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Jacinto MP, Heidenreich D, Müller S, Greenberg MM. Covalent Modification of Bromodomain Proteins by Peptides Containing a DNA Damage-Induced, Histone Post-Translational Modification. Chembiochem 2022; 23:e202200373. [PMID: 36173930 PMCID: PMC9675715 DOI: 10.1002/cbic.202200373] [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: 07/01/2022] [Revised: 09/28/2022] [Indexed: 02/03/2023]
Abstract
An electrophilic 5-methylene-2-pyrrolone modification (KMP ) is produced at lysine residues of histone proteins in nucleosome core particles upon reaction with a commonly formed DNA lesion (C4-AP). The nonenzymatic KMP modification is also generated in the histones of HeLa cells treated with the antitumor agent, bleomycin that oxidizes DNA and forms C4-AP. This nonenzymatic covalent histone modification has the same charge as the N-acetyllysine (KAc ) modification but is more electrophilic. In this study we show that KMP -containing histone peptides are recognized by, and covalently modify bromodomain proteins that are KAc readers. Distinct selectivity preferences for covalent bromodomain modification are observed following incubation with KMP -containing peptides of different sequence. MS/MS analysis of 3 covalently modified bromodomain proteins confirmed that Cys adduction was selective. The modified Cys was not always proximal to the KAc binding site, indicating that KMP -containing peptide interaction with bromodomain protein is distinct from the former. Analysis of protein adduction yields as a function of bromodomain pH at which the protein charge is zero (pI) or cysteine solvent accessible surface area are also consistent with non-promiscuous interaction between the proteins and electrophilic peptides. These data suggest that intracellular formation of KMP could affect cellular function and viability by modifying proteins that regulate genetic expression.
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Affiliation(s)
- Marco Paolo Jacinto
- Chemistry, Johns Hopkins University, 3400 N. Charles St., 21218, Baltimore, MD, USA
| | - David Heidenreich
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Marc M Greenberg
- Chemistry, Johns Hopkins University, 3400 N. Charles St., 21218, Baltimore, MD, USA
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Feng Y, Endo M, Sugiyama H. Nucleosomes and Epigenetics from a Chemical Perspective. Chembiochem 2020; 22:595-612. [PMID: 32864867 DOI: 10.1002/cbic.202000332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/26/2020] [Indexed: 12/19/2022]
Abstract
Nucleosomes, which are the fundamental building blocks of chromatin, are highly dynamic, they play vital roles in the formation of higher-order chromatin structures and orchestrate gene regulation. Nucleosome structures, histone modifications, nucleosome-binding proteins, and their functions are being gradually unravelled with the development of epigenetics. With the continuous development of research approaches such as cryo-EM, FRET and next-generation sequencing for genome-wide analysis of nucleosomes, the understanding of nucleosomes is getting wider and deeper. Herein, we review recent progress in research on nucleosomes and epigenetics, from nucleosome structure to chromatin formation, with a focus on chemical aspects. Basic knowledge of the nucleosome (nucleosome structure, nucleosome position sequence, nucleosome assembly and remodeling), epigenetic modifications, chromatin structure, chemical biology methods and nucleosome, observation nucleosome by AFM, phase separation and nucleosomes are described in this review.
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Affiliation(s)
- Yihong Feng
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Kyoto, 606-8502, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University Yoshida-Ushinomiyacho, Kyoto, 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University Yoshida-Ushinomiyacho, Kyoto, 606-8501, Japan
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Yang K, Greenberg MM. DNA-Protein Cross-Link Formation in Nucleosome Core Particles Treated with Methyl Methanesulfonate. Chem Res Toxicol 2019; 32:2144-2151. [PMID: 31532638 DOI: 10.1021/acs.chemrestox.9b00314] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
N7-Methyl-2'-deoxyguanosine (MdG) is the major damage product in DNA produced by methylating agents, but it often thought to be nontoxic and nonmutagenic. MdG is chemically unstable. An abasic site (AP) is the major product produced from MdG under physiologically relevant conditions. AP formation is frequently considered to be responsible for the cytotoxic effects of MdG, but the reaction is suppressed in nucleosome core particles (NCPs). Recently, it was discovered that histone proteins form reversible DNA-protein cross-links (DPCs) with MdG in reconstituted NCPs, as well as in methylmethanesulfonate (MMS) treated cells. In this study, the formation and reactivity of MdG in MMS treated NCPs was examined at single nucleotide resolution. Sequences consisting of three or more consecutive dGs are more reactive with MMS. The efficiency and selectivity of MdG formation by MMS is largely unaffected within a NCP, although reactivity at several dGs is ∼1.5-2.5-fold higher in NCPs. DPC formation from MdG (DPCMdG) predominates over AP at all positions within the NCP. With few exceptions, DPCMdG yield is strongly dependent upon the accessibility of the major groove containing MdG to lysine-rich histone N-terminal tails. These data indicate that histone-MdG DPC formation will depend upon DNA sequence and translational position within an NCP.
