• Genomics & Informatics
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• 제3권4호
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• pp.154-158
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• 2005

Germ-line mutations of the BRCA1 gene confer an increased risk for breast and ovarian cancers. BRCA1 in female cells is directly related with the maintenance of the inactive X chromosome (Xi). The effect by the loss of the BRCA1 function on the X chromosome gene expression remains unclear in cancer cells. We attempted to investigate the expression pattern of the X-linked genes by performing BRCA1 knockdown via RNA interference in the MCF7 breast cancer cell line. The transcriptional and translational levels of BRCA1 were decreased over 95% in the MCF7 cells after BRCA1 knockdown. The expression patterns of one hundred ninety X-linked genes were profiled by the X chromosome-specific cDNA arrays. A total of seven percent of the X-linked genes (14/190) were aberrantly expressed by over 2-fold in the MCF7-BRCA1 knockdown cells, which contained two up-regulated genes (2/190, 1 %) and 12 down-regulated genes (12/190, 6.3%). It is interesting that 72% of the aberrantly expressed X-linked genes were located on the Xq (10/14,) region. Our data suggests that BRCA1 may not be important to maintain X chromosome inactivation in cancer because the BRCA1 knockdown did increase the expression of the only one percent of X-linked genes in the human breast cancer cells.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2006년도 Principles and Practice of Microarray for Biomedical Researchers
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• pp.98-107
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• 2006

Chromosomal copy number changes (aneuploidies) are common in human populations. The extra chromosome can affect gene expression by whole-genome level. By gene expression microarray analysis, we want to find aberrant gene expression due to aneuploidies in Klinefelter (+X) and Down syndrome (+21). We have analyzed the inactivation status of X-linked genes in Klinefelter Syndrome (KS) by using X-linked cDNA microarray and cSNP analysis. We analyzed the expression of 190 X-linked genes by cDNA microarray from the lymphocytes of five KS patients and five females (XX) with normal males (XY) controls. cDNA microarray experiments and cSNP analysis showed the differentially expressed genes were similar between KS and XX cases. To analyze the differential gene expressions in Down Syndrome (DS), Amniotic Fluid (AF)cells were collected from 12 pregnancies at $16{\sim}18$ weeks of gestation in DS (n=6) and normal (n=6) subjects. We also analysis AF cells for a DNA microarray system and compared the chip data with two dimensional protein gel analysis of amniotic fluid. Our data may provide the basis for a more systematic identification of biological markers of fetal DS, thus leading to an improved understanding of pathogenesis for fetal DS.

• Reproductive and Developmental Biology
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• 제35권3호
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• pp.209-214
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• 2011

Although the function and utility of RNA transcripts derived from matured spermatozoa remains unclear, they might play important roles in the establishment of a paternal genome and subsequently embryo development. Herein, we investigated the expression of X-chromosome linked RNA transcripts in matured bovine spermatozoa. The total RNA was extracted from the matured spermatozoa, and then converted to cDNA. Autosomal genes (ACT-${\beta}$ and H-2A) and X-chromosome linked genes (ANT3, HPRT, MeCP2, RPS4X, XIAP, XIST and ZFX) were analyzed for the characterization of X-chromosome linked RNA transcripts and compared to female fibroblasts by RT-PCR. The transcripts of autosomal genes (ACT-${\beta}$ and H2A) and X-chromosome linked genes (ANT3, HPRT, MeCP2, RPS4X and ZFX) were not detected in spermatozoa. However, XIAP (X-linked inhibitor of apoptosis protein) and XIST (X-chromosome inactive-specific transcript, a kind of paternal imprinted gene) transcripts were detected in spermatozoa, and relative levels of XIAP and XIST transcripts were similar and 0.5-fold lower when compared to female fibroblasts, respectively. Based on the findings, it is summarized that the presence of RNA transcripts of XIAP and XIST in the isolated spermatozoa may imply their role in inhibition of apoptosis and induction of X-chromosome inactivation in embryo development.

• 한국산림과학회지
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• 제84권1호
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• pp.77-86
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• 1995

