• Molecules and Cells
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• 제39권12호
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• pp.855-861
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• 2016

Ginsenosides, which are the active materials of ginseng, have biological functions that include anti-osteoporotic effects. Aqueous ginseng extract inhibits osteoclast differentiation induced by receptor activator of NF-${\kappa}B$ ligand (RANKL). Aqueous ginseng extract produces chromatography peaks characteristic of ginsenosides. Among these peaks, ginsenoside Re is a major component. However, the preventive effects of ginsenoside Re against osteoclast differentiation are not known. We studied the effect of ginsenoside Re on osteoclast differentiation, RANKL-induced tartrate-resistant acid phosphatase (TRAP) activity, and formation of multinucleated osteoclasts in vitro. Ginsenoside Re hampered osteoclast differentiation in a dose-dependent manner. In an in vivo zebrafish model, aqueous ginseng extract and ginsenoside Re had anti-osteoclastogenesis effects. These findings suggest that both aqueous ginseng extract and ginsenoside Re prevent bone resorption by inhibiting osteoclast differentiation. Ginsenoside Re could be important for promoting bone health.

• 한국동물학회:학술대회논문집
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• 한국동물학회 2003년도 한국생물과학협회 학술발표대회
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• pp.199.3-199
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• 2003

No Abstract, See Full Text

• Molecules and Cells
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• 제45권7호
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• pp.512-512
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• 2022

• Genomics & Informatics
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• 제3권3호
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• pp.74-79
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• 2005

The H19 gene, located at human chromosome 11p15.5, is imprinted in most normal human tissues. However, imprinting is often lost in tumors suggesting H19 is a putative tumor suppressor. We analyzed the single nucleotide polymorphisms (SNPs) of a 16 kb region that includes the H19 gene and its imprinting control region (ICR) in the Korean population. To identify SNPs, we directly sequenced this region in 18 Korean subjects. We identified 64 SNPs, of which 7 were in the exons of H19, 2 were in the introns, 14 were in the 3' intergenic region and 41 were in the 5' intergenic region. Of the 64 SNPs, 21 had not previously been reported and thus appear to be unique to the Korean population. The identified SNPs of H19 in the Korean population may eventually be useful as genetic markers associated with various diseases. In this study, 7 of the 64 identified SNPs were at CTCF binding sites in the ICR and may affect regulation of H19 gene imprinting. Thus, several genetic variations of the H19 gene may be important markers in human diseases that involve genomic imprinting, including cancer.

• Interdisciplinary Bio Central
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• 제1권1호
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• pp.4.1-4.7
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• 2009

Introduction: Histone modifications and DNA methylation are the major factors in epigenetic gene regulation. Especially, revealing how histone modifications are related to DNA methylation is one of the challenging problems in this field. In this paper, we address this issue and propose several plausible mechanisms for precise controlling of DNA methylation status at CpG islands. Materials and Methods: To establish the regulatory relationships, we used 38 histone modification types including H2A.Z and CTCF, and DNA methylation status at CpG islands across chromosome 6, 20, and 22 of human CD4+ T cell. We utilized Bayesian network to construct regulatory network. Results and Discussion: We found several meaningful relationships supported by previous studies. In addition, our results show that histone modifications can be clustered into several groups with different regulatory properties. Based on those findings we predicted the status of methylation level at CpG islands with high accuracy, and suggested core-regulatory network to control DNA methylation status.

• Molecules and Cells
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• 제44권12호
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• pp.883-892
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• 2021

Genome-wide chromosome conformation capture (3C)-based high-throughput sequencing (Hi-C) has enabled identification of genome-wide chromatin loops. Because the Hi-C map with restriction fragment resolution is intrinsically associated with sparsity and stochastic noise, Hi-C data are usually binned at particular intervals; however, the binning method has limited reliability, especially at high resolution. Here, we describe a new method called HiCORE, which provides simple pipelines and algorithms to overcome the limitations of single-layered binning and predict core chromatin regions with three-dimensional physical interactions. In this approach, multiple layers of binning with slightly shifted genome coverage are generated, and interacting bins at each layer are integrated to infer narrower regions of chromatin interactions. HiCORE predicts chromatin looping regions with higher resolution, both in human and Arabidopsis genomes, and contributes to the identification of the precise positions of potential genomic elements in an unbiased manner.

• Molecular & Cellular Toxicology
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• 제5권1호
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• pp.58-66
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• 2009

The 2-year rodent carcinogenicity test involves long-term, repetitive dosing of animals that is both time consuming and expensive. Alternative approaches have been attempted using specific transgenic or knockout mice or toxicogenomics to predict carcinogenicity without conducting a 2-year rodent test. In addition, toxicogenomic analysis of carcinogen-treated animals could also enhance our understanding of molecular mechanisms and aid in the diagnosis of acute toxicity induced by carcinogens. Therefore, we investigated transcription profiles after administering the carcinogens 4,4-dimethylformamide (DMF) and 4-biphenylamine (ABP). BALB/c male mice were treated once with DMF (650 mg/kg i.p.) or ABP (120 mg/kg p.o.). Standard blood biochemistry and histological changes were observed. Gene expression profiles in the livers of mice treated with either vehicle or the carcinogens were analyzed using the Affymetrix $GeneChip^{(R)}$ assay. In all, 1,474 differentially expressed genes in DMF- or ABP-treated mice were identified as being either up- or down-regulated over 1.5-fold (P< 0.01), and these genes were analyzed using hierarchical clustering and Ingenuity Pathways Analysis. Of these, 107 genes were consistently regulated in both carcinogen-treated groups. Genes associated with cancer were upregulated (Por, S100a10, Tes, Ctcf, Ddx21, Eapp, Nel, and Pa2g4) or downregulated (Cbs and Gch1). Toxicological function analysis also identified genes involved in organ toxicity, including hepatotoxicity. These data may help to identify molecular markers for acute hepatotoxicity induced by carcinogens.