylation by the methyltransferase human Dot1. Through an alanine scan of the ubiquitin surface, we identified a functional hotspot on ubiquitin that is required for the stimulation of human Dot1 in vitro. Importantly, this result was validated in chromatin from isolated nuclei by using a synthetic biology strategy that allowed selective incorporation of the hotspot-deficient ubiquitin mutant into H2B. The ubiquitin hotspot additionally impacted the regulation of ySet1-mediated H3K4 methylation but was not required for H2B-Ub-induced impairment of chromatin fiber compaction. These data demonstrate the utility of applying chemical ligation technologies to preassembled chromatin and delineate the multifunctionality of ubiquitin as a histone posttranslational modification.
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56
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Stulemeijer IJE, De Vos D, van Harten K, Joshi OK, Blomberg O, van Welsem T, Terweij M, Vlaming H, de Graaf EL, Altelaar AFM, Bakker BM, van Leeuwen F. Dot1 histone methyltransferases share a distributive mechanism but have highly diverged catalytic properties. Sci Rep 2015; 5:9824. [PMID: 25965993 PMCID: PMC4650758 DOI: 10.1038/srep09824] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 03/19/2015] [Indexed: 11/17/2022] Open
Abstract
The conserved histone methyltransferase Dot1 establishes an H3K79 methylation pattern
consisting of mono-, di- and trimethylation states on histone H3 via a distributive
mechanism. This mechanism has been shown to be important for the regulation of the
different H3K79 methylation states in yeast. Dot1 enzymes in yeast, Trypanosoma
brucei (TbDot1A and TbDot1B, which methylate H3K76) and human (hDot1L)
generate very divergent methylation patterns. To understand how these
species-specific methylation patterns are generated, the methylation output of the
Dot1 enzymes was compared by expressing them in yeast at various expression levels.
Computational simulations based on these data showed that the Dot1 enzymes have
highly distinct catalytic properties, but share a distributive mechanism. The
mechanism of methylation and the distinct rate constants have implications for the
regulation of H3K79/K76 methylation. A mathematical model of H3K76 methylation
during the trypanosome cell cycle suggests that temporally-regulated consecutive
action of TbDot1A and TbDot1B is required for the observed regulation of H3K76
methylation states.
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Affiliation(s)
- Iris J E Stulemeijer
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Dirk De Vos
- Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - Kirsten van Harten
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Onkar K Joshi
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Olga Blomberg
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Marit Terweij
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Hanneke Vlaming
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Erik L de Graaf
- Biomolecular Mass Spectrometry and Proteomics Group, The Netherlands Proteomics Centre, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - A F Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics Group, The Netherlands Proteomics Centre, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Barbara M Bakker
- Department of Pediatrics, Systems Biology Centre for Energy Metabolism and Ageing, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen, 9713 GZ, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
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57
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Yang R, Bi X, Li F, Cao Y, Liu CF. Native chemical ubiquitination using a genetically incorporated azidonorleucine. Chem Commun (Camb) 2015; 50:7971-4. [PMID: 24915456 DOI: 10.1039/c4cc03721a] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A robust chemical ubiquitination method was developed. The method employed a genetically incorporated azidonorleucine as an orthogonal lysine precursor for the installation of a Gly residue bearing an Nα-auxiliary which mediated the ligation between ubiquitin(1-75)-thioester and the target protein. To demonstrate our methodology, a model protein, K48-linked diubiquitin, was synthesized with an overall yield of 35%.
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Affiliation(s)
- Renliang Yang
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.
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58
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Chemical tagging and customizing of cellular chromatin states using ultrafast trans-splicing inteins. Nat Chem 2015; 7:394-402. [PMID: 25901817 PMCID: PMC4617616 DOI: 10.1038/nchem.2224] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 02/27/2015] [Indexed: 12/12/2022]
Abstract
Post-translational modification of the histone proteins in chromatin plays a central role in epigenetic control of DNA-templated processes in eukaryotic cells. Developing methods that enable the structure of histones to be manipulated is therefore essential to understand the biochemical mechanisms underlying genomic regulation. Here we present a synthetic biology method to engineer histones bearing site-specific modifications on cellular chromatin using protein trans-splicing. We genetically fused the N-terminal fragment of ultrafast split-intein to the C-terminus of histone H2B, which upon reaction with a complementary synthetic C-intein, generated labeled histone. Using this approach, we incorporated various non-native chemical modifications to chromatin in vivo with temporal control. Furthermore, the time and concentration dependence of protein trans-splicing performed in nucleo enabled us to examine differences in the accessibility of the euchromatin and heterochromatin regions of the epigenome. Finally, we used protein trans-splicing to semi-synthesize a native histone modification, H2BK120 ubiquitination, in isolated nuclei, and show that this can trigger downstream epigenetic cross-talk of H3K79 methylation.
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59
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Affiliation(s)
- Manuel M. Müller
- Department of Chemistry, Princeton University,
Frick Laboratory, Princeton, New Jersey 08544, United States
| | - Tom W. Muir
- Department of Chemistry, Princeton University,
Frick Laboratory, Princeton, New Jersey 08544, United States
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60
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Yi JS, Federation AJ, Qi J, Dhe-Paganon S, Hadler M, Xu X, St. Pierre R, Varca AC, Wu L, Marineau JJ, Smith WB, Souza A, Chory EJ, Armstrong SA, Bradner JE. Structure-guided DOT1L probe optimization by label-free ligand displacement. ACS Chem Biol 2015; 10:667-74. [PMID: 25397901 PMCID: PMC4504433 DOI: 10.1021/cb500796d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
The
DOT1L lysine methyltransferase has emerged as a validated therapeutic
target in MLL-rearranged (MLLr) acute leukemias.
Although S-adenosylmethionine competitive inhibitors have demonstrated
pharmacological proof-of-principle in MLLr-leukemia,
these compounds require further optimization to improve cellular potency
and pharmacokinetic stability. Limiting DOT1L inhibitor discovery
and ligand optimization have been complex biochemical methods often
using radionucleotides and cellular methods requiring prolonged culture.
