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Oh J, Kim S, Kim S, Kim J, Yeom S, Lee JS. An epitope-tagged Swd2 reveals the different requirements of Swd2 concentration in H3K4 methylation and viability. Biochim Biophys Acta Gene Regul Mech 2024; 1867:195009. [PMID: 38331025 DOI: 10.1016/j.bbagrm.2024.195009] [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] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/11/2024] [Accepted: 02/01/2024] [Indexed: 02/10/2024]
Abstract
Swd2/Cps35 is a common component of the COMPASS H3K4 methyltransferase and CPF transcription termination complex in Saccharomyces cerevisiae. The deletion of SWD2 is lethal, which results from transcription termination defects in snoRNA genes. This study isolated a yeast strain that showed significantly reduced protein level of Swd2 following epitope tagging at its N-terminus (9MYC-SWD2). The reduced level of Swd2 in the 9MYC-SWD2 strain was insufficient for the stability of the Set1 H3K4 methyltransferase, H3K4me3 and snoRNA termination, but the level was enough for viability and growth similar to the wildtype strain. In addition, we presented the genes differentially regulated by the essential protein Swd2 under optimal culture conditions for the first time. The expression of genes known to be decreased in the absence of Set1 and H3K4me3, including NAD biosynthetic process genes and histone genes, was decreased in the 9MYC-SWD2 strain, as expected. However, the effects of Swd2 on the ribosome biogenesis (RiBi) genes were opposite to those of Set1, suggesting that the expression of RiBi genes is regulated by more complex relationship between COMPASS and other Swd2-containing complexes. These data suggest that different concentrations of Swd2 are required for its roles in H3K4me3 and viability and that it may be either contributory or contrary to the transcriptional regulation of Set1/H3K4me3, depending on the gene group.
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Affiliation(s)
- Junsoo Oh
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea; Institute of Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Seho Kim
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - SangMyung Kim
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Jueun Kim
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea; Kangwon Institute of Inclusive Technology, Kangwon National University, Chuncheon-si 24341, Republic of Korea
| | - Soojin Yeom
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea; Institute of Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea; Institute of Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea.
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Yeom S, Oh J, Kim D, Lee JS. The 80 th Threonine Residue of Histone H3 Is Important for Maintaining HM Silencing in Saccharomyces cerevisiae. J Microbiol Biotechnol 2024; 34:39-46. [PMID: 37957109 PMCID: PMC10840469 DOI: 10.4014/jmb.2310.10031] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/02/2023] [Accepted: 11/08/2023] [Indexed: 11/15/2023]
Abstract
Gene expression in eukaryotic cells is intricately regulated by chromatin structure and various factors, including histone proteins. In Saccharomyces cerevisiae, transcriptionally silenced regions, such as telomeres and homothallic mating (HM) loci, are essential for genome stability and proper cellular function. We firstly observed the defective HM silencing in alanine substitution mutant of 80th threonine residue of histone H3 (H3T80A). To identify which properties in the H3T80 residue are important for the HM silencing, we created several substitution mutants of H3T80 residue by considering the changed states of charge, polarity, and structural similarity. This study reveals that the structural similarity of the 80th position of H3 to the threonine residue, not the polarity and charges, is the most important thing for the transcriptional silencing in the HM loci.
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Affiliation(s)
- Soojin Yeom
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
- Institute of Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Junsoo Oh
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
- Institute of Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Donghyun Kim
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
- Institute of Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
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Yeom S, Lee DH, Lim SC. Clinical outcomes of sinonasal inverted papilloma: a retrospective analysis of 139 cases. J Laryngol Otol 2023; 137:1154-1157. [PMID: 36876322 DOI: 10.1017/s0022215123000361] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
OBJECTIVES Sinonasal inverted papilloma has a high tendency for recurrence, local bone destruction and risk of malignant transformation. Therefore, complete resection of the tumour is required, and close follow up is essential. This article describes the clinical outcomes, recurrence rate and malignant transformation rate of sinonasal inverted papilloma. METHODS In this study, 139 patients diagnosed with sinonasal inverted papilloma in our hospital from December 2010 to May 2022 were retrospectively analysed. All patients underwent endoscopic surgery. RESULTS Sinonasal inverted papilloma occurred more often in males than in females. The mean age of patients with sinonasal inverted papilloma was 67.3 ± 5.7 years at diagnosis. The most prevalent site of origin was the maxillary sinus (50.4 per cent). The recurrence rate was 5.75 per cent, and the malignant transformation rate was 6.5 per cent. CONCLUSION All patients in this study underwent endoscopic surgery. Meticulous resection and regular long-term follow ups are crucial to reducing sinonasal inverted papilloma recurrence after surgery.
