• Journal of Plant Biotechnology
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• 제44권1호
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• pp.19-26
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• 2017

Rapid progress in epigenetic studies has resulted in genome wide information of genetic functions, other than DNA sequence information. However, insufficient understanding and unclear research direction in epigenetics has failed to attract many researchers. Here, we review the sexual reproduction processes that are particularly related to epigenetics in plants. We aim to elucidate the roles of epigenetic information and molecular mechanisms involved in the complex sexual reproduction process of plants, and examine their biological significance.

• BMB Reports
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• 제55권11호
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• pp.541-546
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• 2022

The repair of DNA double-strand breaks (DSBs) by homologous recombination (HR) is crucial for maintaining genomic integrity and is involved in numerous fundamental biological processes. Post-translational modifications by proteins play an important role in regulating DNA repair. Here, we report that the methyltransferase SET7 regulates HR-mediated DSB repair by methylating TIP60, a histone acetyltransferase and tumor suppressor involved in gene expression and protein stability. We show that SET7 targets TIP60 for methylation at K137, which facilitates DSB repair by promoting HR and determines cell viability against DNA damage. Interestingly, TIP60 demethylation is catalyzed by LSD1, which affects HR efficiency. Taken together, our findings reveal the importance of TIP60 methylation status by SET7 and LSD1 in the DSB repair pathway.

• Molecules and Cells
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• 제20권3호
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• pp.423-428
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• 2005

Immediately after fertilization, a chromatin remodeling process in the oocyte cytoplasm extracts protamine molecules from the sperm-derived DNA and loads histones onto it. We examined how the histone H3-lysine 9 methylation system is established on the remodeled sperm chromatin in mice. We found that the paternal pronucleus was not stained for dimethylated H3-K9 (H3-$m_2K9$) during pronucleus development, while the maternal genome stained intensively. Such H3-$m_2K9$ asymmetry between the parental pronuclei was independent of $HP1{\beta}$ localization and, much like DNA methylation, was preserved to the two-cell stage when the nucleus appeared to be compartmentalized for H3-$m_2K9$. A conspicuous increase in H3-$m_2K9$ level was observed at the four-cell stage, and then the level was maintained without a visible change up to the blastocyst stage. The behavior of H3-$m_2K9$ was very similar, but not identical, to that of 5-methylcytosine during preimplantation development, suggesting that there is some connection between methylation of histone and of DNA in early mouse development.

• Journal of Microbiology and Biotechnology
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• 제18권3호
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• pp.600-610
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• 2008

A cancer-associated antigen gene (CAGE) was identified by serological analysis of a recombinant cDNA expression library (SEREX). The gene was identified by screening cDNA expression libraries of human testis and gastric cancer cell lines with sera from patients with gastric cancer. CAGE was found to contain a D-E-A-D box domain and encodes a putative protein of 630 amino acids with possible helicase activity. The CAGE gene is widely expressed in various cancer tissues and cancer cell lines. Demethylation plays a role in the activation of CAGE in certain cancer cell lines where the gene is not expressed. The functional roles of CAGE in tumorigenesis, the molecular mechanisms of CAGE expression, and cell motility are also discussed.

• Biotechnology and Bioprocess Engineering:BBE
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• 제11권4호
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• pp.337-343
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• 2006

Trimethylamine dehydrogenase (TMADH, EC 1.5.99.7), an iron-sulfur flavoprotein that catalyzes the oxidative demethylation of trimethylamine to form dimethylamine and formaldehyde, was purified from Methylophaga sp. strain SK1. The active TMADH was purified 12.3-fold through three purification steps. The optimal pH and temperature for enzyme activity was determined to be 8.5 and $55^{\circ}C$, respectively. The $V_{max}\;and\;K_m$ values were 7.9 nmol/min/mg protein and 1.5 mM. A genomic DNA of 2,983 bp from Methylophaga sp. strain SK1 was cloned, and DNA sequencing revealed the open reading frame (ORF) of the gene coding for TMADH. The ORF contained 728 amino acids with extensive identity (82%) to that of Methylophilus methylotrophus $W_3A_1$.