We therefore developed a new suite of assay technologies that allows
comparative assessment of chemical tools for DOT1L in a miniaturized
format. Coupling these assays with structural information, we developed
new insights into DOT1L ligand binding and identified several functionalized
probes with increased cellular potency (IC50 values ∼10
nM) and excellent selectivity for DOT1L. Together these assay technologies
define a platform capability for discovery and optimization of small-molecule
DOT1L inhibitors.
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Affiliation(s)
- Joanna S. Yi
- Department
of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States
- Department
of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States
- Department
of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States
| | - Alexander J. Federation
- Department
of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States
| | - Jun Qi
- Department
of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States
| | - Sirano Dhe-Paganon
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States
| | - Michael Hadler
- Human
Oncology and Pathogenesis Program, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Xiang Xu
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States
| | - Roodolph St. Pierre
- Department
of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States
| | - Anthony C. Varca
- Department
of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States
| | - Lei Wu
- Shanghai ChemPartner Co. Ltd., 998 Hailei Road, Zhangjiang Hi-Tech Park, Pudong
New Area, Shanghai, 201203, China
| | - Jason J. Marineau
- Department
of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States
| | - William B. Smith
- Department
of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States
| | - Amanda Souza
- Department
of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States
| | - Emma J. Chory
- Department
of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States
| | - Scott A. Armstrong
- Human
Oncology and Pathogenesis Program, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - James E. Bradner
- Department
of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts, United States
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61
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Holt M, Muir T. Application of the protein semisynthesis strategy to the generation of modified chromatin. Annu Rev Biochem 2015; 84:265-90. [PMID: 25784050 DOI: 10.1146/annurev-biochem-060614-034429] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Histone proteins are subject to a host of posttranslational modifications (PTMs) that modulate chromatin structure and function. Such control is achieved by the direct alteration of the intrinsic physical properties of the chromatin fiber or by regulating the recruitment and activity of a host of trans-acting nuclear factors. The sheer number of histone PTMs presents a formidable barrier to understanding the molecular mechanisms at the heart of epigenetic regulation of eukaryotic genomes. One aspect of this multifarious problem, namely how to access homogeneously modified chromatin for biochemical studies, is well suited to the sensibilities of the organic chemist. Indeed, recent years have witnessed a critical role for synthetic protein chemistry methods in generating the raw materials needed for studying how histone PTMs regulate chromatin biochemistry. This review focuses on what is arguably the most powerful, and widely employed, of these chemical strategies, namely histone semisynthesis via the chemical ligation of peptide fragments.
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Affiliation(s)
- Matthew Holt
- Department of Chemistry, Frick Laboratory, Princeton University, Princeton, New Jersey 08544; ,
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62
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Wang JX, Fang GM, He Y, Qu DL, Yu M, Hong ZY, Liu L. Peptideo-Aminoanilides as Crypto-Thioesters for Protein Chemical Synthesis. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408078] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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63
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Wang JX, Fang GM, He Y, Qu DL, Yu M, Hong ZY, Liu L. Peptideo-Aminoanilides as Crypto-Thioesters for Protein Chemical Synthesis. Angew Chem Int Ed Engl 2014; 54:2194-8. [DOI: 10.1002/anie.201408078] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/18/2014] [Indexed: 12/29/2022]
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64
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Swalm BM, Knutson SK, Warholic NM, Jin L, Kuntz KW, Keilhack H, Smith JJ, Pollock RM, Moyer MP, Scott MP, Copeland RA, Wigle TJ. Reaction coupling between wild-type and disease-associated mutant EZH2. ACS Chem Biol 2014; 9:2459-64. [PMID: 25154026 DOI: 10.1021/cb500548b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
EZH2 and EZH1 are protein methyltransferases (PMTs) responsible for histone H3, lysine 27 (H3K27) methylation. Trimethylation of H3K27 (H3K27me3) is a hallmark of many cancers, including non-Hodgkin lymphoma (NHL). Heterozygous EZH2 point mutations at Tyr641, Ala677, and Ala687 have been observed in NHL. The Tyr641 mutations enhance activity on H3K27me2 but have weak or no activity on unmethylated H3K27, whereas the Ala677 and Ala687 mutations use substrates of all methylation states effectively. It has been proposed that enzymatic coupling of the wild-type and mutant enzymes leads to the oncogenic H3K27me3 mark in mutant-bearing NHL. We show that coupling with the wild-type enzyme is needed to achieve H3K27me3 for several mutants, but that others are capable of achieving H3K27me3 on their own. All forms of PRC2 (wild-type and mutants) display kinetic signatures that are consistent with a distributive mechanism of catalysis.
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Affiliation(s)
- Brooke M. Swalm
- Epizyme, Inc. 400 Technology Square,
Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Sarah K. Knutson
- Epizyme, Inc. 400 Technology Square,
Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Natalie M. Warholic
- Epizyme, Inc. 400 Technology Square,
Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Lei Jin
- Epizyme, Inc. 400 Technology Square,
Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Kevin W. Kuntz
- Epizyme, Inc. 400 Technology Square,
Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Heike Keilhack
- Epizyme, Inc. 400 Technology Square,
Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Jesse J. Smith
- Epizyme, Inc. 400 Technology Square,
Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Roy M. Pollock
- Epizyme, Inc. 400 Technology Square,
Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Mikel P. Moyer
- Epizyme, Inc. 400 Technology Square,
Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Margaret Porter Scott
- Epizyme, Inc. 400 Technology Square,
Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Robert A. Copeland
- Epizyme, Inc. 400 Technology Square,
Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Tim J. Wigle
- Epizyme, Inc. 400 Technology Square,
Fourth Floor, Cambridge, Massachusetts 02139, United States
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65
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Torres-Kolbus J, Chou C, Liu J, Deiters A. Synthesis of non-linear protein dimers through a genetically encoded Thiol-ene reaction. PLoS One 2014; 9:e105467. [PMID: 25181502 PMCID: PMC4152134 DOI: 10.1371/journal.pone.0105467] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/21/2014] [Indexed: 11/19/2022] Open
Abstract
Site-specific incorporation of bioorthogonal unnatural amino acids into proteins provides a useful tool for the installation of specific functionalities that will allow for the labeling of proteins with virtually any probe. We demonstrate the genetic encoding of a set of alkene lysines using the orthogonal PylRS/PylTCUA pair in Escherichia coli. The installed double bond functionality was then applied in a photoinitiated thiol-ene reaction of the protein with a fluorescent thiol-bearing probe, as well as a cysteine residue of a second protein, showing the applicability of this approach in the formation of heterogeneous non-linear fused proteins.
