• Molecules and Cells
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• 제38권11호
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• pp.925-935
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• 2015

DNA methylation is a well-characterized epigenetic modification that plays central roles in mammalian development, genomic imprinting, X-chromosome inactivation and silencing of retrotransposon elements. Aberrant DNA methylation pattern is a characteristic feature of cancers and associated with abnormal expression of oncogenes, tumor suppressor genes or repair genes. Ten-eleven-translocation (TET) proteins are recently characterized dioxygenases that catalyze progressive oxidation of 5-methylcytosine to produce 5-hydroxymethylcytosine and further oxidized derivatives. These oxidized methylcytosines not only potentiate DNA demethylation but also behave as independent epigenetic modifications per se. The expression or activity of TET proteins and DNA hydroxymethylation are highly dysregulated in a wide range of cancers including hematologic and non-hematologic malignancies, and accumulating evidence points TET proteins as a novel tumor suppressor in cancers. Here we review DNA demethylation-dependent and -independent functions of TET proteins. We also describe diverse TET loss-of-function mutations that are recurrently found in myeloid and lymphoid malignancies and their potential roles in hematopoietic transformation. We discuss consequences of the deficiency of individual Tet genes and potential compensation between different Tet members in mice. Possible mechanisms underlying facilitated oncogenic transformation of TET-deficient hematopoietic cells are also described. Lastly, we address non-mutational mechanisms that lead to suppression or inactivation of TET proteins in cancers. Strategies to restore normal 5mC oxidation status in cancers by targeting TET proteins may provide new avenues to expedite the development of promising anti-cancer agents.

• 원예과학기술지
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• 제33권1호
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• pp.83-92
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• 2015

xBrassicoraphanus line BB#5, a new synthetic intergeneric hybrid between Brassica rapa L. ssp. pekinensis and Raphanus sativus L. var. rafiphera induced by N-methyl-N-nitroso-urethane mutagenesis in microspore culture, shows high seed fertility and morphological uniformity. Dual-color fluorescence in situ hybridization (FISH) using 5S and 45S rDNA probes and genomic in situ hybridization (GISH) using B. rapa genomic DNA probe were carried out to analyze the chromosome composition and the meiosis pairing pattern compared to its parental lines. The somatic chromosome complement is 2n = 38, which consists of 17 metacentric and two submetacentric chromosomes with lengths of 2.18 to $5.01{\mu}m$. FISH karyotype analysis showed five and eight pairs of 5S and 45S rDNA loci. GISH meiosis pairing analysis showed that 19 complete bivalents were most frequent and accounted for 42% of the 100 pollen mother cells examined. Based on chromosome number, size, morphology, rDNA distribution, and meiosis pairing pattern, both parental genomes of B. rapa and R. sativus appear to exist in xBrassicoraphanus line BB#5, demonstrating its genome integrity. Such stable chromosome constitutions and meiotic pairing patterns in somatic and meiotic cells are very rare in natural and synthetic intergeneric hybrids. Chromosomal studies and genetic and phenotypic changes in allopolyploids a re discussed. The results p resented h erein will b e usef ul f or f urther g enomic s tudy o f xBrassicoraphanus lines and their improvement as promising new breeding varieties.

• BMB Reports
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• 제48권12호
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• pp.685-690
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• 2015

The eukaryotic genome is packed into chromatin, which is important for the genomic integrity and gene regulation. Chromatin structures are maintained through assembly and disassembly of nucleosomes catalyzed by histone chaperones. Asf1 (anti-silencing function 1) is a highly conserved histone chaperone that mediates histone transfer on/off DNA and promotes histone H3 lysine 56 acetylation at globular core domain of histone H3. To elucidate the role of Asf1 in the modulation of chromatin structure, we screened and identified small molecules that inhibit Asf1 and H3K56 acetylation without affecting other histone modifications. These pyrimidine-2,4,6-trione derivative molecules inhibited the nucleosome assembly mediated by Asf1 in vitro, and reduced the H3K56 acetylation in HeLa cells. Furthermore, production of HSV viral particles was reduced by these compounds. As Asf1 is implicated in genome integrity, cell proliferation, and cancer, current Asf1 inhibitor molecules may offer an opportunity for the therapeutic development for treatment of diseases.

