• International Journal of Stem Cells
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• v.15 no.3
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• pp.301-310
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• 2022

Background and Objectives: RUNX2 plays an essential role during the odontoblast differentiation of dental pulp stem cells (DPSCs). RUNX2 Exon 5 is an alternative exon and essential for RUNX2 transcriptional activity. This study aimed to investigate the regulatory mechanisms of RUNX2 exon 5 alternative splicing in human DPSCs. Methods and Results: The regulatory motifs of RUNX2 exon 5 were analyzed using the online SpliceAid program. The alternative splicing of RUNX2 exon 5 in DPSCs during mineralization-induced differentiation was analyzed by RT-PCR. To explore the effect of splicing factor YBX1 on exon 5 alternative splicing, gaining or losing function of YBX1 was performed by transfection of YBX1 overexpression plasmid or anti-YBX1 siRNA in DPSCs. Human RUNX2 exon 5 is evolutionarily conserved and alternatively spliced in DPSCs. There are three potential YBX1 binding motifs in RUNX2 exon 5. The inclusion of RUNX2 exon 5 and YBX1 expression level increased significantly during mineralization-induced differentiation in DPSCs. Overexpression of YBX1 significantly increased the inclusion of RUNX2 exon 5 in DPSCs. In contrast, silence of YBX1 significantly reduced the inclusion of exon 5 and the corresponding RUNX2 protein expression level. Knockdown of YBX1 reduced the expression of alkaline phosphatase (ALP) and osteocalcin (OC) and the mineralization ability of DPSCs, while overexpression of YBX1 increased the expression of ALP and OC and the mineralization ability of DPSCs. Conclusions: Human RUNX2 exon 5 is conserved evolutionarily and alternatively spliced in DPSCs. Splicing factor YBX1 promotes the inclusion of RUNX2 exon 5 and improves the mineralization ability of DPSCs.

• Proceedings of the Korean Statistical Society Conference
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• 2004.11a
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• pp.79-84
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• 2004

We use principal component analysis (PCA) to identify exons of a gene and further analyze their internal structures. The PCA is conducted on the short-time Fourier transform (STFT) based on the 64 codon sequences and the 4 nucleotide sequences. By comparing to independent component analysis (ICA), we can differentiate between the exon and intron regions, and how they are correlated in terms of the square magnitudes of STFTs. The experiment is done on the gene F56F11.4 in the chromosome III of C. elegans. For this data, the nucleotide based PCA identifies the exon and intron regions clearly. The codon based PCA reveals a weak internal structure in some exon regions, but not the others. The result of ICA shows that the nucleotides thymine (T) and guanine (G) have almost all the information of the exon and intron regions for this data. We hypothesize the existence of complex exon structures that deserve more detailed analysis.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.2
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• pp.511-516
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• 2012

Background: We investigated the association between polymorphisms in the $p53$ tumor suppressor gene and breast cancer risk in women especially in the Southern part of India. Methods: Genotyping was performed for 50 breast cancer women and 50 controls to determine the status of $p53$ exon 4 codon 72 polymorphism and exon 7 codon 249 mutation and their possible role in breast cancer risk. Results: Frequency of Arg/Arg at codon 72 was 18% in controls and 28% in patients, Arg/Pro frequency was 56% and 66%, Pro/Pro genotype was 8% in controls and 8% in patients. No significance was observed for breast cancer risk with either Arg/Arg or Pro/Pro genotype in codon 72 polymorphism. Similarly, mutation analysis of exon 7 codon 249 revealed that 72% of breast cancer patients have mutation, which is not statistically significant. However, there is a strong association between increase in exon 7 codon 249 mutation and exposure to pollution. Conclusion: The results suggested that there is no risk for exon 4 with Arg/Arg or Pro/Pro polymorphisms in the $p53$ gene and there is no strong correlation between breast cancer patients and mutation in exon 7 codon 249 in South Indian women.

