• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.61-68
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• 2000

Now that the complete genomes of numerous organisms have been ascertained, key problems in molecular biology include determining the functions of the genes in each organism, the relationships that exist among these genes, and the regulatory mechanisms that control their operation. These problems can be partially addressed by using machine learning methods to induce predictive models from available data. My group is applying and developing machine learning methods for several tasks that involve characterizing gene regulation. In one project, for example, we are using machine learning methods to identify transcriptional control elements such as promoters, terminators and operons. In another project, we are using learning methods to identify and characterize sets of genes that are affected by tumor promoters in mammals. Our approach to these tasks involves learning multiple models for inter-related tasks, and applying learning algorithms to rich and diverse data sources including sequence data, microarray data, and text from the scientific literature.

• YAKHAK HOEJI
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• v.49 no.3
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• pp.205-211
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• 2005

The 3' UTR (3' untranslated region) plays important roles in controlling gene expression through regulating 3' polyadenylation, mRNA export, subcellular localization, translational efficiency, and mRNA stability. Changes in the 3' UTR sequence in an expressed transcript can result in functional changes of the genes that are expressed in pathological conditions compared with those genes expressed in normal physiologic conditions. A genome-wide survey of 3' UTR variation was performed for the genes expressed during hematopoietic differentiation from CD34+ stem/progenitor cells to CD 15 + myeloid progenitor cells. Wide-spread differential usage of the 3' UTR was observed from the genes expressed during this cellular transition. This study implies that the 3' UTR can be a highly coordinated region for post-transcriptional regulation of the function of expressed genes.

• Molecules and Cells
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• v.28 no.5
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• pp.407-415
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• 2009

The sirtuins are a protein family named after the first identified member, S. cerevisiae Sir2p. Sirtuins are protein deacetylases whose activity is dependent on $NAD^+$ as a cosubstrate. They are structurally defined by two central domains that together form a highly conserved catalytic center, which catalyzes the transfer of an acetyl moiety from acetyllysine to $NAD^+$, yielding nicotinamide, the unique metabolite O-acetyl-ADP-ribose and deacetylated lysine. One or more sirtuins are present in virtually all species from bacteria to mammals. Here we describe a phylogenetic analysis of sirtuins. Based on their phylogenetic relationship, sirtuins can be grouped into over a dozen classes and subclasses. Humans, like most vertebrates, have seven sirtuins: SIRT1-SIRT7. These function in diverse cellular pathways, regulating transcriptional repression, aging, metabolism, DNA damage responses and apoptosis. We show that these seven sirtuins arose early during animal evolution. Conserved residues cluster around the catalytic center of known sirtuin family members.

• Archives of Pharmacal Research
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• v.22 no.3
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• pp.229-231
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• 1999

Recessive oncogenes are genetic functions important in the regulation of tissue growth and differentiation. These genetic functions are defined on the basis of the phenotype expressed by homozygotes. Defining the role of these genes in normal developmental and physiological processes is important to the development of accurate models of the normal regulation of growth and differentiation. Drosophila can be a good system to investigate the neoplastic mechanism of oncogenes and provide a greater understanding in the developmental progression of both invertebrates and vertebrates and vertebrates. The lethal (2) giant larvae gene is a recessive oncogene of Drosophila and temperature sensitive mutations of this gene have been isolated. Here, the application of temperature-sensitive mutations in Drosophila oncogene studies is discussed.

• Animal Bioscience
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• v.34 no.8
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• pp.1271-1282
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• 2021

Genome-wide studies provide considerable insights into the genetic background of animals; however, the inheritance of several heritable factors cannot be elucidated. Epigenetics explains these heritabilities, including those of genes influenced by environmental factors. Knowledge of the mechanisms underlying epigenetics enables understanding the processes of gene regulation through interactions with the environment. Recently developed next-generation sequencing (NGS) technologies help understand the interactional changes in epigenetic mechanisms. There are large sets of NGS data available; however, the integrative data analysis approaches still have limitations with regard to reliably interpreting the epigenetic changes. This review focuses on the epigenetic mechanisms and profiling methods and multi-omics integration methods that can provide comprehensive biological insights in animal genetic studies.