임목을 대상으로 삽입된 외래 유전자의 공간적, 시기별 발현 특성을 이해하기 위한 기초연구로서 온실에서 생육 중인 형질전환된 2년생 잡종 포플러 (Populus alba X P. grandidentata) Hansen 클론을 대상으로 삽입된 외래 유전자의 발현정도를 각 기관별로 조사하였다. Agrobacterium binary vector pRT45, pRT102 및 pRT104에 의해서 형질전환된 3계통의 형질전환체 Tr15, Tr345, Tr665 모두는 선발가능한 표식 유전자로서 nos promoter-NPT II 유전자가 대상 식물체의 genome에 삽입되어 있으며, 그외에, pin2 promoter-CAT 유전자(pRT45), nos promoter-PIN2 유전자(pRT102), Cauliflower Mosaic Virus 35s promoter-PIN2 유전자(pRT104)가 3계통의 형질전환체에 제각각 삽입되어 있는 잡종 포플러이다. 이들 3계통의 형질전환 포플러 식물체의 DNA를 PCR 검정 기법을 이용하여 분석해 본 결과 선발 가능한 표식 유전자인 NPT-II가 삽입되어 있음이 입증되었다 발현 정도를 비교 분석하기 위해서 NPT-ELISA 검정을 실시하였다. 삽입된 NPT II 유전자는 형질전환된 포플러의 잎, 엽병, 형성층 조직, 줄기의 목질부, 뿌리에서 발현되었으며, 발현 정도는 형질전환된 식물체의 계통에 따라서, 그리고 형진전환된 식물체의 부위에 따라서 다양하게 나타났다. pRT45에 의해서 형질전환된 Tr15 형질전환체의 경우, 늙은 잎과 엽병에서 NPT II 유전자가 가장 높은 수준으로 발현되었으며, 어린 잎과 뿌리 조직에서 가장 낮게 발현되었다. 삽입된 외래 유전자가 각 식물체간에, 각 기관에 따라서 각각 상이한 발현 정도를 나타내는 이와 같은 결과는 형질전환된 식물체에 대한 효과적인 선발과정이 요구됨을 의미함은 물론이고, 형질전환 식물체의 발달 과정에 따라서 삽입된 외래 유전자가 공간적, 시기적으로 각각 다르게 발현할 수 있다는 것을 나타낸다.

• Reproductive and Developmental Biology
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• 제34권3호
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• pp.193-199
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• 2010

We report here the production of transgenic chickens that can regulate human erythropoietin (hEPO) gene expression. The glycoprotein hormone hEPO is an essential for viability and growth of the erythrocytic progenitors. Retrovirus vector system used in this study has two features including tetracycline-controllable promoter and woodchuck hepatitis virus posttranscriptional regulator element (WPRE). The former is for to reduce the possibility of physiological disturbance due to constitutional and unregulated expression of hEPO gene in the transgenic chicken. The latter is for maximum expression of the foreign gene when we turn-on the gene expression. A replication-defective Moloney murine leukemia virus (MoMLV)-based vectors packaged with vesicular stomatitis virus G glycoprotein (VSV-G) was injected beneath the blastoderm of non-incubated chicken embryos (stage X). Out of 325 injected eggs, 28 chicks hatched after 21 days of incubation and 16 hatched chicks were found to express the hEPO gene delivered by the vector. The biological activity of the recombinant hEPO in transgenic chicken serum was comparable to its commercially available counterpart. The recombinant hEPO in transgenic chicken serum had N- and O-linked carbohydrate simillar to that produced from in vitro cultured cells transformed with hEPO gene.

• Genomics & Informatics
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• 제14권1호
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• pp.34-40
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• 2016

Due to advances in omics technologies, numerous genome-wide studies on human samples have been published, and most of the omics data with the associated clinical information are available in public repositories, such as Gene Expression Omnibus and ArrayExpress. While analyzing several public datasets, we observed that errors in gender information occur quite often in public datasets. When we analyzed the gender description and the methylation patterns of gender-specific probes (glucose-6-phosphate dehydrogenase [G6PD], ephrin-B1 [EFNB1], and testis specific protein, Y-linked 2 [TSPY2]) in 5,611 samples produced using Infinium 450K HumanMethylation arrays, we found that 19 samples from 7 datasets were erroneously described. We also analyzed 1,819 samples produced using the Affymetrix U133Plus2 array using several gender-specific genes (X (inactive)-specific transcript [XIST], eukaryotic translation initiation factor 1A, Y-linked [EIF1AY], and DEAD [Asp-Glu-Ala-Asp] box polypeptide 3, Y-linked [DDDX3Y]) and found that 40 samples from 3 datasets were erroneously described. We suggest that the users of public datasets should not expect that the data are error-free and, whenever possible, that they should check the consistency of the data.

• Asian-Australasian Journal of Animal Sciences
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• 제19권2호
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• pp.165-170
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• 2006

