• Genomics & Informatics
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• v.13 no.2
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• pp.40-44
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• 2015

DNA microarray and next-generation sequencing provide data that can be used for the genetic analysis of multiple quantitative traits such as gene expression levels, transcription factor binding profiles, and epigenetic signatures. In particular, chromatin opening is tightly coupled with gene transcription. To understand how these two processes are genetically regulated and associated with each other, we examined the changes of chromatin accessibility and gene expression in response to genetic variation by means of quantitative trait loci mapping. Regulatory patterns commonly observed in yeast and human across different technical platforms and experimental designs suggest a higher genetic complexity of transcription regulation in contrast to a more robust genetic architecture of chromatin regulation.

• Proceedings of the Korean Society of Toxicology Conference
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• 2003.10b
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• pp.155-156
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• 2003

RNA was isolated from mucosal tissue of the duodenum, jejunum, ileum and colon after perfusion. The gene expression profiles were measured using Affymetrix GeneChip(R) analysis. Prodrug valacyclovir permeability was 5-fold and 2-fold higher than the parent drug acyclovir in the jejunum and ileum, respectively.(omitted)

• BMB Reports
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• v.52 no.1
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• pp.70-85
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• 2019

Reduction of insulin/insulin-like growth factor 1 (IGF1) signaling (IIS) extends the lifespan of various species. So far, several longevity mouse models have been developed containing mutations related to growth signaling deficiency by targeting growth hormone (GH), IGF1, IGF1 receptor, insulin receptor, and insulin receptor substrate. In addition, p70 ribosomal protein S6 kinase 1 (S6K1) knockout leads to lifespan extension. S6K1 encodes an important kinase in the regulation of cell growth. S6K1 is regulated by mechanistic target of rapamycin (mTOR) complex 1. The v-myc myelocytomatosis viral oncogene homolog (MYC)-deficient mice also exhibits a longevity phenotype. The gene expression profiles of these mice models have been measured to identify their longevity mechanisms. Here, we summarize our knowledge of long-lived mouse models related to growth and discuss phenotypic characteristics, including organ-specific gene expression patterns.

• Reproductive and Developmental Biology
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• v.30 no.2
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• pp.143-156
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• 2006

Major characteristics of embryonic stem cells (ESCs) are sustaining of sternness and pluripotency by self-renewal. In this report, transcriptional profiles of the molecules in the developmentally important signaling pathways including Wnt, BMP4, $TGF-\beta$, RTK, Hh, Notch, and JAK/STAT signaling pathways were investigated to understand the self-renewal of mouse ESCs (mESCs), J1 line, and compared with the NIH3T3 cell line and mouse embryonic fibroblast (MEF) cells as controls. In the Wnt signaling pathway, the expression of Wnt3 was seen widely in mESCs, suggesting that the ligand may be an important regulator for self-renewal in mESCs. In the Hh signaling pathway, the expression of Gli and N-myc were observed extensively in mESCs, whereas the expression levels of in a Shh was low, suggesting that intracellular molecules may be essential for the self-renewal of mESCs. IGF-I, IGF-II, IGF-IR and IGF-IIR of RTK signaling showed a lower expression in mESCs, these molecules related to embryo development may be restrained in mESCs. The expression levels of the Delta and HESS in Notch signaling were enriched in mESCs. The expression of the molecules related to BMP and JAK-STAT signaling pathways were similar or at a slightly lower level in mESCs compared to those in MEF and NIH3T3 cells. It is suggested that the observed differences in gene expression profiles among the signaling pathways may contribute to the self-renewal and differentiation of mESCs in a signaling-specific manner.

• Archives of Pharmacal Research
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• v.27 no.4
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• pp.422-428
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• 2004

Expressed sequence tags (ESTs) were generated from two 3'-directed CDNA libraries constructed from quiescent and activated rat hepatic stellate cell (HSC) to analyze the expression profiles of active genes in both cells. From quiescent and activated HSC, 694 ESTs and 779 ESTs, respectively, were obtained after excluding those having shorter than 30 bp. Amonq ESTs obtained from quiescent and activated HSC, 68 and 73 kinds of ESTs (186 clones and 236 clones), respectively, appeared more than once, implying that their genes are expressed highly in each cell type. 52 among 73 ESTs appeared only in the activated HSC 47 amonq 68 ESTs only in the normal HSC, and 21 in both cells. The genes of these 52 ESTs were assumed to be expressed more highly in the activated HSC. To confirm the high expression of genes of which the ESTs appeared more than twice in the activated HSC, northern hybridization was carried out with RNAs derived from rat normal and fibrotic liver using each of 18 EST DNAs as probe. 13 ESTs showed more intense bands with RNA isolated from the fibrotic liver than normal liver. From these results, we confirm the positive correlation between abundance of transcript in activated HSCs and the expression level in fibrotic liver, The expression profile of the transcripts serves as an important tool in understanding the biological properties of HSC.

