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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
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Genomics & Informatics
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Korea Genome Organization
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Volume & Issues
Volume 3, Issue 4 - Dec 2005
Volume 3, Issue 3 - Sep 2005
Volume 3, Issue 2 - Jun 2005
Volume 3, Issue 1 - Mar 2005
Selecting the target year
Genomic Features of Retroelements and Implications for Human Disease
Kim, Heui-Soo ;
Genomics & Informatics, volume 3, issue 4, 2005, Pages 133~141
Most of the endogenous retroviral genes integrated into the primate genome after the split of New World monkeys in the Oligocene era, approximately 33 million years ago. Because they can change the structure of adjacent genes and move between and within chromosomes they may play important roles in evolutionas well as in many kinds of disease and the creation of genetic polymorphism. Comparative analysis of HERVs (human endogenous retroviruses) and their LTR (long terminal repeat) elements in the primate genomes will help us to understand the possible impact of HERV elements in the evolution and phylogeny of primates. For example, HERV-K LTR and SINE-R elements have been identified that have been subject to recent change in the course of primate evolution. They are specific elements to the human genome and could be related to biological function. The HERV-M element is related to the superfamily of HERV-K and is integrated into the periphilin gene as the truncated form, 5'LTR-gag-pol-3'LTR. PCR and RT-PCR approaches indicated that the insertion of various retrotransposable elements in a common ancestor genome may make different transcript variants in different primate species. Examination of the HERV-W elementrevealed that env fragments were detected on human chromosomes 1, 3-7, 12, 14, 17, 20, and X, whilst the pol fragments were detected on human chromosomes 2-8, 10-15, 20, 21, X, and Y. Bioinformatic blast search showed that almost full-length of the HERV-W family was identified on human chromosomes 1-8, 11-15, 17, 18, 21, and X. Expression analysis of HERV-W genes (gag, pol, and env) in human tissues by RT-PCR indicated that gag and pol were expressed in specific tissues, whilst env was constituitively expressed in all tissues examined. DNA sequence based phylogenetic analysis indicated that the gag, pol and env genes have evolved independently during primate evolution. It will thus be of considerable interest to expand the current HERV gene information of various primates and disease tissues.
Comparative Genomics Study of Interferon-
Receptor-1 in Humans and Chimpanzees
Kim, Il-Chul ; Chi, Seung-Wook ; Kim, Dae-Won ; Choi, Sang-Haeng ; Chae, Sung-Hwa ; Park, Hong-Seog ;
Genomics & Informatics, volume 3, issue 4, 2005, Pages 142~148
The immune response-related genes have been suggested to be the most favorable genes for positive selection during evolution. Comparing the entire DNA sequence of chimpanzee chromosome 22 (PTR22) with human chromosome 21 (HSA21), we have identified 15 orthologs having indel in their coding sequences. Among them, interferon-
receptor-1 gene (IFNAR1), an immuneresponse-related gene, is subjected to comparative genomic analysis. Chimpanzee IFNAR1 showed the same genomic structure as human IFNAR1 (11 exons and 10 introns) except the 3 bp insertion in exon 4. The sequence alignment of IFNAR1 coding sequence indicated that 'ISPP' amino acid sequence motif is highly conserved in chimpanzee and other animals including mouse and chicken. However, the human IFNAR1 shows that one proline residue is missing in the sequence motif. The homology modeling of the IFNAR1 structures suggests that the proline deletion in human IFNAR1 leads to the formation of the following
-helix, whereas two sequential prolines in chimpanzee IFNAR1 inhibit it. As a result, human IFNAR1 may adopt a characteristic structure distinct from chimpanzee IFNAR1. This human specific trait could contribute to specific immune response in the most optimized manner for humans. Further molecular biological studies on the IFNAR1 will help us to gain insights into the molecular implication of species-specific host-pathogen interaction in primate evolution.
Genetic Variants of IL-13 and IL-4 in the Korean Population: Polymorphisms, Haplotypes and Linkage Disequilibrium
Ryu, Ha-Jung ; Jung, Ho-Youl ; Park, Jung-Sun ; Kim, Jun-Woo ; Kim, Hyung-Tae ; Park, Choon-Sik ; Han, Bok-Ghee ; Koh, In-Song ; Park, Chan ; Kimm, Ku-Chan ; Oh, Berm-Seok ; Lee, Jong-Keuk ;
Genomics & Informatics, volume 3, issue 4, 2005, Pages 149~153
Asthma is an inflammatory airways disease characterized by bronchial hyperresponsiveness and airways obstruction, which results from a complex interaction of genetic and environmental factors. Interleukin (IL)-13 and IL-4 are important in IgE synthesis and allergic inflammation, therefore genes encoding IL-13 and IL-4 are candidates for predisposition to asthma. In the present study, we screened single-nucleotide polymorphisms (SNPs) in IL-13 and IL-4 and examined whether they are risk factors for asthma. We resequenced all exons and the promoter region in 12 asthma patients and 12 normal controls, and identified 18 SNPs including 2 novel SNPs. The linkage disequilibrium(LD) pattern was evaluated with 16 common SNPs, and haplotypes were also estimated within the block. Although IL-13 and IL-4 are localized within 27 kb on chromosome 5q31 and share many biological profiles, this region was partitioned into 2 blocks. One SNP and three SNPs were determined as haplotype-taggingSNPs (htSNPs) within IL-13 and IL-4 haplotype-block, respectively. No significant associations were observed between any of the SNPs or haplotypes and development of asthma in small number of Korean subjects. However, the genetic variants of IL-13 and IL-4 would provide valuable strategies for the genotyping studies in large population.