• 한국발생생물학회지:발생과생식
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• 제14권4호
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• pp.253-259
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• 2010

DNA 메틸화 (DNA methylation)는 유전자의 발현을 조절하는 대표적인 후생학적 조절기작 (epigenetic regulation) 중에 하나이다. DNA 메틸화 양상은 생식세포 형성과정 및 배 발생단계에서 탈메틸화 (demethylation)와 de novo 메틸화의 드라마틱한 변화가 일어난다. 또한 이러한 DNA 메틸화는 배아줄기세포 (embryonic stem cells, ESCs)에서 특징적인 양상을 보이는 것으로 알려져 있다. 본 연구에서는 생쥐 수정란 유래 배아줄기세포와 체세포핵이식 배아줄기세포 (nuclear transplanted ESCs)를 이용해서 대표적 각인유전자 (imprinting genes)로 알려진 Snrpn, Igf2r, H19 유전자들에 대한 메틸화 양상을 알아보고자 하였다. 연구 결과 H19 유전자에 대해서는 DNA 메틸화 양상은 수정란 유래 배아줄기세포와 체세포핵이식 배아줄기세포에서 비슷한 경향을 보였으나, Snrpn과 Igf2r의 경우에는 체세포핵이식 배아줄기세포에서 과메틸화 (hypermethylation) 경향을 보였다.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.221-221
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• 2022

Chromosome breakage occurred by DNA methylation inhibitor. Zebularine is known as DNA methylation inhibitor and suitable for water solubility among different DNA methylation inhibitors as 5-Azacytidine and 5-aza-2'-deoxycytidine. We used zebularine as mutagen according to different methods by roots absorption and seed imbibition. After zebularine treatment, DNA methylation inhibitor, we observed mitotic chromosome behavior what is different according to two different treatment methods. First, seed imbibition treatment in 1,000 μM of zebularine solution for 72 hours in dark conditions. The second treatment to seedlings of Keumkang was also treated in 1,000 μM of zebularine solution for 72 hours after germination. Root and shoot showed different elongations in each treatment. Root absorption treatment(3.01±0.48, 2.00±0.26) showed the shortest elongation in root and shoot than control(8.16±0.61, 4.03±0.48) and seed imbibition treatment(4.33±0.80, 2.48±0.36). It can be explained root tip meristematic cell activity was damaged by DNA methylation inhibitor. Primary root tips were collected in DW for 24 hours at low temperature(0℃) and fixed in fixation solution for 3 days to chromosome observation in mitosis. Mitotic index, chromosome structure and chromosome aberration were observed by phase-contrast microscope. Mitotic index of the control(0.29) showed twice mitotic cells as the treated groups(imbibition 0.15, absorption 0.14). Observation of chromosomes showed some short chromosomes and loosen chromosomes affected by zebularine. It is considered because of zebularine damage DNA in mitosis. We observed "gap by chromosome breakage" in chromosomes that have loose parts between centromere and telomere. It seems demethylation of zebularine occurs chromosome breakage.

• Journal of Periodontal and Implant Science
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• 제47권2호
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• pp.66-76
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• 2017

Purpose: Oral wound healing requires gingival fibroblasts to respond to local growth factors. Epigenetic silencing through DNA methylation can potentially decrease the responsiveness of gingival fibroblasts to local growth factors. In this study, our aim was to determine whether the inhibition of DNA methylation sensitized gingival fibroblasts to transforming growth factor-${\beta}1$ (TGF-${\beta}1$). Methods: Gingival fibroblasts were exposed to 5-aza-2'-deoxycytidine (5-aza), a clinically approved demethylating agent, before stimulation with TGF-${\beta}1$. Gene expression changes were evaluated using quantitative polymerase chain reaction (PCR) analysis. DNA methylation was detected by methylation-sensitive restriction enzymes and PCR amplification. Results: We found that 5-aza enhanced TGF-${\beta}1$-induced interleukin-11 (IL11) expression in gingival fibroblasts 2.37-fold (P=0.008). 5-aza had no significant effects on the expression of proteoglycan 4 (PRG4) and NADPH oxidase 4 (NOX4). Consistent with this, 5-aza caused demethylation of the IL11 gene commonly next to a guanosine (CpG) island in gingival fibroblasts. The TGF-${\beta}$ type I receptor kinase inhibitor SB431542 impeded the changes in IL11 expression, indicating that the effects of 5-aza require TGF-${\beta}$ signaling. 5-aza moderately increased the expression of TGF-${\beta}$ type II receptor (1.40-fold; P=0.009), possibly enhancing the responsiveness of fibroblasts to TGF-${\beta}1$. As part of the feedback response, 5-aza increased the expression of the DNA methyltransferases 1 (DNMT1) (P=0.005) and DNMT3B (P=0.002), which are enzymes responsible for gene methylation. Conclusions: These in vitro data suggest that the inhibition of DNA methylation by 5-aza supports TGF-${\beta}$-induced IL11 expression in gingival fibroblasts.