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Affiliation(s)
- Jessica Torres-Kolbus
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Chungjung Chou
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Jihe Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alexander Deiters
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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66
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Nguyen UTT, Bittova L, Müller MM, Fierz B, David Y, Houck-Loomis B, Feng V, Dann GP, Muir TW. Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Nat Methods 2014; 11:834-40. [PMID: 24997861 PMCID: PMC4130351 DOI: 10.1038/nmeth.3022] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 06/01/2014] [Indexed: 12/11/2022]
Abstract
Elucidating the molecular details of how chromatin-associated factors deposit, remove and recognize histone post-translational modification (PTM) signatures remains a daunting task in the epigenetics field. We introduce a versatile platform that greatly accelerates biochemical investigations into chromatin recognition and signaling. This technology is based on the streamlined semisynthesis of DNA-barcoded nucleosome libraries with distinct combinations of PTMs. Chromatin immunoprecipitation of these libraries, once they have been treated with purified chromatin effectors or the combined chromatin recognizing and modifying activities of the nuclear proteome, is followed by multiplexed DNA-barcode sequencing. This ultrasensitive workflow allowed us to collect thousands of biochemical data points revealing the binding preferences of various nuclear factors for PTM patterns and how preexisting PTMs, alone or synergistically, affect further PTM deposition via cross-talk mechanisms. We anticipate that the high throughput and sensitivity of the technology will help accelerate the decryption of the diverse molecular controls that operate at the level of chromatin.
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Affiliation(s)
- Uyen T. T. Nguyen
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
| | - Lenka Bittova
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
| | - Manuel M. Müller
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
| | - Beat Fierz
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
| | - Yael David
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
| | - Brian Houck-Loomis
- The Rockefeller University, New York, NY 10065, United States; current address: New York Genome Center, New York, NY 10013, United States
| | - Vanessa Feng
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
| | - Geoffrey P. Dann
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
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67
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The challenge of producing ubiquitinated proteins for structural studies. Cells 2014; 3:639-56. [PMID: 24926903 PMCID: PMC4092866 DOI: 10.3390/cells3020639] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 12/14/2022] Open
Abstract
Protein ubiquitination is an important post-translational modification involved in several essential signalling pathways. It has different effects on the target protein substrate, i.e., it can trigger the degradation of the protein in the proteasome, change the interactions of the modified protein with its partners, or affect its localization and activity. In order to understand the molecular mechanisms underlying the consequences of protein ubiquitination, scientists have to face the challenging task of producing ubiquitinated proteins for structural characterization with X-ray crystallography and/or nuclear magnetic resonance (NMR) spectroscopy. These techniques require milligrams of homogeneous samples of high purity. The strategies proposed so far for the production of ubiquitinated proteins can be divided into two groups, i.e., chemical (or non-enzymatic) and enzymatic methodologies. In this review, we summarize the still very sparse examples available in the literature that describe successful production of ubiquitinated proteins amenable for biochemical and structural studies, and discuss advantages and disadvantages of the techniques proposed. We also give a perspective of the direction in which the field might evolve.
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68
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Pick H, Kilic S, Fierz B. Engineering chromatin states: chemical and synthetic biology approaches to investigate histone modification function. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:644-56. [PMID: 24768924 DOI: 10.1016/j.bbagrm.2014.04.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/26/2014] [Accepted: 04/16/2014] [Indexed: 01/11/2023]
Abstract
Patterns of histone post-translational modifications (PTMs) and DNA modifications establish a landscape of chromatin states with regulatory impact on gene expression, cell differentiation and development. These diverse modifications are read out by effector protein complexes, which ultimately determine their functional outcome by modulating the activity state of underlying genes. From genome-wide studies employing high-throughput ChIP-Seq methods as well as proteomic mass spectrometry studies, a large number of PTMs are known and their coexistence patterns and associations with genomic regions have been mapped in a large number of different cell types. Conversely, the molecular interplay between chromatin effector proteins and modified chromatin regions as well as their resulting biological output is less well understood on a molecular level. Within the last decade a host of chemical approaches has been developed with the goal to produce synthetic chromatin with a defined arrangement of PTMs. These methods now permit systematic functional studies of individual histone and DNA modifications, and additionally provide a discovery platform to identify further interacting nuclear proteins. Complementary chemical- and synthetic-biology methods have emerged to directly observe and modulate the modification landscape in living cells and to readily probe the effect of altered PTM patterns on biological processes. Herein, we review current methodologies allowing chemical and synthetic biological engineering of distinct chromatin states in vitro and in vivo with the aim of obtaining a molecular understanding of histone and DNA modification function. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
- Horst Pick
- Fondation Sandoz Chair in Biophysical Chemistry of Macromolecules, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Sinan Kilic
- Fondation Sandoz Chair in Biophysical Chemistry of Macromolecules, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Beat Fierz
- Fondation Sandoz Chair in Biophysical Chemistry of Macromolecules, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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69
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Fierz B. Synthetic chromatin approaches to probe the writing and erasing of histone modifications. ChemMedChem 2014; 9:495-504. [PMID: 24497444 DOI: 10.1002/cmdc.201300487] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/18/2014] [Indexed: 11/11/2022]
Abstract
Posttranslational modifications (PTMs) of chromatin are involved in gene regulation, thereby contributing to cell differentiation, lineage determination, and organism development. Discrete chromatin states are established by the action of a large set of enzymes that catalyze the deposition, propagation, and removal of histone PTMs, thereby modulating gene expression. Given their central role in determining and maintaining cellular phenotype, as well as in controlling chromatin processes such as DNA repair, the dysregulation of these enzymes can have serious consequences, and can result in cancer and neurodegenerative diseases. Thus, such chromatin regulator proteins are promising drug targets. However, they are often present in large, modular protein complexes that specifically recognize target chromatin regions and exhibit intricate regulation through preexisting histone marks. This renders the study of their enzymatic mechanisms complex. Recent developments in the chemical production of defined chromatin substrates show great promise for improving our understanding of the activity of chromatin regulator complexes at the molecular level. Herein I discuss examples highlighting the application of synthetic chromatin to study the enzymatic mechanisms and regulatory pathways of these crucial protein complexes in detail, with potential implications for assay development in pharmacological research.