• Journal of Pharmaceutical Investigation
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• v.39 no.6
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• pp.411-416
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• 2009

The aim of this study was to investigate the frequency of the SNPs on PEPT1 exon 5 and 16 and to analyze haplotype frequency on PEPT1 exon 5 and 16 in Korean population. A total of 519 healthy subjects was genotyped for PEPT1, using pyrosequencing analysis and polymerase chain reaction-based diagnostic tests. Haplotype was statistically inferred using an algorithm based on the expectation-maximization (EM). PEPT1 exon 5 G381A genotyping revealed that the frequency for homozygous wild-type (G/G), heterozygous (G/A) and homozygous mutant-type (A/A) was 30.4, 53.4 and 16.2%, respectively. PEPT1 exon 16 G1287C genotyping revealed that the frequency for homozygous G/G, heterozygous G/C and homozygous C/C type was 88.8, 10.0 and 1.2%, respectively. Based on these genotype data, haplotype analysis between PEPT1 exon 5 G381A and exon 16 G1287C using HapAnalyzer and PL-EM has proceeded. The result has revealed that linkage disequilibrium between alleles is not obvious (|D'|=0.3667).

• Genomics & Informatics
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• v.4 no.1
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• pp.33-39
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• 2006

Alternative splicing (AS) is an important mechanism of producing transcriptome diversity and microarray techniques are being used increasingly to monitor the splice variants. There exist three types of microarrays interrogating AS events-junction, exon, and tiling arrays. Junction probes have the advantage of monitoring the splice site directly. Johnson et al., performed a genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays (Science 302:2141-2144, 2003), which monitored splicing at every known exon-exon junctions for more than 10,000 multi-exon human genes in 52 tissues and cell lines. Here, we describe an algorithm to deduce the relative concentration of isoforms from the junction array data. Non-negative Matrix Factorization (NMF) is applied to obtain the transcript structure inferred from the expression data. Then we choose the transcript models consistent with the ECgene model of alternative splicing which is based on mRNA and EST alignment. The probe-transcript matrix is constructed using the NMF-consistent ECgene transcripts, and the isoform abundance is deduced from the non-negative least squares (NNLS) fitting of experimental data. Our method can be easily extended to other types of microarrays with exon or junction probes.

• The Journal of the Korea institute of electronic communication sciences
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• v.16 no.4
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• pp.675-682
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• 2021

In an environment in which a limited type and number of sensors are used, a demand for acquiring various context information may appear. In this study, a new method for acquiring various context information than before was proposed in an environment in which a limited number of sensors are required. To this end, a clue was obtained from the Exon-Intron theory, which is gaining great interest in the field of biology, and a method for acquiring various context information was proposed based on this. By applying Exon-Intron's selective cutting and combining method, events of each sensor were efficiently cut and each event data was combined and utilized, thereby realizing the diversification of the acquired context information.

• Journal of Life Science
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• v.14 no.6 s.67
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• pp.1009-1017
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• 2004

Sialyltransferases cloned so far show the remarkable tissue-specific expression, which is correlated with the existence of cell type-specific sialylated sugar structure in glycoconjugates. In the previous studies, we found various mRNA isoforms of human sialyltransferases generated by alternative splicing and alternative promoter utilization. To understand the regulatory mechanisms for specific expression of human sialyltransferase genes and for production of their mRNA isoforms, in this study, we have isolated and characterized five kinds of human sialyltransferase genes: hST3Gal II, hST8Sia II, hST8Sia III, hST8Sia IV, and hST8Sia V. The hST3Gal II gene is composed of six exons, which span over 17kb, with exons ranging in size from 46 to over 1017 bp. The hST8Sia III gene comprises over 10 kb, and consists of only four exons, which is much smaller and simpler than other human sialyltransferase genes. In contrast, three genes (hST8Sia II, hST8Sia IV and hST8Sia V) span more than 70 kb, and comprise five or more exons. All exon-intron boundaries follow the GT-AG rule. In particular, the sialylmotif L, which is a highly conserved region in all cloned sialyltransferases, was found in one exon of hST8Sia III, whereas this motif is encoded by discrete exons in the other human sialyltransferases. Exon structures of these sialyltransferase genes show the structural diversity, as found in other human sialyltransferase genes reported so far. We determined the transcription start site of hST3Gal II gene by the 5'-RACE and cap site hunting experiments.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.3
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• pp.315-320
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• 2016