• Journal of Acupuncture Research
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• v.23 no.4
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• pp.135-148
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• 2006

Objectives : Juglandis Semen herbal acupuncture solution(JSS) has a broad array of clinical applications in oriental medicine, including treatment of chronic musculoskeletal diseases such as arthritis. This study was performed to investigate the global gene expression profiles using microarray assay in RAW 264.7 cell line treated with JSS and to advance our understanding of the pharmacologic effect of Jss. Methods : Change of the gene expression profile in RAW cell line following treatment with JSS alone, with lipopolysaccharide(LPS) alone, or with LPS plus JSS was investigated with a cut-off level of 2 fold change in the expression. Results : Of the 8170 genes profiled in this study, 95 were upragulated and 42 downregulated following JSS treatment, 51 were upragulated and 21 downregulated following LPS treatment, and 88 were upregulated and 69 downregulated following costimulation of JSS and LPS. Conclusion : JSS treatment induced upregulation of some genes including IL-10 with its possible implication in an antiinflammatory action of JSS. However, further research on expression profile changes induced by JSS treatment is expected.

• Development and Reproduction
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• v.15 no.4
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• pp.331-338
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• 2011

MicroRNAs (miRNAs) function as a key regulator of diverse cellular functions. To find out novel miRNAs that promote the differentiation of mouse embryonic stem cells (mESCs), we compared the miRNAs expression profiles of mESCs under self-renewal vs. differentiation states. We noticed that miR-222 was highly expressed during the differentiation of mESCs. Quantitative RT-PCR analysis revealed that expression of miR-222 was up-regulated during the embryonic bodies formation and retinoic acid -dependent differentiation. When miR-222 was suppressed by antogomiR-222, the differentiation of mESCs was delayed compared to control. Self-renewal marker expression or cell proliferation was not affected but the expression of lineage specific marker was suppressed by the treatment of miR-222 inhibitor during the differentiation of mESCs. Taken together, these results suggest that miR-222 functions to promote the differentiation of mESCs by regulating expression of differentiation related genes.

• Biomedical Science Letters
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• v.12 no.1
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• pp.53-56
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• 2006

The suprachiasmatic nucleus (SCN) of the anterior hypothalamus is the circadian pacemaker entrained to the 24-hr day by environmental time cues. Major circadian genes such as mPeriod ($mPer1{\sim}3$) and mCryptochrome ($mCry1{\sim}2$) are actively transcribed by the action of CLOCK/BMAL heterodimers, and in turn, these are being suppressed by the mPER/mCRY complex. In the study, the locomotor activity rhythms of mPer1 Knockout (KO) mice are measured, and the expression profiles of Heat Shock Protein 105kDa (HSP 105) genes in the SCN were measured by in situ hybridization. In agreement with previous reports, the locomotor activity rhythm of mPer1 KO mice was much shorter than that of wildtype. In addition, the total bout of activity of mPer1 KO was less in comparison to control mice. The expression of HSP 105 in the SCN of mPer1 KO mice was ranged from CT6 to CT22, with a peak level at CT14, implying that the gene are under the control of circadian clock. However, the expression of HSP 105 in the SCN of wildtype could not be detected in our study. Further analysis will reveal the direct or indirect regulation by mPer1 on the expression in the SCN and the role of the gene in the circadian clock.

• The Plant Pathology Journal
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• v.25 no.2
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• pp.172-178
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• 2009

To obtain global gene expression profiles of Arabidopsis thaliana by acid stress, seedlings were subjected to low pH stress. Using Affymetrix AH1 chips covering 24,000 genes, we analyzed gene expression patterns. Fifty-four genes were up-regulated, and 38 were down-regulated more than 3-fold after 2 h of acid stress (pH 3.0). Several defense and abiotic stress-related genes were recognized among the up-regulated genes and peroxidase and extensin genes were identified among the down-regulated genes. After 12 h treatment, relatively fewer genes showed changed expression, indicating that plants seem to adjust themselves to this abiotic stress. Most of the up-regulated genes are already known to be involved in abiotic stress responses and pathogen attacks, especially wounding. However, down-regulated genes for the members of extensins and peroxidases are specific to the acid treatment. These results suggest that acid treatment turns on genes involved in stress responses, especially in wounding and turns off genes very specific for the acid stress.

• Journal of Microbiology and Biotechnology
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• v.16 no.4
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• pp.543-549
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• 2006

DNA microarray was used to study the transcription profiling of Escherichia coli adapting to acetate as a sole carbon source. Bacteria grown in glucose minimal media were used as a reference. The dynamic expression levels of 3,497 genes were monitored at seven time points during this adaptation. Among the central metabolic genes, the glycolytic and glucose phosphotransferase genes were repressed as the bacteria entered stationary phase, whereas the glyoxylate pathway, TCA cycle, and gluconeogenic genes were induced. Distinct induction or repression patterns were recognized among different pathway genes. For example, the repression of glycolytic genes and the induction of gluconeogenic ones started immediately after glucose was depleted. On the other hand, the regulation of the pentose phosphate pathway genes and glyoxylate genes gradually responded to the glucose depletion or was more related to growth in acetate. When the whole genome was considered, many of the CRP, FadR, and Cra regulons were immediately responsive to the glucose depletion, whereas the $\sigma^s$, Lrp, and IHF regulons were gradually responsive to the glucose depletion. The expression profiling also provided differential regulations between isoenzymes; for example, malic enzymes A (sfcA) and B (maeB). The expression profiles of three genes were confirmed with RT-PCR.