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Tozaki T, Kwak HG, Nakamura K, Takasu M, Ishii H, Ohnuma A, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Kusano K, Hirata M, Nirasawa T, Nagata SI. Sequence determination of phosphorothioated oligonucleotides using MALDI-TOF mass spectrometry for controlling gene doping in equestrian sports. Drug Test Anal 2021; 14:175-180. [PMID: 34418319 DOI: 10.1002/dta.3154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/23/2021] [Accepted: 08/17/2021] [Indexed: 11/07/2022]
Abstract
In human and equestrian sporting events, one method of gene doping is the illegal use of therapeutic oligonucleotides to alter gene expression. In this study, we aimed to identify therapeutic oligonucleotides via sequencing using matrix-assisted laser desorption/ionisation-time-of-flight mass spectrometry (MALDI-TOF MS). As a model of therapeutic oligonucleotides, 22 bp-long phosphorothioated oligonucleotides (PSOs) were used. By using a Clarity OTX kit for extracting short-length oligonucleotides, a spectrum of singly charged PSO with a mean intensity of 6.08 × 104 (standard deviation: 4.34 × 103 ) was detected from 500 pmol PSO in 1 ml horse plasma using the linear negative mode of MALDI-TOF MS. In addition, a 17 bp sequence was determined using in-source decay (ISD) mode, indicating that 500 pmol of a PSO in 1 ml plasma is the detection limit for sequencing. Using the determined sequences (17 bp), a targeted gene for PSO was singly identified on the horse reference genome, EquCab2.0, via a GGGenome search. These procedures can be potentially used to identify therapeutic oligonucleotides, whose nucleotides are unknown, for gene doping control.
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Affiliation(s)
- Teruaki Tozaki
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi, Japan.,Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan
| | - Ho-Geun Kwak
- Daltonics Division, Bruker Japan K.K., Yokohama, Kanagawa, Japan
| | - Kotono Nakamura
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan
| | - Masaki Takasu
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan
| | - Hideaki Ishii
- Drug Analysis Department, Laboratory of Racing Chemistry, Tochigi, Japan
| | - Aoi Ohnuma
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi, Japan
| | - Mio Kikuchi
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi, Japan
| | - Taichiro Ishige
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi, Japan
| | - Hironaga Kakoi
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi, Japan
| | - Kei-Ichi Hirota
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi, Japan
| | - Kanichi Kusano
- Equine Department, Japan Racing Association, Tokyo, Japan
| | - Minoru Hirata
- Daltonics Division, Bruker Japan K.K., Yokohama, Kanagawa, Japan
| | - Takashi Nirasawa
- Daltonics Division, Bruker Japan K.K., Yokohama, Kanagawa, Japan
| | - Shun-Ichi Nagata
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi, Japan
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Kwak HG, Suzuki T, Dohmae N. Global mapping of post-translational modifications on histone H3 variants in mouse testes. Biochem Biophys Rep 2017; 11:1-8. [PMID: 28955761 PMCID: PMC5614684 DOI: 10.1016/j.bbrep.2017.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 05/23/2017] [Indexed: 11/17/2022] Open
Abstract
Mass spectrometry (MS)-based characterization is important in proteomic research for verification of structural features and functional understanding of gene expression. Post-translational modifications (PTMs) such as methylation and acetylation have been reported to be associated with chromatin remodeling during spermatogenesis. Although antibody- and MS-based approaches have been applied for characterization of PTMs on H3 variants during spermatogenesis, variant-specific PTMs are still underexplored. We identified several lysine modifications in H3 variants, including testis-specific histone H3 (H3t), through their successful separation with MS-based strategy, based on differences in masses, retention times, and presence of immonium ions. Besides methylation and acetylation, we detected formylation as a novel PTM on H3 variants in mouse testes. These patterns were also observed in H3t. Our data provide high-throughput structural information about PTMs on H3 variants in mouse testes and show possible applications of this strategy in future proteomic studies on histone PTMs. Various post-translational modifications in histone H3 variants were characterized in the mouse testes. We specifically identified similar modified patterns based on immonium ions. Novel modified lysines in testis-specific H3 histone, H3t, were verified. Our approach will be helpful for the discovery of other novel or specific modifications during spermatogenesis.