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Affiliation(s)
- Beat Fierz
- Fondation Sandoz Chair in Biophysical Chemistry of Macromolecules, École Polytechnique Fédérale de Lausanne, 1015 Lausanne (Switzerland)
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70
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Boll E, Drobecq H, Ollivier N, Raibaut L, Desmet R, Vicogne J, Melnyk O. A novel PEG-based solid support enables the synthesis of >50 amino-acid peptide thioesters and the total synthesis of a functional SUMO-1 peptide conjugate. Chem Sci 2014. [DOI: 10.1039/c3sc53509f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Bis(2-sulfanylethyl)amino PEG resin gives access to large peptide thioester segments and to functional SUMO-1 conjugates.
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Affiliation(s)
- Emmanuelle Boll
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
| | - Hervé Drobecq
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
| | - Nathalie Ollivier
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
| | - Laurent Raibaut
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
| | - Rémi Desmet
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
| | - Jérome Vicogne
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
| | - Oleg Melnyk
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
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71
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Abstract
In eukaryotic cells, many proteins undergo extensive post-translational modifications (PTMs) such as methylation, acetylation, phosphorylation, glycosylation, and ubiquitination. Among these, ubiquitination is a particularly interesting PTM from both structural and functional viewpoints. In ubiquitination, the C-terminal carboxyl group of the small ubiquitin protein is attached to the ε-amine of a lysine residue of a substrate protein through an isopeptide bond. Ubiquitination has been shown to be involved in the regulation of many cellular processes including protein degradation and gene expression. And dysfunction of these processes is implicated in many human diseases. Despite many years of intensive research, a large number of protein ubquitination events remain poorly characterized. The challenge lies with the tremendous difficulties in isolating homogeneously modified proteins from biological samples for structural and functional studies. Enzymatic ubiquitination in vitro often has limited practical value due to the large number of substrate-specific E3 ligases and the difficulties in identifying or isolating these enzymes. Chemical approaches to the preparation of ubiquitinated proteins provide a powerful solution, and the development of such approaches has been the subject of intense research by many research laboratories. This review summarizes the methodological developments of protein chemical ubiquitination in recent years.
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Affiliation(s)
- Renliang Yang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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72
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Li YT, Liang J, Li JB, Fang GM, Huang Y, Liu L. New semi-synthesis of ubiquitin C-terminal conjugate with 7-amino-4-methylcoumarin. J Pept Sci 2013; 20:102-7. [DOI: 10.1002/psc.2568] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 08/27/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Yi-Tong Li
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology; Peking University, Shenzhen Graduate School; Shenzhen 518055 China
- Tsinghua-Peking Center for Life Sciences, Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Jun Liang
- Tsinghua-Peking Center for Life Sciences, Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Jia-Bin Li
- Tsinghua-Peking Center for Life Sciences, Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Ge-Min Fang
- Tsinghua-Peking Center for Life Sciences, Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Yong Huang
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology; Peking University, Shenzhen Graduate School; Shenzhen 518055 China
- Tsinghua-Peking Center for Life Sciences, Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Department of Chemistry; Tsinghua University; Beijing 100084 China
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73
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Haj-Yahya N, Haj-Yahya M, Castañeda CA, Spasser L, Hemantha HP, Jbara M, Penner M, Ciechanover A, Fushman D, Brik A. Modifying the Vicinity of the Isopeptide Bond To Reveal Differential Behavior of Ubiquitin Chains with Interacting Proteins: Organic Chemistry Applied to Synthetic Proteins. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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74
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Haj-Yahya N, Haj-Yahya M, Castañeda CA, Spasser L, Hemantha HP, Jbara M, Penner M, Ciechanover A, Fushman D, Brik A. Modifying the vicinity of the isopeptide bond to reveal differential behavior of ubiquitin chains with interacting proteins: organic chemistry applied to synthetic proteins. Angew Chem Int Ed Engl 2013; 52:11149-53. [PMID: 24006204 DOI: 10.1002/anie.201306118] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Indexed: 01/08/2023]
Abstract
In every direction: Chemical protein synthesis allows the construction of 14 di-ubiquitin analogues modified in the vicinity of the isopeptide bond to examine their behavior with deubiquitinases and ubiquitin binding domains. The results set the ground for the generation of unique probes for studying the interactions of these chains with various ubiquitin-interacting proteins.
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Affiliation(s)
- Najat Haj-Yahya
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105 (Israel) http://www.bgu.ac.il/∼abrik
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75
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Napper AD, Watson VG. Targeted drug discovery for pediatric leukemia. Front Oncol 2013; 3:170. [PMID: 23847761 PMCID: PMC3703567 DOI: 10.3389/fonc.2013.00170] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 06/13/2013] [Indexed: 12/31/2022] Open
Abstract
Despite dramatic advances in the treatment of pediatric leukemia over the past 50 years, there remain subsets of patients who respond poorly to treatment. Many of the high-risk cases of childhood leukemia with the poorest prognosis have been found to harbor specific genetic signatures, often resulting from chromosomal rearrangements. With increased understanding of the genetic and epigenetic makeup of high-risk pediatric leukemia has come the opportunity to develop targeted therapies that promise to be both more effective and less toxic than current chemotherapy. Of particular importance is an understanding of the interconnections between different targets within the same cancer, and observations of synergy between two different targeted therapies or between a targeted drug and conventional chemotherapy. It has become clear that many cancers are able to circumvent a single specific blockade, and pediatric leukemias are no exception in this regard. This review highlights the most promising approaches to new drugs and drug combinations for high-risk pediatric leukemia. Key biological evidence supporting selection of molecular targets is presented, together with a critical survey of recent progress toward the discovery, pre-clinical development, and clinical study of novel molecular therapeutics.