• Applied Biological Chemistry
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• 제48권4호
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• pp.331-334
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• 2005

본 연구는 일반적으로 사용되는 DNA 추출방법들에 대한 효율을 비교하기 위해 수행하였다. 원료 옥수수 및 이를 가공한 시료들로부터 DNA추출을 하였으며, 추출된 DNA의 형상, 농도 및 순도 측정 그리고 PCR 분석 결과를 비교하였다. 5가지 방법으로 옥수수의 DNA를 추출한 결과, 추출방법에 따른 DNA 형상의 차이가 거의 없는 것을 확인하였으나, 각각의 시료들로부터 추출된 DNA의 양은 시료 g당 $0.25{\mu}g$부터 $234.0{\mu}g$까지 매우 다양하게 나타났다. 5가지 방법으로 옥수수 시료들의 DNA를 추출한 결과, CTAB법과 DNeasy plant Maxi 키트를 이용한 DNA 추출방법이 높은 수율을 보였다.

• 한국수정란이식학회지
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• 제25권2호
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• pp.111-116
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• 2010

Sperm chromatin integrity is essential for successful fertilization and development of an embryo. Reported here is a quantification of DNA fragments which is intimately associated with reproductive potential to provide one of criteria for sperm chromatin integrity. Three sperm populations were considered: CONTROL (no treatment), UV irradiation (48mW/$cm^2$, 1h) and $H_2O_2$ (oxidative stress induced by hydrogen peroxide, 10 mM, 50 mM and 100 mM). DNA fragments in boar sperm were evaluated by using ligation-mediated quantitative real-time polymerase chain reaction (LM-qPCR) assay, which relies on real-time qPCR to provide a measure of blunt 5' phosphorylated double strand breaks in genomic DNA. The results in agarose gel electrophoresis showed no significant DNA fragmentation and no dose-dependent response to $H_2O_2$. However, the remarkable difference in shape and position was observed in melting curve of LM-qPCR. This result supported that the melting curve analysis of LM-qPCR presented here, could be more sensitive and accurate than previous DNA fragmentation assay method.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2005년도 International Meeting of the Microbiological Society of Korea
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• pp.105-109
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• 2005

Heat Shock Transcription Factor (HSF), and the promoter heat Shock Element (HSE), are among the most highly conserved transcriptional regulatory elements in nature. HSF mediates the transcriptional response of eukaryotic cells to heat, infection and inflammation, pharmacological agents, and other stresses. While HSF is essential for cell viability in yeast, oogenesis and early development in Drosophila, extended life-span in C. elegans, and extra-embryonic development and stress resistance in mammals, little is known about its full range of biological target genes. We used whole genome analyses to identify virtually all of the direct transcriptional targets of yeast HSF, representing nearly three percent of the genomic loci. The majority of the identified loci are heat-inducibly bound by yeast HSF, and the target genes encode proteins that have a broad range of biological functions including protein folding and degradation, energy generation, protein secretion, maintenance of cell integrity, small molecule transport, cell signaling, and transcription. Approximately 30% of the HSF direct target genes are also induced by the diauxic shift, in which glucose levels begin to be depleted. We demonstrate that phosphorylation of HSF by Snf1 kinase is responsible for expression of a subset of HSF targets upon glucose starvation.

• Journal of Computing Science and Engineering
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• 제4권4호
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• pp.291-312
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• 2010

The last decades a large amount of research has been done in the genomics domain which has and is generating terabytes, if not exabytes, of information stored globally in a very fragmented way. Different databases use different ways of storing the same data, resulting in undesired redundancy and restrained information transfer. Adding to this, keeping the existing databases consistent and data integrity maintained is mainly left to human intervention which in turn is very costly, both in time and money as well as error prone. Identifying a fixed conceptual dictionary in the form of a conceptual model thus seems crucial. This paper presents an effort to integrate the mutational data from the established genomic data source HGMD into a conceptual model driven database HGDB, thereby providing useful lessons to improve the already existing conceptual model of the human genome.