X-linked Gene Expression Profiles by RNAi-Mediated BRCA1 Knockdown in MCF7 Cells
Song, Min-Ae ; Park, Jung-Hoon ; Ahn, Hee-Jeong ; Ko, Jung-Jae ; Lee, Su-Man ;
Genomics & Informatics, volume 3, issue 4, 2005, Pages 154~158
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.
Estimating the Genetic Epidemiology Parameters of Selected Cancers in Korea Population - The Korean Twin Study -
Sung, Jooh-On ;
Genomics & Informatics, volume 3, issue 4, 2005, Pages 159~165
The Korean Twin Register (n=154,783 pairs) was reported in 2002 as the first nationwide twin study in Korea and the largest study in Asia. The Twin Register has the information of disease outcomes since 1990, and basic clinical and questionnaire data from biennial health examination provided by Korea National Health Service. The author attempted to calculate some of the genetic parameters of cancers in this population. Common cancers in Korea known to have familial aggregation (colon and breast) and cancers of which familial aggregation is unclear (stomach cancer) were examined for their familial recurrence risks. There were 699 stomach cancers, 438 breast and 491 colorectal cancers cases in the twin register between 1991 and 2003. Like-sex twins showed recurrence risks (
) of 5.1 (95% CI 3.7-6.9) for stomach cancers, 15.5 (95% CI1 0.9-20.2) for female breast cancers, and 28.1 (95% CI 23.5-34.4) for colon cancers. Colorectal cancers of female like-sex twins show significantly higher familial recurrence risk 40.7 (95% CI 34.6-47.4), suggesting higher genetic contribution in women than in men. The results show increased familial risks compared with previous studies from the same register and are largely compatible with other studies. The data of the Twin Register could be used for estimating population level genetic parameters, as well as base of the various studies.
A Cotwin Control Study of Smoking and Risk Factors of Metabolic Syndrome
Sung, Jooh-On ; Cho, Sung-Il ; Choi, Ji-Sook ; Song, Yun-Mi ; Lee, Ka-Young ; Choi, Eun-Young ; Ha, Mi-Na ; Kim, Yeon-Ju ; Shin, Eun-Kyung ;
Genomics & Informatics, volume 3, issue 4, 2005, Pages 166~171
Background: Smoking effects are relatively well-documented, especially on cancers and cardiovascular diseases. However, the direction and magnitude of association between smoking and obesity remain unclear. Conflicting results so far are thought to stem from the multiple confounding structure of smoking and other obesogenic life style characteristics. Methods: Cotwin control study is a genomic epidemiology design, in which the other twin (=cotwin) serves as a control of the twin. Cotwin control study, discordant for smoking habits can provide powerful evidence of association between smoking and obesity by completely matching genomic information, intrauterine environment, and almost all environmental factors. We selected 3,697 like-sex twin pairs (2,762 male and 935 female pairs) out of 63,666 pairs of adult twins in the existing Korea Twin and Family Register, whose smoking habits are discordant. We used the information of obesity as body mass index (BMI,
) blood pressure, and blood cholesterol level at the time or later than the smoking information. Paired t-test was done to compare the smoking effects. Results: Lifetime smoking rate was 80.1 % (47.9 current smoker) for men and 10% (1.7% current smoker) for women. Among 2,762 and 935 male and female like-sex twin pairs, 363 male pairs and 20 female pairs correspond to the definition of smoker-nonsmoker pair. The male smokers demonstrated increase in BMI by 0.47, while female smokers show slight decrease (by 0.13), which were not statistically significant. Diastolic and systolic blood pressure, and cholesterol level were slightly increased among smokers by 1.85 mmHg, 0.62 mmHg, and 1.28 mg/dl for men. For women, the results show increase in diastolic blood pressure (3.42mmHg) and cholesterol level (1.25 mg/dl), and systolic pressure (8.17 mmHg). Conclusion: The results refute the possibility that smoking can reduce BMI. Considering the direct adverse effect of smoking, it should be emphasized that smoking do not decrease obesity and thus increase overall metabolic syndrome.
Specificity of Intracellular Trans-Splicing Reaction by hTERT-Targeting Group I Intron
Jung, Heung-Su ; Kwon, Byung-Su ; Lee, Seong-Wook ;
Genomics & Informatics, volume 3, issue 4, 2005, Pages 172~174
Recent anti-cancer approaches have been based to target tumor-specifically associated and/or causative molecules such as RNAs or proteins. As this specifically targeted anti-cancer modulator, we have previously described a novel human cancer gene therapeutic agent that is Tetrahymena group I intron-based trans-splicing ribozyme which can reprogram and replace human telomerase reverse transcriptase (hTERT) RNA to selectively induce tumor-specific cytotoxicity in cancer cells expressing the target RNA. Moreover, the specific ribozyme has been shown to efficiently retard tumor tissues in xenograft mice which had been inoculated with hTERT-expressing human cancer cells. In this study, we assessed specificity of trans-splicing reaction in cells to evaluate the therapeutic feasibility of the specific ribozyme. In order to analyze the trans-spliced products by the specific ribozyme in hTERT-positive cells, RT, 5'-end RACE-PCR, and sequencing reactions of the spliced RNAs were employed. Then, whole analyzed products resulted from reactions only with the hTERT RNA. This study suggested that the developed ribozyme perform highly specific RNA replacement of the target RNA in cells, hence trans-splicing ribozyme will be one of specific agents for genetic approach to revert cancer.