Using the somatic cell hybrid panel (SCHP) and radiation hybrid (IMpRH) panel, porcine SOCS2 gene was mapped at SSC5 (1/2) q21-q24 and closely linked with SW1383 marker (47 cR in distance), while SOCS3 gene was assigned to SSC12p11-(2/3p13) and closely linked with SW2490 (43 cR). The reverse transcriptase-polymerase chain reaction (RT-PCR) was performed to detect the expression of these two genes in the different tissues and the results showed that both SOCS2 and SOCS3 genes were widely expressed in tissues investigated (heart, liver, spleen, lung, kidney skeletal muscle, fat and brain), although some tissues showed lower gene expression. Moreover, SOCS2 and SOCS3 genes had different expression levels at different stages, in different tissues and in different breeds. A G/A substitution, which can be recognized by restriction enzyme of Cfr421, was observed in 5' untranslated region (5'-UTR) of SOCS2 gene. The allele frequencies was investigated by PCR-restriction fragment length polymorphism (PCR-RFLP) method and it showed that the allele frequency among Dahuabai, Erhualian, Yushan, Qingping, Large white and Landrace tested were different. Association analysis in a cross experimental populations revealed no significant association between the SOCS2 gene polymorphism and the economic traits investigated. The full-length coding regions (CDs) of porcine SOCS3 gene was obtained by RT-PCR.

• 한국어병학회지
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• 제36권2호
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• pp.191-211
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• 2023

Rock bream iridovirus (RBIV) causes high mortality and economic losses in rock bream (Oplegnathus fasciatus) aquaculture industry in Korea. Although, the immune responses of rock bream under RBIV infection have been studied, there is not much information at the different stages of infection (initial, middle and recovery). Gene expression profiling of rock bream under different RBIV infection stages was investigated using a microarray approaches. In total, 5699 and 6557 genes were significantly up- or down-regulated over 2-fold, respectively, upon RBIV infection. These genes were grouped into categories such as innate immune responses, adaptive immune responses, complements, lectin, antibacterial molecule, stress responses, DNA/RNA binding, energy metabolism, transport and cell cycle. Interestingly, hemoglobins (α and β) appears to be important during pathogenesis; it is highly up-regulated at the initial stage and is gradually decreased when the pathogen most likely multiplying and fish begin to die at the middle or later stage. Expression levels were re-elevated at the recovery stage of infection. Among up-regulated genes, interferon-related genes were found to be responsive in most stages of RBIV infection. Moreover, X-linked inhibitor of apoptosis (XIAP)-associated factor 1 (XAF1) expression was high, whereas expression of apoptosis-relate genes were low. In addition, stress responses were highly induced in the virus infection. The cDNA microarray data were validated using quantative real-time PCR. Our results provide novel inslights into the broad immune responses triggered by RBIV at different infection stages.

• 생명과학회지
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• 제11권3호
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• pp.279-283
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• 2001

Amyotrophic lateral sclerosis(ALS) is a progressive neurologic disorder resulting from the degeneration of upper and lower motor neurons, and is inherited in 10% of cases. About 20% of familial ALS, clinically indistinguishable from sporadic ALS, is caused by mutations of Cu/Zn superoxide dismutase on chromosome 21q22.21 inherited as an autosomal dominant trait. We now report a new locus in the non-SOD1 dominantly inherited ALS. We screened a large ALS family with 11 affected individuals and one obligate gene carrier with genome-wide ABI polymorphic markers using the ABI 377 automated system. No evidence of linkage was obtained with the autosomal markers. We next screened this family with X chromosome markers as there was no evidence of male-to-male tran-smission of the disease. Linkage was established with several X chromosome markers with a lod score up to 3.8; almost the maximum possible score in this family. Our finding imply that a gene for the dominant expression of a neuronal degeneration is coded on X chromosome and raise the question of the role of X-linked genes that escape inactivation in this pathogenesis. More importantly, our finding that a gene causing ALS is localized on X-chromosome has direct investigational relevance to sporadic ALS, where epidemiological studies show male gender predominance(1.3:1) and earlier onset in men by 5-10 years.

• Molecules and Cells
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• 제37권5호
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• pp.357-364
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• 2014

Medulloblastoma, the most common malignant brain tumor in children, is a disease whose mechanisms are now beginning to be uncovered by high-throughput studies of somatic mutations, mRNA expression patterns, and epigenetic profiles of patient tumors. One emerging theme from studies that sequenced the tumor genomes of large cohorts of medulloblastoma patients is frequent mutation of RNA binding proteins. Proteins which bind multiple RNA targets can act as master regulators of gene expression at the post-transcriptional level to co-ordinate cellular processes and alter the phenotype of the cell. Identification of the target genes of RNA binding proteins may highlight essential pathways of medulloblastomagenesis that cannot be detected by study of transcriptomics alone. Furthermore, a subset of RNA binding proteins are attractive drug targets. For example, compounds that are under development as anti-viral targets due to their ability to inhibit RNA helicases could also be tested in novel approaches to medulloblastoma therapy by targeting key RNA binding proteins. In this review, we discuss a number of RNA binding proteins, including Musashi1 (MSI1), DEAD (Asp-Glu-Ala-Asp) box helicase 3 X-linked (DDX3X), DDX31, and cell division cycle and apoptosis regulator 1 (CCAR1), which play potentially critical roles in the growth and/or maintenance of medulloblastoma.