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Affiliation(s)
- S Yeom
- Department of Otolaryngology - Head and Neck Surgery, Chonnam National University Medical School and Hwasun Hospital, Hwasun, South Korea
| | - D H Lee
- Department of Otolaryngology - Head and Neck Surgery, Chonnam National University Medical School and Hwasun Hospital, Hwasun, South Korea
| | - S C Lim
- Department of Otolaryngology - Head and Neck Surgery, Chonnam National University Medical School and Hwasun Hospital, Hwasun, South Korea
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Oh J, Yeom S, Park J, Lee JS. The regional sequestration of heterochromatin structural proteins is critical to form and maintain silent chromatin. Epigenetics Chromatin 2022; 15:5. [PMID: 35101096 PMCID: PMC8805269 DOI: 10.1186/s13072-022-00435-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/06/2022] [Indexed: 12/20/2022] Open
Abstract
Budding yeast Saccharomyces cerevisiae and fission yeast Schizosaccharomyces pombe are good models for heterochromatin study. In S. pombe, H3K9 methylation and Swi6, an ortholog of mammalian HP1, lead to heterochromatin formation. However, S. cerevisiae does not have known epigenetic silencing markers and instead has Sir proteins to regulate silent chromatin formation. Although S. cerevisiae and S. pombe form and maintain heterochromatin via mechanisms that appear to be fundamentally different, they share important common features in the heterochromatin structural proteins. Heterochromatin loci are localized at the nuclear periphery by binding to perinuclear membrane proteins, thereby producing distinct heterochromatin foci, which sequester heterochromatin structural proteins. In this review, we discuss the nuclear peripheral anchoring of heterochromatin foci and its functional relevance to heterochromatin formation and maintenance.
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Affiliation(s)
- Junsoo Oh
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, 1 Kangwondeahak-gil, Chuncheon, 24341, Republic of Korea
| | - Soojin Yeom
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, 1 Kangwondeahak-gil, Chuncheon, 24341, Republic of Korea
| | - Jiyeon Park
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, 1 Kangwondeahak-gil, Chuncheon, 24341, Republic of Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, 1 Kangwondeahak-gil, Chuncheon, 24341, Republic of Korea.
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Yeom S, Oh J, Lee JS. Spreading-dependent or independent Sir2-mediated gene silencing in budding yeast. Genes Genomics 2022; 44:359-367. [PMID: 35034281 DOI: 10.1007/s13258-021-01203-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 12/02/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND In the budding yeast Saccharomyces cerevisiae, a silent chromatin structure is formed at three distinct loci, including telomeres, rDNA, and mating-type loci, which silence the expression of genes within their structures. Sir2 is the only common factor, regulating the three silent chromatin regions. S. cerevisiae has 32 telomeres, but studies on gene silencing in budding yeast have been performed using some reporter genes, artificially inserted in the telomeric regions. Therefore, insights into the global landscape of Sir-dependent silencing of genes within the silent chromatin regions are required. OBJECTIVE This study aimed to obtain global insights into Sir2-dependent gene silencing on all silent chromatin regions in budding yeast. METHODS RNA-sequencing was performed to identify genes that are silenced by Sir2. By comparing with the chromatin immunoprecipitation-sequencing (ChIP-seq) of Sir2 in the wild-type strain, we confirmed Sir2-regulated genes. RESULTS Using Sir2 ChIP-seq data, we identified that the Sir2 binding domain length caused by Sir2 spreading from the chromosomal end is different in each telomere in budding yeast. Expression of most subtelomeric genes increased in the ∆sir2 strain. Some Sir2-regulated subtelomeric genes were positioned within the telomeric Sir2-binding domain, while the others were outside the Sir2-binding domain. In addition, Sir2 was bound to the mating-type loci and rDNA region, and gene expression increased in the ∆sir2 strain. CONCLUSION We concluded that S. cerevisiae has two modes of Sir2-mediated gene silencing: one is dependent on chromatin binding and spreading of Sir2, and the other is independent of spreading of Sir2.