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Affiliation(s)
- Andrew D Napper
- High-Throughput Screening and Drug Discovery Laboratory, Nemours Center for Childhood Cancer Research, A.I. duPont Hospital for Children , Wilmington, DE , USA
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76
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Kim J, Kim JA, McGinty RK, Nguyen UTT, Muir TW, Allis CD, Roeder RG. The n-SET domain of Set1 regulates H2B ubiquitylation-dependent H3K4 methylation. Mol Cell 2013; 49:1121-33. [PMID: 23453808 DOI: 10.1016/j.molcel.2013.01.034] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 12/28/2012] [Accepted: 01/23/2013] [Indexed: 12/22/2022]
Abstract
Past studies have documented a crosstalk between H2B ubiquitylation (H2Bub) and H3K4 methylation, but little (if any) direct evidence exists explaining the mechanism underlying H2Bub-dependent H3K4 methylation on chromatin templates. Here, we took advantage of an in vitro histone methyltransferase assay employing a reconstituted yeast Set1 complex (ySet1C) and a recombinant chromatin template containing fully ubiquitylated H2B to gain valuable insights. Combined with genetic analyses, we demonstrate that the n-SET domain within Set1, but not Swd2, is essential for H2Bub-dependent H3K4 methylation. Spp1, a homolog of human CFP1, is conditionally involved in this crosstalk. Our findings extend to the human Set1 complex, underscoring the conserved nature of this disease-relevant crosstalk pathway. As not all members of the H3K4 methyltransferase family contain n-SET domains, our studies draw attention to the n-SET domain as a predictor of an H2B ubiquitylation-sensing mechanism that leads to downstream H3K4 methylation.
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Affiliation(s)
- Jaehoon Kim
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
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77
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Fierz B, Kilic S, Hieb AR, Luger K, Muir TW. Stability of nucleosomes containing homogenously ubiquitylated H2A and H2B prepared using semisynthesis. J Am Chem Soc 2012; 134:19548-51. [PMID: 23163596 DOI: 10.1021/ja308908p] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Post-translational modifications (PTMs) of histones are an essential feature in the dynamic regulation of chromatin. One of these modifications, ubiquitylation, has been speculated to directly influence the stability of the nucleosome, which represents the basic building block of chromatin. Here we report a strategy for the semisynthesis of site-specifically ubiquitylated histone H2A (uH2A). This branched protein was generated through a three-piece expressed protein ligation approach including a traceless ligation at valine. uH2A could be efficiently incorporated into nucleosomes, thereby opening the way to detailed biochemical and biophysical studies on the function of this PTM. Accordingly, we used uH2A, as well as a previously generated ubiquitylated H2B, in chaperone-coupled nucleosome stability assays to demonstrate that the direct effect of ubiquitylated histones on nucleosomal stability is in fact modest.
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Affiliation(s)
- Beat Fierz
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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78
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Haj-Yahya M, Eltarteer N, Ohayon S, Shema E, Kotler E, Oren M, Brik A. N-methylation of isopeptide bond as a strategy to resist deubiquitinases. Angew Chem Int Ed Engl 2012; 51:11535-9. [PMID: 23065695 DOI: 10.1002/anie.201205771] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 08/23/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Mahmood Haj-Yahya
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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79
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Haj-Yahya M, Eltarteer N, Ohayon S, Shema E, Kotler E, Oren M, Brik A. N-Methylation of Isopeptide Bond as a Strategy to Resist Deubiquitinases. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205771] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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80
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Li YM, Yang MY, Huang YC, Li YT, Chen PR, Liu L. Ligation of expressed protein α-hydrazides via genetic incorporation of an α-hydroxy acid. ACS Chem Biol 2012; 7:1015-22. [PMID: 22424086 DOI: 10.1021/cb300020s] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Expressed protein ligation bridges the gap between synthetic peptides and recombinant proteins and thereby significantly increases the size and complexity of chemically synthesized proteins. Although the intein-based expressed protein ligation method has been extensively used in this regard, the development of new expressed protein ligation methods may improve the flexibility and power of protein semisynthesis. In this study a new alternative version of expressed protein ligation is developed by combining the recently developed technologies of hydrazide-based peptide ligation and genetic code expansion. Compared to the previous intein-based expressed protein ligation method, the new method does not require the use of protein splicing technology and generates recombinant protein α-hydrazides as ligation intermediates that are more chemically stable than protein α-thioesters. Furthermore, the use of an evolved mutant pyrrolysyl-tRNA synthetase(PylRS), ACPK-RS, from M. barkeri shows an improved performance for the expression of recombinant protein backbone oxoesters. By using HdeA as a model protein we demonstrate that the hydrazide-based method can be used to synthesize proteins with correctly folded structures and full biological activity. Because the PylRS-tRNACUAPyl system is compatible with both prokaryotic and eukaryotic cells,the strategy presented here may be readily expanded to manipulate proteins produced in mammalian cells. The new hydrazide-based method may also supplement the intein-based expressed protein ligation method by allowing for a more flexible selection of ligation site.
