• Animal cells and systems
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• v.5 no.1
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• pp.71-75
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• 2001

Spin is an abundant maternal transcript comprising up to 0.2% of the total mRNA stock in mouse oocyte, whose protein product is associated with the meiotic spindle. We have identified a new isoform of Spin transcript containing a distinct 5'-untranslated region and the N-terminus of encoded protein. Northern blot and RT-PCR analysis showed that the new isoform is expressed in embryos and most of adult tissues, while the previously identified transcript is expressed solely in mouse oocyte. We thus designated these two Spin isoforms as somatic type and oocyte type, respectively. To investigate the underlying mechanism for the differential expression, genomic structure of Spin was examined. Spin exists as multiple copies in the genome, some of which appears to be pseudogenes, and characterization of Spin genomic clones indicates that oocyte- and somatic-isoforms were generated by alternative splicing. The complex organization of Spin genomic locus and its multifaceted control of expression provide a good model to study the molecular mechanisms of elaborate genome usage in mammals.

• Korean Journal of Agricultural Science
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• v.36 no.2
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• pp.159-165
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• 2009

This study was conducted to identify the PERV (Porcine Endogenous Retrovirus) integration sites and their characterizations using the porcine genomic sequence information. Total 114 Mb (4.2%) sequence of the 2.7 Gb pig genome was investigated for the PERV sequences. As the results, 8 PERV sequences were identified and their genomic structures were deduced from the BLAST searches against previously known PERV genes. Seven PERVs have internal deletions in the protein coding region and they will not be functional. The other one also has internal deletions in the gag and env genes, indicating this PERV is also defective. Even though we could not identify the functional PERVs in this study, the results presented here can be used for the fundamental research materials for controlling PERV infections in relation to xenotransplantation using porcine organs and tissues.

• The Korean Journal of Physiology and Pharmacology
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• v.21 no.2
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• pp.267-273
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• 2017

The p53-inducible gene 3 (PIG3), initially identified as a gene downstream of p53, plays an important role in the apoptotic process triggered by p53-mediated reactive oxygen species (ROS) production. Recently, several studies have suggested that PIG3 may play a role in various types of cancer. However, the functional significance of PIG3 in cancer remains unclear. Here, we found that PIG3 was highly expressed in human colon cancer cell lines compared to normal colon-derived fibroblasts. Therefore, we attempted to elucidate the functional role of PIG3 in colon cancer. PIG3 overexpression increases the colony formation, migration and invasion ability of HCT116 colon cancer cells. Conversely, these tumorigenic abilities were significantly decreased in in vitro studies with PIG3 knockdown HCT116 cells. PIG3 knockdown also attenuated the growth of mouse xenograft tumors. These results demonstrate that PIG3 is associated with the tumorigenic potential of cancer cells, both in vitro and in vivo, and could play a key oncogenic role in colon cancer.

• Genomics & Informatics
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• v.7 no.3
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• pp.159-162
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• 2009

Human personal genome sequencing can be done with high efficiency by aligning a huge number of short reads derived from various next generation sequencing (NGS) technologies to the reference genome sequence. One of the major obstacles is the incompleteness of human reference genome. We tried to analyze the effect of hidden gene duplication on the NGS data using the known example of hydin gene. Hydin2, a duplicated copy of hydin on chromosome 16q22, has been recently found to be localized to chromosome 1q21, and is not included in the current version of standard human genome reference. We found that all of eight personal genome data published so far do not contain hydin2, and there is large number of nsSNPs in hydin. The heterozygosity of those nsSNPs was significantly higher than expected. The sequence coverage depth in hydin gene was about two fold of average depth. We believe that these unique finding of hydin can be used as useful indicators to discover new hidden multiplication in human genome.

• Genomics & Informatics
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• v.14 no.4
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• pp.187-195
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• 2016

In genetic association studies with high-dimensional genomic data, multiple group testing procedures are often required in order to identify disease/trait-related genes or genetic regions, where multiple genetic sites or variants are located within the same gene or genetic region. However, statistical testing procedures based on an individual test suffer from multiple testing issues such as the control of family-wise error rate and dependent tests. Moreover, detecting only a few of genes associated with a phenotype outcome among tens of thousands of genes is of main interest in genetic association studies. In this reason regularization procedures, where a phenotype outcome regresses on all genomic markers and then regression coefficients are estimated based on a penalized likelihood, have been considered as a good alternative approach to analysis of high-dimensional genomic data. But, selection performance of regularization procedures has been rarely compared with that of statistical group testing procedures. In this article, we performed extensive simulation studies where commonly used group testing procedures such as principal component analysis, Hotelling's $T^2$ test, and permutation test are compared with group lasso (least absolute selection and shrinkage operator) in terms of true positive selection. Also, we applied all methods considered in simulation studies to identify genes associated with ovarian cancer from over 20,000 genetic sites generated from Illumina Infinium HumanMethylation27K Beadchip. We found a big discrepancy of selected genes between multiple group testing procedures and group lasso.