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Affiliation(s)
- Kun Yang
- Department of Chemistry , Johns Hopkins University , 3400 N. Charles Street , Baltimore , Maryland 21218 , United States
| | - Marc M Greenberg
- Department of Chemistry , Johns Hopkins University , 3400 N. Charles Street , Baltimore , Maryland 21218 , United States
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Byrne SR, Yang K, Rokita SE. Effect of Nucleosome Assembly on Alkylation by a Dynamic Electrophile. Chem Res Toxicol 2019; 32:917-925. [PMID: 30882212 DOI: 10.1021/acs.chemrestox.9b00057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Quinone methides are reactive electrophiles that are generated during metabolism of various drugs, natural products, and food additives. Their chemical properties and cellular effects have been described previously, and now their response to packaging DNA in a nucleosome core is described. A model bisquinone methide precursor (bisQMP) was selected based on its ability to form reversible adducts with guanine N7 that allow for their redistribution and transfer after quinone methide regeneration. Assembly of Widom's 601 DNA with the histone octamer of H2A, H2B, H3, and H4 from Xenopus laevis significantly suppressed alkylation of the DNA. This result is a function of DNA packaging since addition of the octamer without nucleosome reconstitution only mildly protected DNA from alkylation. The lack of competition between nucleophiles of DNA and the histones was consistent with the limited number of adducts formed by the histones as detected by tryptic digestion and ultraperformance liquid chromatography-mass spectrometry. Only three peptide adducts were observed after reaction with a monofunctional analogue of bisQMP, and only two peptide adducts were observed after reaction with bisQMP. Histone reaction was also suppressed when reconstituted into the nucleosome core particle. However, bisQMP was capable of cross-linking the DNA and histones in moderate yields (∼20%) that exceeded expectations derived from reaction of cisplatin, nitrogen mustards, and diepoxybutane. The core histones also demonstrated a protective function against dynamic alkylation by trapping the reactive quinone methide after its spontaneous regeneration from DNA adducts.
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Affiliation(s)
- Shane R Byrne
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
| | - Kun Yang
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
| | - Steven E Rokita
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
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Zou T, Hashiya F, Wei Y, Yu Z, Pandian GN, Sugiyama H. Direct Observation of H3-H4 Octasome by High-Speed AFM. Chemistry 2018; 24:15998-16002. [DOI: 10.1002/chem.201804010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Tingting Zou
- Department of Science; Graduate School of Science; Kyoto University, Sakyo; Kyoto 606-8502 Japan
| | - Fumitaka Hashiya
- Department of Science; Graduate School of Science; Kyoto University, Sakyo; Kyoto 606-8502 Japan
| | - Yulei Wei
- Department of Science; Graduate School of Science; Kyoto University, Sakyo; Kyoto 606-8502 Japan
| | - Zutao Yu
- Department of Science; Graduate School of Science; Kyoto University, Sakyo; Kyoto 606-8502 Japan
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Material Sciences (iCeMS); Kyoto University; Yoshida Ushinomiya-cho Sakyo Kyoto 606-8501 Japan
| | - Hiroshi Sugiyama
- Department of Science; Graduate School of Science; Kyoto University, Sakyo; Kyoto 606-8502 Japan
- Institute for Integrated Cell-Material Sciences (iCeMS); Kyoto University; Yoshida Ushinomiya-cho Sakyo Kyoto 606-8501 Japan
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Zou T, Kizaki S, Sugiyama H. Investigating Nucleosome Accessibility for MNase, FeII
Peplomycin, and Duocarmycin B2
by Using Capillary Electrophoresis. Chembiochem 2018; 19:664-668. [DOI: 10.1002/cbic.201700643] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Tingting Zou
- Department of Science; Graduate School of Science; Kyoto University; Sakyo Kyoto 606-8502 Japan
| | - Seiichiro Kizaki
- Department of Science; Graduate School of Science; Kyoto University; Sakyo Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of Science; Graduate School of Science; Kyoto University; Sakyo Kyoto 606-8502 Japan
- Institute for Integrated Cell-Material Sciences (iCeMS); Kyoto University; Yoshida Ushinomiya-cho Sakyo Kyoto 606-8501 Japan
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Saha A, Kizaki S, Han JH, Yu Z, Sugiyama H. UVA irradiation of BrU-substituted DNA in the presence of Hoechst 33258. Bioorg Med Chem 2018; 26:37-40. [PMID: 29170027 DOI: 10.1016/j.bmc.2017.11.011] [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: 09/19/2017] [Revised: 11/02/2017] [Accepted: 11/04/2017] [Indexed: 01/15/2023]
Abstract
Given that our knowledge of DNA repair is limited because of the complexity of the DNA system, a technique called UVA micro-irradiation has been developed that can be used to visualize the recruitment of DNA repair proteins at double-strand break (DSB) sites. Interestingly, Hoechst 33258 was used under micro-irradiation to sensitize 5-bromouracil (BrU)-labelled DNA, causing efficient DSBs. However, the molecular basis of DSB formation under UVA micro-irradiation remains unknown. Herein, we investigated the mechanism of DSB formation under UVA micro-irradiation conditions. Our results suggest that the generation of a uracil-5-yl radical through electron transfer from Hoechst 33258 to BrU caused DNA cleavage preferentially at self-complementary 5'-AABrUBrU-3' sequences to induce DSB. We also investigated the DNA cleavage in the context of the nucleosome to gain a better understanding of UVA micro-irradiation in a cell-like model. We found that DNA cleavage occurred in both core and linker DNA regions although its efficiency reduced in core DNA.
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Affiliation(s)
- Abhijit Saha
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Seiichiro Kizaki
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Ji Hoon Han
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Zutao Yu
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida Ushinomiya-cho, Sakyo, Kyoto 606-8502, Japan.
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