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Affiliation(s)
- Yi-Ming Li
- Tsinghua-Peking
Center for Life Sciences, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Mai-Yun Yang
- Beijing National Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules Center, Peking-Tsinghua Center for Life Sciences, and Department of Chemical Biology, Peking University, Beijing 100871, China
| | - Yi-Chao Huang
- Tsinghua-Peking
Center for Life Sciences, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yi-Tong Li
- Tsinghua-Peking
Center for Life Sciences, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Peng R. Chen
- Beijing National Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules Center, Peking-Tsinghua Center for Life Sciences, and Department of Chemical Biology, Peking University, Beijing 100871, China
| | - Lei Liu
- Tsinghua-Peking
Center for Life Sciences, Department of Chemistry, Tsinghua University, Beijing 100084, China
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81
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82
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Spasser L, Brik A. Chemistry and Biology of the Ubiquitin Signal. Angew Chem Int Ed Engl 2012; 51:6840-62. [DOI: 10.1002/anie.201200020] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Indexed: 01/07/2023]
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83
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Whitcomb SJ, Fierz B, McGinty RK, Holt M, Ito T, Muir TW, Allis CD. Histone monoubiquitylation position determines specificity and direction of enzymatic cross-talk with histone methyltransferases Dot1L and PRC2. J Biol Chem 2012; 287:23718-25. [PMID: 22619169 DOI: 10.1074/jbc.m112.361824] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
It is well established that chromatin is a destination for signal transduction, affecting many DNA-templated processes. Histone proteins in particular are extensively post-translationally modified. We are interested in how the complex repertoire of histone modifications is coordinately regulated to generate meaningful combinations of "marks" at physiologically relevant genomic locations. One important mechanism is "cross-talk" between pre-existing histone post-translational modifications and enzymes that subsequently add or remove modifications on chromatin. Here, we use chemically defined "designer" nucleosomes to investigate novel enzymatic cross-talk relationships between the most abundant histone ubiquitylation sites, H2AK119ub and H2BK120ub, and two important histone methyltransferases, Dot1L and PRC2. Although the presence of H2Bub in nucleosomes greatly stimulated Dot1L methylation of H3K79, we found that H2Aub did not influence Dot1L activity. In contrast, we show that H2Aub inhibited PRC2 methylation of H3K27, but H2Bub did not influence PRC2 activity. Taken together, these results highlight how the position of nucleosome monoubiquitylation affects the specificity and direction of cross-talk with enzymatic activities on chromatin.
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Affiliation(s)
- Sarah J Whitcomb
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York 10065, USA
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84
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Abstract
Chromatin is extensively chemically modified and thereby acts as a dynamic signaling platform controlling gene function. Chromatin regulation is integral to cell differentiation, lineage commitment and organism development, whereas chromatin dysregulation can lead to age-related and neurodegenerative disorders as well as cancer. Investigating chromatin biology presents a unique challenge, as the issue spans many disciplines, including cell and systems biology, biochemistry and molecular biophysics. In recent years, the application of chemical biology methods for investigating chromatin processes has gained considerable traction. Indeed, chemical biologists now have at their disposal powerful chemical tools that allow chromatin biology to be scrutinized at the level of the cell all the way down to the single chromatin fiber. Here we present recent examples of how this rapidly expanding palette of chemical tools is being used to paint a detailed picture of chromatin function in organism development and disease.
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85
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Luo M. Current chemical biology approaches to interrogate protein methyltransferases. ACS Chem Biol 2012; 7:443-63. [PMID: 22220966 DOI: 10.1021/cb200519y] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein methyltransferases (PMTs) play various physiological and pathological roles through methylating histone and nonhistone targets. However, most PMTs including more than 60 human PMTs remain to be fully characterized. The current approaches to elucidate the functions of PMTs have been diversified by many emerging chemical biology technologies. This review focuses on progress in these aspects and is organized into four discussion modules (assays, substrates, cofactors, and inhibitors) that are important to elucidate biological functions of PMTs. These modules are expected to provide general guidance and present emerging methods for researchers to select and combine suitable PMT-activity assays, well-defined substrates, novel SAM surrogates, and PMT inhibitors to interrogate PMTs.
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Affiliation(s)
- Minkui Luo
- Molecular Pharmacology
and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, New
York 10065, United States
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86
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Abstract
Regulation of gene transcription is vitally important for the maintenance of normal cellular homeostasis. Failure to correctly regulate gene expression, or to deal with problems that arise during the transcription process, can lead to cellular catastrophe and disease. One of the ways cells cope with the challenges of transcription is by making extensive use of the proteolytic and nonproteolytic activities of the ubiquitin-proteasome system (UPS). Here, we review recent evidence showing deep mechanistic connections between the transcription and ubiquitin-proteasome systems. Our goal is to leave the reader with a sense that just about every step in transcription-from transcription initiation through to export of mRNA from the nucleus-is influenced by the UPS and that all major arms of the system--from the first step in ubiquitin (Ub) conjugation through to the proteasome-are recruited into transcriptional processes to provide regulation, directionality, and deconstructive power.
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Affiliation(s)
- Fuqiang Geng
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8240, USA.
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87
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Wakeman TP, Wang Q, Feng J, Wang XF. Bat3 facilitates H3K79 dimethylation by DOT1L and promotes DNA damage-induced 53BP1 foci at G1/G2 cell-cycle phases. EMBO J 2012; 31:2169-81. [PMID: 22373577 DOI: 10.1038/emboj.2012.50] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 02/07/2012] [Indexed: 11/09/2022] Open
Abstract
The methyltransferase DOT1L methylates histone H3 at K79 to facilitate specific biological events. H3K79 dimethylation (H3K79-2Me) by DOT1L influences the DNA damage response by promoting 53BP1 recruitment to DNA damage sites; however, it is unclear if this methylation is required as 53BP1 interacts with dimethylated H4 (H4K20-2Me) with a much higher affinity. We demonstrate that H3K79-2Me, while negligible during S-phase, is required for ionizing radiation (IR)-induced 53BP1 foci formation during G1/G2-phases when H4K20-2Me levels are low. Further, we describe an essential role for HLA-B-associated transcript 3 (Bat3) in regulating this process in U2OS cells. Bat3 co-localizes with DOT1L at histone H3, and Bat3 knockdown results in decreased DOT1L-H3 interaction and H3K79-2Me, leading to a reduction in IR-induced 53BP1 foci formation, defects in DNA repair and increased sensitivity to IR. We demonstrate that a conserved Bat3 ubiquitin-like motif and a conserved DOT1L ubiquitin-interacting motif promote DOT1L-Bat3 interaction to facilitate efficient H3K79-2Me and IR-induced 53BP1 foci formation during G1/G2-phases. Taken together, our findings identify a novel role for Bat3 in regulating DOT1L function, which plays a critical role in DNA damage response.