• Proceedings of the Korean Society of Applied Pharmacology
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• 1998.11a
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• pp.140-140
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• 1998

The aim of this study was to find out the effect of hypoxic condition on the regulation of cyplal gene expression. pcyplal-Luc construct was cloned and transfected into Hepa I cells. When Hepa-I cells containing pcyplal-Luc were treated by DFO (desferrioxamine) which is iron-chelating agent, the stimulatory effect of luciferase by TCDD was decreased. This inhibitory effect of desferrioxamine on the luciferase activity was dose dependent and abolished by concomitant treatment with N$\^$G/-nitro-ι-arginine. And when cobalt chloride which is known as a hypoxia inducing chemical was administrated, the stimulatory effect of luciferase by TCDD was also decreased. This inhibitory effect of cobalt chloride on the luciferase activity was dose dependent and abolished by concomitant treatment with N$\^$G/-nitro-ι-arginine. These data showed that hypoxic condition down regulates cyplal gene expression and this might be through nitric oxide action.

• IMMUNE NETWORK
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• v.22 no.5
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• pp.39.1-39.18
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• 2022

RNA metabolism plays a central role in regulating of T cell-mediated immunity. RNA processing, modifications, and regulations of RNA decay influence the tight and rapid regulation of gene expression during T cell phase transition. Thymic selection, quiescence maintenance, activation, differentiation, and effector functions of T cells are dependent on selective RNA modulations. Recent technical improvements have unveiled the complex crosstalk between RNAs and T cells. Moreover, resting T cells contain large amounts of untranslated mRNAs, implying that the regulation of RNA metabolism might be a key step in controlling gene expression. Considering the immunological significance of T cells for disease treatment, an understanding of RNA metabolism in T cells could provide new directions in harnessing T cells for therapeutic implications.

• Reproductive and Developmental Biology
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• v.35 no.3
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• pp.215-219
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• 2011

Acyl-CoA synthetase 4(ACSL4) is an arachidonate-preferring enzyme abundant in steroidogenic tissues and postulated to modulate eicosanoid production. The human and mouse ACSL4 gene are mapped on chromosome X. The female mice heterozygous for ACSL4 deficiency became pregnant less frequent1y and produced small litters, with 40% of embryos surviving gestation. In this study, we examined the regulation of ACS4 by estradiol-$17{\beta}$ and progesterone (P4) in the human endometrial cancer cell line HTB-1B. ACSL4 mRNA was increased in a dose-dependent manner. Also, expression of ACSL4 gene was up-regulated in a time-dependent manner in HTB-1B cells. However, combined treatment with progesterone and estradiol-$17{\beta}$ modestly decreased the levels of ACS4L mRNA as compared with the estradiol-$17{\beta}$ and progesterone respectively. Overall, these results suggest that the ACSL4 gene is regulated by progesterone and estradiol-$17{\beta}$ in the HTB-1B cells.

• Journal of Microbiology and Biotechnology
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• v.16 no.5
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• pp.795-798
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• 2006

The phosphoenolpyruvate-dependent carbohydrate phosphotransferase system (PTS) is responsible for the simultaneous transfer and phosphorylation of various carbon sources in Escherichia coli. The ptsG gene encoding the enzyme $IICB^{Glc}$, the membrane component of the glucose-specific PTS, is repressed by Mlc and activated by the CRP cAMP complex; various other factors, such as Fis, FruR, and ArcA, are also known to be involved in ptsG regulation. Thus, in an attempt to discover a novel gene affecting the regulation of ptsG, a mutant with a decreased ptsG transcription in the presence of glucose compared with the wild-type strain was screened using transposon random mutagenesis. The mutant was found to have a transposon insertion in yhjV, a putative gene encoding a transporter protein whose function is yet unknown.

• Journal of fish pathology
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• v.16 no.2
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• pp.111-118
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• 2003

Androgen plays an important role in the regulation of gonadotropin production in vertebrates . We have investigated the transcriptional pattern of androgen receptor (AR) in a variety of tissues in maturing male and female goldfish by RT-PCR. Specific primer for AR was designed based on goldfish AR gene from the GenBank (accession number AY090897). AR was shown 10 be maturity- and tissue-dependent gene expression pattern in goldfish. In immature male goldfish, significantly higher transcript level of AR was observed in the pituitary und testis , compared [0 brain and liver. Mature male goldfish showed a similar expression pattern to immature male goldfish. Interestingly. when compare to male goldfish, female goldfish showed AR mRNA expression that was found 10 be weak in pituitary, and very low expression in brain. They could not be found 10 have expression in any other tissues. Taken together. the- transcriptional analysis of AR depending on the tissue, sex. and maturity of a goldfish provides the opportunity for the study of goldfish reproductive physiology ,The results provided for the first time a comparison of the tissue distribution of AR mRNA in sexually maturating male and female goldfish.