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Key Words
- DTT, dithiothreitol
- ESI-TRAP, electrospray TRAP
- FDR, false discovery rate
- H2SO4, sulfuric acid
- HCD, high-energy collision dissociation
- HFBA, heptafluorobutyric acid
- HPLC, high performance liquid chromatography
- ISD, in source decay
- MALDI, matrix-assisted laser desorption/ionization
- MS, mass spectrometry
- Mass spectrometry
- PTMs, post-translational modifications
- Post-translational modification
- RP, reverse phase
- SDS-PAGE, sodium dodecyl sulfate-polyacrylamide gel electrophoresis
- Spermatogenesis
- TCA, trichloroacetic acid
- TFA, trifluoroacetic acid
- Testis-specific H3 histone
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Abstract
Various histones, including testis-specific histones, exist during spermatogenesis and some of them have been reported to play a key role in chromatin remodeling. Mass spectrometry (MS)-based characterization has become the important step to understand histone structures. Although individual histones or partial histone variant groups have been characterized, the comprehensive analysis of histone variants has not yet been conducted in the mouse testis. Here, we present the comprehensive separation and characterization of histone variants from mouse testes by a top-down approach using MS. Histone variants were successfully separated on a reversed phase column using high performance liquid chromatography (HPLC) with an ion-pairing reagent. Increasing concentrations of testis-specific histones were observed in the mouse testis and some somatic histones increased in the epididymis. Specifically, the increase of mass abundance in H3.2 in the epididymis was inversely proportional to the decrease in H3t in the testis, which was approximately 80%. The top-down characterization of intact histone variants in the mouse testis was performed using LC-MS/MS. The masses of separated histone variants and their expected post-translation modifications were calculated by performing deconvolution with information taken from the database. TH2A, TH2B and H3t were characterized by MS/MS fragmentation. Our approach provides comprehensive knowledge for identification of histone variants in the mouse testis that will contribute to the structural and functional research of histone variants during spermatogenesis.
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Affiliation(s)
- Ho-Geun Kwak
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
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Shinagawa T, Huynh LM, Takagi T, Tsukamoto D, Tomaru C, Kwak HG, Dohmae N, Noguchi J, Ishii S. Disruption of Th2a and Th2b genes causes defects in spermatogenesis. Development 2015; 142:1287-92. [PMID: 25742800 DOI: 10.1242/dev.121830] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The variant histones TH2A and TH2B are abundant in the testis, but their roles in spermatogenesis remain elusive. Here, we show that male mutant mice lacking both Th2a and Th2b genes were sterile, with few sperm in the epididymis. In the mutant testis, the lack of TH2B was compensated for by overexpression of H2B, whereas overexpression of H2A was not observed, indicating a decrease in the total histone level. Mutant mice exhibited two defects: incomplete release of cohesin at interkinesis after meiosis I and histone replacement during spermiogenesis. In the mutant testis, secondary spermatocytes at interkinesis accumulated and cohesin was not released normally, suggesting that the retained cohesion of sister chromatids delayed the subsequent entry into meiosis II. In addition, impaired chromatin incorporation of TNP2 and degenerated spermatids were observed in the mutant testis. These results suggest that a loss of TH2A and TH2B function in chromatin dynamics or a decrease in the total histone levels causes defects in both cohesin release and histone replacement during spermatogenesis.
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Affiliation(s)
- Toshie Shinagawa
- Laboratory of Molecular Genetics, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan CREST Research Project of JST (Japan Science and Technology Agency), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Linh My Huynh
- Laboratory of Molecular Genetics, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan CREST Research Project of JST (Japan Science and Technology Agency), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Tsuyoshi Takagi
- Laboratory of Molecular Genetics, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan CREST Research Project of JST (Japan Science and Technology Agency), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Daisuke Tsukamoto
- Laboratory of Molecular Genetics, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan CREST Research Project of JST (Japan Science and Technology Agency), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Chinatsu Tomaru
- Laboratory of Molecular Genetics, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan CREST Research Project of JST (Japan Science and Technology Agency), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Ho-Geun Kwak
- Global Research Cluster, RIKEN, Graduate School of Science and Engineering, Saitama University, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Naoshi Dohmae
- Global Research Cluster, RIKEN, Graduate School of Science and Engineering, Saitama University, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Junko Noguchi
- Division of Animal Sciences, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Shunsuke Ishii
- Laboratory of Molecular Genetics, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan CREST Research Project of JST (Japan Science and Technology Agency), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
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