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Affiliation(s)
- Timothy P Wakeman
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
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88
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Designer proteins: applications of genetic code expansion in cell biology. Nat Rev Mol Cell Biol 2012; 13:168-82. [DOI: 10.1038/nrm3286] [Citation(s) in RCA: 271] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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89
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Abstract
Protein ubiquitination, the covalent attachment of ubiquitin to target proteins, has emerged as one of the most prevalent posttranslational modifications (PTMs), regulating nearly every cellular pathway. The diversity of signaling associated with this particular PTM stems from the myriad ways in which a target protein can be modified by ubiquitin, e.g., monoubiquitin, multi-monoubiquitin, and polyubiquitin linkages. In this Review, we focus on developments in both enzymatic and chemical methods that engender ubiquitin with new chemical and physical properties. Moreover, we highlight how these methods have enabled studies directed toward (i) characterizing enzymes responsible for reversing the ubiquitin modification, (ii) understanding the influence of ubiquitin on protein function and crosstalk with other PTMs, and (iii) uncovering the impact of polyubiquitin chain linkage and length on downstream signaling events.
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Affiliation(s)
- Eric R. Strieter
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706,
United States
| | - David A. Korasick
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706,
United States
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90
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Dhall A, Chatterjee C. Chemical approaches to understand the language of histone modifications. ACS Chem Biol 2011; 6:987-99. [PMID: 21827195 DOI: 10.1021/cb200142c] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Genomic DNA in the eukaryotic cell nucleus is present in the form of chromatin. Histones are the principal protein component of chromatin, and their post-translational modifications play important roles in regulating the structure and function of chromatin and thereby in determining cell development and disease. An understanding of how histone modifications translate into downstream cellular events is important from both developmental and therapeutic perspectives. However, biochemical studies of histone modifications require access to quantities of homogenously modified histones that cannot be easily isolated from natural sources or generated by enzymatic methods. In the past decade, chemical synthesis has proven to be a powerful tool in translating the language of histone modifications by providing access to uniformly modified histones and by the development of stable analogues of thermodynamically labile modifications. This Review highlights the various synthetic and semisynthetic strategies that have enabled biochemical and biophysical characterization of site-specifically modified histones.
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Affiliation(s)
- Abhinav Dhall
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Champak Chatterjee
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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91
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Abstract
In this issue of Molecular Cell, Wu et al. (2011) reveal that ubiquitylation of histone 2B lysine 34 stimulates histone methyltransferase activity on nucleosomes, a finding with implications for the general mechanism by which monoubiquitylation may influence subsequent modification activities.
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Affiliation(s)
- Michael Werner
- Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58(th) St., Chicago, IL 60637, USA
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92
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Virdee S, Kapadnis PB, Elliott T, Lang K, Madrzak J, Nguyen DP, Riechmann L, Chin JW. Traceless and site-specific ubiquitination of recombinant proteins. J Am Chem Soc 2011; 133:10708-11. [PMID: 21710965 PMCID: PMC3135006 DOI: 10.1021/ja202799r] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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Protein ubiquitination is a post-translational modification that regulates almost all aspects of eukaryotic biology. Here we discover the first routes for the efficient site-specific incorporation of δ-thiol-l-lysine (7) and δ-hydroxy-l-lysine (8) into recombinant proteins, via evolution of a pyrrolysyl-tRNA synthetase/tRNACUA pair. We combine the genetically directed incorporation of 7 with native chemical ligation and desulfurization to yield an entirely native isopeptide bond between substrate proteins and ubiquitin. We exemplify this approach by demonstrating the synthesis of a ubiquitin dimer and the first synthesis of ubiquitinated SUMO.
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Affiliation(s)
- Satpal Virdee
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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93
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Affiliation(s)
- Tomasz Fekner
- Department of Chemistry, The Ohio State University, 484 W 12th Avenue, Columbus, OH 43210, USA
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94
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Frederiks F, van Welsem T, Oudgenoeg G, Heck AJR, Janzen CJ, van Leeuwen F. Heterologous expression reveals distinct enzymatic activities of two DOT1 histone methyltransferases of Trypanosoma brucei. J Cell Sci 2011; 123:4019-23. [PMID: 21084562 DOI: 10.1242/jcs.073882] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Dot1 is a highly conserved methyltransferase that modifies histone H3 on the nucleosome core surface. In contrast to yeast, flies, and humans where a single Dot1 enzyme is responsible for all methylation of H3 lysine 79 (H3K79), African trypanosomes express two DOT1 proteins that methylate histone H3K76 (corresponding to H3K79 in other organisms) in a cell-cycle-regulated manner. Whereas DOT1A is essential for normal cell cycle progression, DOT1B is involved in differentiation and control of antigenic variation of this protozoan parasite. Analysis of DOT1A and DOT1B in trypanosomes or in vitro, to understand how H3K76 methylation is controlled during the cell cycle, is complicated by the lack of genetic tools and biochemical assays. To eliminate these problems, we developed a heterologous expression system in yeast. Whereas Trypanosoma brucei DOT1A predominantly dimethylated H3K79, DOT1B trimethylated H3K79 even in the absence of dimethylation by DOT1A. Furthermore, DOT1A activity was selectively reduced by eliminating ubiquitylation of H2B. The tail of histone H4 was not required for activity of DOT1A or DOT1B. These findings in yeast provide new insights into possible mechanisms of regulation of H3K76 methylation in Trypanosoma brucei.