Porcine beta-defensin-1 (PBD-1) gene plays an important role in the innate immunity of pigs. The peptide encoded by this gene is an antimicrobial peptide that has direct activity against a wide range of microbes. This peptide is involved in the co-creation of an antimicrobial barrier in the oral cavity of pigs. The objective of the present study was to detect polymorphisms, if any, in exon-1 and exon-2 regions of PBD-1 gene in Large White Yorkshire (LWY) and native Ankamali pigs of Kerala, India. Blood samples were collected from 100 pigs and genomic DNA was isolated using phenol chloroform method. The quantity of DNA was assessed in a spectrophotometer and quality by gel electrophoresis. Exon-1 and exon-2 regions of PBD-1 gene were amplified by polymerase chain reaction (PCR) and the products were subjected to single strand conformation polymorphism (SSCP) analysis. Subsequent silver staining of the polyacrylamide gels revealed three unique SSCP banding patterns in each of the two exons. The presence of single nucleotide polymorphisms (SNPs) was confirmed by nucleotide sequencing of the PCR products. A novel SNP was found in the 5'-UTR region of exon-1 and a SNP was detected in the mature peptide coding region of exon-2. In exon-1, the pooled population frequencies of GG, GT, and TT genotypes were 0.67, 0.30, and 0.03, respectively. GG genotype was predominant in both the breeds whereas TT genotype was not detected in LWY breed. Similarly, in exon-2, the pooled population frequencies of AA, AG, and GG genotypes were 0.50, 0.27, and 0.23, respectively. AA genotype was predominant in LWY pigs whereas GG genotype was predominant in native pigs. These results suggest that there exists a considerable genetic variation at PBD-1 locus and further association studies may help in development of a PCR based genotyping test to select pigs with better immunity.

• Journal of the Korean Chemical Society
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• v.50 no.2
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• pp.116-122
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• 2006

In this study we extracted DNA from 100 tissues of breast cancer patients and 103 normals. Then we confirmed single-nucleotide polymorphism(SNP) using PCR-DHPLC(polymerase chain reaction-denaturing high performance liquid chromatogrphy).Also, we studied SNP of samples using several columns to identify relation between packing materials of column and resolution.As a result, we identified 4 C/A, C/G genotypes(4%) in exon 5 and 37 T del genotypes(37%) in exon 8 among 100 breast cancer tissues and 2 in exon 5, 9 in exon 8 among 103 normal samples.In resolution test, we confirmed that PS-DVB(poly styrene-divinylbenzen) column is more efficient than C18 column.

• Journal of Gastric Cancer
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• v.6 no.4
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• pp.214-220
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• 2006

Purpose: p53 is one of the most commonly mutated genes in human tumors. The aim of this study was to analyze p53 mutation in gastric cancer and its correlations with the clinicopathologic variables to clarify the usefulness of p53 mutation as a prognostic factor. Materials and Methods: Specimens from 331 patients with gastric cancer who underwent a gastrectomy between March 1999 and April 2001 at the Kyungpook National University Hospital were used. p53 gene mutations were assessed by using a polymerase chain-reaction single-strand conformation polymorphism (PCR-SSCP) analysis. The correlations between p53 gene mutation and clinocopathologic parameters were analyzed. Results: p53 mutations were found in 66 (19.9%) tumors. Among those 66 cases, mutations were seen in 23 tumors at axon 5, in 8 at exon 6, in 21 at exon 7, and in 17 at exon 8. Two mutations were shown in 3 tumors. Thiriy-six (23.1%) of 156 intestinal-type tumors and 19 (13.1%) of 145 diffuse-type tumors showed p53 gene mutation (P=0.007). The frequency of p53 gene mutation didn't show any significant differences according to age, sex, stage, location, or gross type. Exon 5 mutations showed more frequently in intestinal-type tumors than in diffuse-type tumors (9.7% vs. 2.8%, P=0.024), and p53 mutation were more frequent in lymph nodes metastasis group than lymph nodes non-metastasis group with statistical significance (25.0% vs 15.6%, P=0.034). The five-year survival rate showed no statistically significant difference with p53 mutation (P=0.704). Conclusion: p53 mutations assessed by PCR-SSCP had little value as a prognostic factor after gastrectomy in patients with gastric cancer.