• 한국발생생물학회지:발생과생식
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• 제7권2호
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• pp.61-68
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• 2003

포유동물의 초기 발생과정 중 접합체가 전능성이나 다능성을 가지기 위해서는 전반적인 DNA 메틸화를 포함하는 후성 유전학적 리프로그래밍의 복잡한 과정을 거쳐야만 한다. 본 연구팀에서는 공여핵의 후성 유전학적 리프로그래밍 과정을 조사하기 위하여 소 복제수정란에서 메틸화 양상을 분석하였다. 복제수정란의 비정상적인 메틸화 양상이 다양한 반복염기서열에서 관찰되었지만 single-copy유전자들의 염기서열은 정상적인 메틸화 양상을 보여주었다. 전반적으로 복제수정란의 전반적인 메틸화 상태는 정상수정란과 완전히 다른 양상을 보여주었다. 또한 복제 배반포의 영양외배엽세포에서 특이적으로 높은 메틸화 수준은 현 복제동물에서 빈번히 나타나는 불완전한 태반형성에 작용할 수 있을 것이다. 결론적으로 복제수정란의 비정상적 발생은 공여핵의 불완전한 후성 유전학적 리프로그래밍에 기인할 수 있다는 사실을 제시하게 되었다. 이러한 공여핵의 후성 유전학적 과정의 이해는 복제수정란의 비정상적 발생을 보다 분명히 밝힐 수 있을 것이다.

• BMB Reports
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• 제56권6호
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• pp.347-352
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• 2023

The protein family of poly (ADP-ribose) polymerases (PARPs) is comprised of multifunctional nuclear enzymes. Several PARP inhibitors have been developed as new anticancer drugs to combat resistance to chemotherapy. Herein, we characterized PARP4 mRNA expression profiles in cisplatin-sensitive and cisplatin-resistant ovarian cancer cell lines. PARP4 mRNA expression was significantly upregulated in cisplatin-resistant ovarian cancer cell lines, and this upregulation was associated with the hypomethylation of specific cytosine-phosphate-guanine (CpG) sites (cg18582260 and cg17117459) on its promoter. Reduced PARP4 expression was restored by treating cisplatin-sensitive cell lines with a demethylation agent, implicating the epigenetic regulation of PARP4 expression by promoter methylation. Depletion of PARP4 expression in cisplatin-resistant cell lines reduced cisplatin chemoresistance and promoted cisplatin-induced DNA fragmentation. The differential mRNA expression and DNA methylation status at specific PARP4 promoter CpG sites (cg18582260 and cg17117459) according to cisplatin responses, was further validated in primary ovarian tumor tissues. The results showed significantly increased PARP4 mRNA expressions and decreased DNA methylation levels at specific PARP4 promoter CpG sites (cg18582260 and cg17117459) in cisplatin-resistant patients. Additionally, the DNA methylation status at cg18582260 CpG sites in ovarian tumor tissues showed fairly clear discrimination between cisplatin-resistant patients and cisplatin-sensitive patients, with high accuracy (area under the curve = 0.86, P = 0.003845). Our findings suggest that the DNA methylation status of PARP4 at the specific promoter site (cg18582260) may be a useful diagnostic biomarker for predicting the response to cisplatin in ovarian cancer patients.