• Journal of Microbiology and Biotechnology
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• v.10 no.6
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• pp.823-828
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• 2000

The complete nucleotide sequence of hepatitis B virus DNA isolated from Korean patient serum was determined and characterized, and its phylogenetic relation was then investigated. The viral genome was 3,215 base pairs long and included four well known open reading frames (i.e. surface antigens, core antigens, X protein and DNA polymerase). The sequence of the surface antigen showed that the HBV genome under investigation, designated HBV 315, was characteristic of subtype adr. A phylogenetic analysis using the total genome sequence revealed that HBV315 was grouped into genomic group C together with isolates from Japan, China, Thailand, Polynesia, and New Caledonia. The mean percent similarity between HBV315 and other HBV isolates in genomic group C was 97.25%, and that with other genomic groups ranged from 86.16% to 91.25%. The predicted amino acid sequences of HBV315 were compared with two closely related subtype adr isolates, M38636 and D12980. The results showed that the X gene product was identical in the three strains, while there were significant amino acid sequence differences between HBV315 and M38636 in the Pre-S1 and Pre-S2 regions.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.10
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• pp.1368-1374
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• 2005

To investigate the genetic relationships among various cattle breeds, bovine mtDNA D-loop region was used in 411 animals of 18 cattle breeds, including 8 Asian Bos taurus, 7 European Bos taurus, 1 Asian Bos indicus, and 2 African Bos indicus. The size of amplified PCR products from mtDNA D-loop region was 964 bp and the products were digested by 15 different restriction enzymes. Two different band patterns were identified in eight restriction enzymes (BstXI, Hae III, Msp I, Apa I, Taq I, Alu I, BamH I, EcoN I) and the rest of restriction enzymes showed more than 3 different band patterns among which Apo I and MspR9 resulted in 7 different restriction patterns. The genotypes, number of haplotype, effective number of haplotype, and degree of heterozygosity were analyzed. Based on all the PCR-RFLP data, different haplotypes were constructed and analyzed for calculating genetic distances between these breeds using Nei's unbiased method and constructing a phylogenetic tree.

• Journal of Microbiology and Biotechnology
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• v.13 no.5
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• pp.783-788
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• 2003

A 27 bp $tRNA^{Gly}$ region (att1) was identified as the integration site for a 12,384 bp Pfl-derived genomic island containing 15 open reading frames (ORFs) from PA0715 to PA0729 in P. aeruginosa strain PAOl. Homologous island was observed in P. aeruginosa strain PA14, but not in P. aeruginosa strain K (PAK). We isolated the Pfl island from PA14, and determined its 10,657 bp sequences containing 14 ORFs, with significant sequence variations near the borders. In contrast to the PAO1 Pfl island, the PA14 Pfl island was integrated at the 10 bp att2 site between PA1191 and PA1192. The attl site of PA14, however, was still occupied by a third genetic segment, whereas both attl and att2 sites of PAK remained unutilized. These results exemplify an extensive genomic variation of Pfl-related islands involving differential genetic organizations and differential att site utilizations.

• Molecules and Cells
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• v.24 no.1
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• pp.105-112
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• 2007

Most neuroblastoma cells have chromosomal aberrations such as gains, losses, amplifications and deletions of DNA. Conventional approaches like fluorescence in situ hybridization (FISH) or metaphase comparative genomic hybridization (CGH) can detect chromosomal aberrations, but their resolution is low. In this study we used array-based comparative genomic hybridization to identify the chromosomal aberrations in human neuroblastoma SH-SY5Y cells. The DNA microarray consisting of 4000 bacterial artificial chromosome (BAC) clones was able to detect chromosomal regions with aberrations. The SH-SY5Y cells showed chromosomal gains in 1q12~ q44 (Chr1:142188905-246084832), 7 (over the whole chro-mosome), 2p25.3~p16.3 (Chr2:18179-47899074), and 17q 21.32~q25.3 (Chr17:42153031-78607159), while chromosomal losses detected were the distal deletion of 1p36.33 (Chr1:552910-563807), 14q21.1~q21.3 (Chr14:37666271-47282550), and 22q13.1~q13.2 (Chr22:36885764-4190 7123). Except for the gain in 17q21 and the loss in 1p36, the other regions of gain or loss in SH-SY5Y cells were newly identified.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.6
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• pp.762-766
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• 2005

This study was conducted to establish an individual identification system comprising of 19 microsatellite markers located on different bovine autosomes. The markers were typed on 257 animals from five cattle breeds. In total, 112 alleles were detected from the genotyping of 19 microsatellite markers. The average heterozygosities ranged from 0.292 to 0.824 and the polymorphic information content (PIC) ranged from 0.274 to 0.817 in Hanwoo. We found that there were differences in allele frequencies in Hanwoo when compared with other cattle breeds. The calculated cumulative power of discrimination (CPD) was 99.999% when nine microsatellite loci were used for analysis in the individual identification system. Also the matching probability, the probability that two unrelated animals would show the same genotypes, was estimated to be $0.44{\times}10^{-9}$. Therefore, the nine markers used in this study will be used for individual identification in two million Hanwoo individuals.