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Affiliation(s)
- Soojin Yeom
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, 1 Kangwondeahak-gil, Chuncheon, 24341, Republic of Korea
| | - Junsoo Oh
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, 1 Kangwondeahak-gil, Chuncheon, 24341, Republic of Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, 1 Kangwondeahak-gil, Chuncheon, 24341, Republic of Korea.
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Yeom S, Lee J. The maintenance of HM silencing is regulated by arginine residues of histone H4 tail in
S. cerevisiae. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.622.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Soojin Yeom
- Kangwon national universityChuncheonRepublic of Korea
- CFRL(Critical Zone Frontier Research Laboratory)ChuncheonRepublic of Korea
| | - Jung‐Shin Lee
- Kangwon national universityChuncheonRepublic of Korea
- CFRL(Critical Zone Frontier Research Laboratory)ChuncheonRepublic of Korea
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Yeom S, Oh J, Lee EJ, Lee JS. Positive Charge of Arginine Residues on Histone H4 Tail Is Required for Maintenance of Mating Type in Saccharomyces cerevisiae. J Microbiol Biotechnol 2018; 28:1573-1579. [PMID: 30176714 DOI: 10.4014/jmb.1807.07044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Transcriptional gene silencing is regulated by the chromatin structure, which is by various factors including histones. Saccharomyces cerevisiae contains transcriptionally silenced regions such as telomeric regions and hidden mating (HM) loci. The positively-charged amino acids on the histone H4 tail were reported to be critical for the telomeric silencing in yeast, by interacting with Dot1, a specific methyltransferase for the 79th. lysine on histone H3. However, Dot1 did not affect gene silencing within HM loci, but whether the positively-charged amino acids on the H4 tail affect HM silencing has not been defined. To elucidate the function of the H4 tail on HM silencing, we created several MATa-type yeast strains bearing the substitution of arginine with alanine or lysine on the histone H4 tail and checked the sensitivity of MATa-type yeast to alpha pheromone. The arginine point mutants substituted by alanine (R17A, R19A, and R23A) did not show sensitivity to alpha pheromone, but only two arginine mutants substituted by lysine (R17K and R19K) restored the sensitivity to alpha pheromone-like wild type. These data suggested that the basic property of arginine at 17th and 19th positions in the histone H4 tail is critical for maintaining HM silencing, but that of the 23rd arginine is not. Our data implicated that the positive charge of two arginine residues on the histone H4 tail is required for HM silencing in a manner independent of Dot1.
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Affiliation(s)
- Soojin Yeom
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea.,Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon 24341, Republic of Korea.,Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Junsoo Oh
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea.,Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon 24341, Republic of Korea.,Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Eun-Jin Lee
- Department of Genetic Engineering and Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea.,Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon 24341, Republic of Korea.,Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea
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Byun J, An H, Yeom S, Choi G. 127 NDRG1 regulates proliferation of endothelial cells of infantile hemangioma. J Invest Dermatol 2018. [DOI: 10.1016/j.jid.2018.03.132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Yeom S, Eoh J, Hong J, Jeong JY. Experimental Evaluation of Helical-Type Sodium-to-Air Heat Exchanger Performance for Thermal Sizing Design Code Validation. NUCL TECHNOL 2017. [DOI: 10.13182/nt16-30] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- S. Yeom
- Korea Atomic Energy Research Institute, 111, Daedeok-daero 989beon-gil, Yuseong-gu, Daejeon 305-353, Korea
| | - J. Eoh
- Korea Atomic Energy Research Institute, 111, Daedeok-daero 989beon-gil, Yuseong-gu, Daejeon 305-353, Korea
| | - J. Hong
- Korea Atomic Energy Research Institute, 111, Daedeok-daero 989beon-gil, Yuseong-gu, Daejeon 305-353, Korea
| | - J.-Y. Jeong
- Korea Atomic Energy Research Institute, 111, Daedeok-daero 989beon-gil, Yuseong-gu, Daejeon 305-353, Korea
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Park C, Nam E, Yeom S. 339 POSTER Implication of tumor suppressor maspin in the eradication of lung cancer. EJC Suppl 2006. [DOI: 10.1016/s1359-6349(06)70344-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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