• Childhood Kidney Diseases
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• 제12권1호
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• pp.11-22
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• 2008

Telomeres consist of tandem guanine-thymine(G-T) repeats in most eukaryotic chromosomes. Human telomeres are predominantly linear, double stranded DNA as they ended in 30-200 nucleotides(bases,b) 3'-overhangs. In DNA replication, removal of the terminal RNA primer from the lagging strand results in a 3'-overhang of uncopied DNA. This is because of bidirectional DNA replication and specificity of unidirectional DNA polymerase. After the replication, parental and daughter DNA strands have unequal lengths due to a combination of the end-replication problem and end-processing events. The gradual chromosome shortening is observed in most somatic cells and eventually leads to cellular senescence. Telomere shortening could be a molecular clock that signals the replicative senescence. The shortening of telomeric ends of human chromosomes, leading to sudden growth arrest, triggers DNA instability as biological switches. In addition, telomere dysfunction may cause chronic allograft nephropathy or kidney cancers. The renal cell carcinoma(RCC) in women may be less aggressive and have less genomic instability than in man. Younger patients with telomere dysfunction are at a higher risk for RCC than older patients. Thus, telomeres maintain the integrity of the genome and are involved in cellular aging and cancer. By studying the telomeric DNA, we may characterize the genetic determinants in diseases and discover the tools in molecular medicine.

• Journal of Microbiology
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• 제39권2호
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• pp.102-108
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• 2001

DNA damage response has a central role in the maintenance of genomic integrity while mutations in related genes may result in a range of disorders including neoplasic formations. The uvsZl characterized in this report is a navel uvs mutation in Aspergillus nidulans, resulting in a nucleotide excision repair (NER) phenotype: UV-sensitivity before DNA synthesis (quiescent cells), high UV-induced mutation frequency and probable absence of involvement with mitotic and meiotic recombinations. The mutation is recessive and nan-allelic to the previously characterized uvsA101 mutation, also located on the paba-y interval on chromosome I. uvsZl skewed wild-type sensitivity to MMS, which suggests non-involvement of this mutation with BER. Epitasis tests showed that the uvsZ gene product is probably involved in the same repair pathways as UVSB or UVSH proteins. Although mutations in these proteins result in an NER phenotype, UVSB is related with cell cycle control and UVSH is associated with the post-replicational repair pathway. The epistatic interaction among uvsZl and uvsB413 and uvsH77 mutations indicates that different repair systems may be related with the common steps of DNA damage response in Aspergillus nidulans.

• Molecules and Cells
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• 제40권2호
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• pp.143-150
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• 2017

Homologous recombination (HR) is necessary for maintenance of genomic integrity and prevention of various mutations in tumor suppressor genes and proto-oncogenes. Rad51 and Rad54 are key HR factors that cope with replication stress and DNA breaks in eukaryotes. Rad51 binds to single-stranded DNA (ssDNA) to form the presynaptic filament that promotes a homology search and DNA strand exchange, and Rad54 stimulates the strand-pairing function of Rad51. Here, we studied the molecular dynamics of Rad51 and Rad54 during the cell cycle of HeLa cells. These cells constitutively express Rad51 and Rad54 throughout the entire cell cycle, and the formation of foci immediately increased in response to various types of DNA damage and replication stress, except for caffeine, which suppressed the Rad51-dependent HR pathway. Depletion of Rad51 caused severe defects in response to postreplicative stress. Accordingly, HeLa cells were arrested at the G2-M transition although a small amount of Rad51 was steadily maintained in HeLa cells. Our results suggest that cell cycle progression and proliferation of HeLa cells can be tightly controlled by the abundance of HR proteins, which are essential for the rapid response to postreplicative stress and DNA damage stress.