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Affiliation(s)
- Floor Frederiks
- Division of Gene Regulation, The Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands
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95
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Abstract
Epigenetics, broadly defined as the inheritance of non-Mendelian phenotypic traits, can be more narrowly defined as heritable alterations in states of gene expression ("on" versus "off") that are not linked to changes in DNA sequence. Moreover, these alterations can persist in the absence of the signals that initiate them, thus suggesting some kind of "memory" to epigenetic forms of regulation. How, for example, during early female mammalian development, is one X chromosome selected to be kept in an active state, while the genetically identical sister X chromosome is "marked" to be inactive, even though they reside in the same nucleus, exposed to the same collection of shared trans-factors? Once X inactivation occurs, how are these contrasting chromatin states maintained and inherited faithfully through subsequent cell divisions? Chromatin states, whether active (euchromatic) or silent (heterochromatic) are established, maintained, and propagated with remarkable precision during normal development and differentiation. However, mistakes made in establishing and maintaining these chromatin states, often executed by a variety of chromatin-remodeling activities, can lead to mis-expression or mis-silencing of critical downstream gene targets with far-reaching implications for human biology and disease, notably cancer. Though chromatin biologists have identified many of the "inputs" that are important for controlling chromatin states, the detailed mechanisms by which these processes work remain largely opaque, in part due to the staggering complexity of the chromatin polymer, the physiologically relevant form of our genome. The primary objective of this article is to serve as a "call to arms" for chemists to contribute to the development of the precision tools needed to answer pressing molecular problems in this rapidly moving field.
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Affiliation(s)
- C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA.
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96
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Histone H2B ubiquitylation disrupts local and higher-order chromatin compaction. Nat Chem Biol 2011; 7:113-9. [PMID: 21196936 PMCID: PMC3078768 DOI: 10.1038/nchembio.501] [Citation(s) in RCA: 353] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 11/10/2010] [Indexed: 11/25/2022]
Abstract
Regulation of chromatin structure involves histone post-translational modifications which can modulate intrinsic properties of the chromatin fiber to change the chromatin state. We used chemically defined nucleosome arrays to demonstrate that H2B ubiquitylation (uH2B), a modification associated with transcription, interferes with chromatin compaction and leads to an open and biochemically accessible fiber conformation. Importantly, these effects were specific for ubiquitin, as compaction of chromatin modified with a similar ubiquitin-sized protein, Hub1, was only weakly affected. Applying a fluorescence based method we found that uH2B acts through a mechanism distinct from H4 tail acetylation (acH4), a modification known to disrupt chromatin folding. Finally, incorporation of both uH2B and acH4 in nucleosomes resulted in synergistic inhibition of higher order chromatin structure formation, possibly a result of their distinct mode of action.
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97
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Frederiks F, Stulemeijer IJE, Ovaa H, van Leeuwen F. A modified epigenetics toolbox to study histone modifications on the nucleosome core. Chembiochem 2010; 12:308-13. [PMID: 21243718 DOI: 10.1002/cbic.201000617] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Indexed: 11/06/2022]
Abstract
In the eukaryotic cell nucleus, the DNA is packaged in a structure called chromatin. The fundamental building block of chromatin is the nucleosome, which is composed of DNA wrapped around an octamer of four distinct histone proteins. Post-translational modifications (PTMs) of histone proteins can affect chromatin structure and function and thereby play critical roles in regulating gene expression. Most histone PTMs are found in unstructured histone tails that protrude from the nucleosome core. As a consequence, (synthetic) peptide truncations of these tails provide convenient substrates for the analysis of histone binding proteins and modifying enzymes. Modifications located on residues that reside in the nucleosome core are more difficult to study because short peptides do not recapitulate this defined structured state well. Methylation of histone H3 on Lys79 (H3K79), mediated by the Dot1 enzyme, is an example of such a core PTM. This modification, which is highly conserved, is linked to human leukemia, and pharmacological modulation of Dot1 activity could be a strategy to treat leukemia. Here we review the available and emerging genetic, biochemical, and chemical methods that together are starting to reveal the function and regulation of this and other histone modifications on the nucleosome core.
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Affiliation(s)
- Floor Frederiks
- Division of Gene Regulation, Netherlands Cancer Institute, Netherlands Proteomics Centre, Amsterdam, The Netherlands
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98
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Genetically Directing ɛ-N, N-Dimethyl-l-Lysine in Recombinant Histones. ACTA ACUST UNITED AC 2010; 17:1072-6. [DOI: 10.1016/j.chembiol.2010.07.013] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Revised: 07/16/2010] [Accepted: 07/20/2010] [Indexed: 11/21/2022]
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99
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Yang R, Pasunooti KK, Li F, Liu XW, Liu CF. Synthesis of K48-linked diubiquitin using dual native chemical ligation at lysine. Chem Commun (Camb) 2010; 46:7199-201. [PMID: 20737108 DOI: 10.1039/c0cc01382j] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dual native chemical ligation at lysine strategy was revised by replacing the acid-labile Cbz protecting group with photolabile NVOC at the 4-mercaptolysine side chain. The optimized strategy was subsequently applied to the synthesis of K48-linked diubiquitin.
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Affiliation(s)
- Renliang Yang
- Division of Chemical Biology and Biotechnology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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100
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Chandrasekharan MB, Huang F, Sun ZW. Histone H2B ubiquitination and beyond: Regulation of nucleosome stability, chromatin dynamics and the trans-histone H3 methylation. Epigenetics 2010; 5:460-8. [PMID: 20523115 DOI: 10.4161/epi.5.6.12314] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Regulation of Set1-COMPASS-mediated H3K4 methylation and Dot1-mediated H3K79 methylation by H2BK123 ubiquitination (H2Bub1) is an evolutionarily conserved trans-histone crosstalk mechanism. How H2Bub1 impacts chromatin structure and affects Set1-COMPASS/Dot1 functions has not been fully defined. Ubiquitin was proposed to bind proteins to physically bridge H2Bub1 with Set1-COMPASS/Dot1. Alternatively, the bulky ubiquitin was thought to be a "wedge" that loosens the nucleosome for factor access. Contrary to the latter possibility, recent discoveries provide evidence for nucleosome stabilization by H2Bub1 via preventing the constant H2A-H2B eviction. Recent data has also uncovered a "docking-site" on H2B for Set1-COMPASS. Collectively, these findings invoke a model, where ubiquitin acts as a "glue" to bind the nucleosome together for supporting Set1-COMPASS/Dot1 functions. This review provides an overview of these novel findings. Additionally, how H2Bub1 and its deubiquitination might alter the chromatin dynamics during transcription is discussed. Possible models for nucleosome stabilization by ubiquitin are also provided.
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Affiliation(s)
- Mahesh B Chandrasekharan
- Department of Biochemistry and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
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