• Genomics & Informatics
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• 제2권2호
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• pp.86-91
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• 2004

Even though it represents $6-13\%$ of human genomic DNA, Alu sequences are rarely found in coding regions. When in exon region, over $80\%$ of them are found in 3' untranslated region (UTR). Pseudogenes are an important component of human genome. Their functions are not clearly known and the mechanism of how they are generated is still debatable. Both the Alu and Pseudogenes are important research problems in molecular biology. mRNA is thought to be a prime source of pseudogene and active research is going on its molecular mechanism. We report, for the first time, that mRNAs containing Alu repeats at 3' UTR has a significantly high correlation with processed pseudogenes, suggesting a possibility that Alu containing mRNAs have a high tendency to become processed pseudogenes. It is known that about $10\%$ of all human genes have been transposed. Transposed genes at 3' UTR without Alu repeat have about two processed pseudogenes per gene on average while we found with statistical significance that a transposed gene with Alu had over three processed Pseudogenes on average. Therefore, we propose Alu repeats as a new and important factor in the generation of pseudogenes.

• Journal of Animal Science and Technology
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• 제60권10호
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• pp.25.1-25.10
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• 2018

The central dogma of gene expression propounds that DNA is transcribed to mRNA and finally gets translated into protein. Only 2-3% of the genomic DNA is transcribed to protein-coding mRNA. Interestingly, only a further minuscule part of genomic DNA encodes for long non-coding RNAs (lncRNAs) which are characteristically more than 200 nucleotides long and can be transcribed from both protein-coding (e.g. H19 and TUG1) as well as non-coding DNA by RNA polymerase II. The lncRNAs do not have open reading frames (with some exceptions), 3`-untranslated regions (3'-UTRs) and necessarily these RNAs lack any translation-termination regions, however, these can be spliced, capped and polyadenylated as mRNA molecules. The flexibility of lncRNAs confers them specific 3D-conformations that eventually enable the lncRNAs to interact with proteins, DNA or other RNA molecules via base pairing or by forming networks. The lncRNAs play a major role in gene regulation, cell differentiation, cancer cell invasion and metastasis and chromatin remodeling. Deregulation of lncRNA is also responsible for numerous diseases in mammals. Various studies have revealed their significance as biomarkers for prognosis and diagnosis of cancer. The aim of this review is to overview the salient features, evolution, biogenesis and biological importance of these molecules in the mammalian system.

• 한국식물병리학회:학술대회논문집
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• 한국식물병리학회 2003년도 정기총회 및 추계학술발표회
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• pp.76.2-77
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• 2003

The complete nucleotide sequences of genomic RNA of an isolate of soybean mosaic virus (SMV-CN18), which has ability to overcome Rsv resistance of soybean, have been determined. A large open reading frame encodes a polyprotein of 3068 amino acids with a predicted Mr of 350 kDa. Based on comparison with the proposed cleavage site of other potyviral polyproteins, nine mature proteins are predicted as a following order, P1, HC-Pro, P3, CI, 6K, VPg, NIa, NIb and coat protein (CP). The mature proteins of the strain share various amino acid identity with known SMV-G2, -G7 and -N strain, with the greatest variability occurring in the P1 (91 ％, 88 ％, 96％)and the lowest variability in the CP (100 ％, 99 ％, 100 ％). In addition, 5' untranslated region determined by 5' RACE is much more various than any coding regions. Difference in amino acid sequences throughout the genome is discussed in relation to resistance and susceptibility of soybean cultivars to SMV-CNl8.

• Asian Pacific Journal of Cancer Prevention
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• 제15권22호
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• pp.9557-9565
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• 2014

MiRNAs are endogenous, single stranded ~22-nucleotide non-coding RNAs (ncRNAs) which are transcribed by RNA polymerase II and mediate negative post-transcriptional gene regulation through binding to 3'untranslated regions (UTR), possibly open reading frames (ORFs) or 5'UTRs of target mRNAs. MiRNAs are involved in the normal physiology of eukaryotic cells, so dysregulation may be associated with diseases like cancer, and neurodegenerative, heart and other disorders. Among all cancers, lung cancer, with high incidence and mortality worldwide, is classified into two main groups: non-small cell lung cancer and small cell lung cancer. Recent promising studies suggest that gene expression profiles and miRNA signatures could be a useful step in a noninvasive, low-cost and repeatable screening process of lung cancer. Similarly, every stage of lung development during fetal life is associated with specific miRNAs. Since lung development and lung cancer phenomena share the same physiological, biological and molecular processes like cell proliferation, development and shared mRNA or expression regulation pathways, and according to data adopted from various studies, they may have partially shared miRNA signature. Thus, focusing on lung cancer in relation to lung development in miRNA studies might provide clues for lung cancer diagnosis and prognosis.

• 한국임상수의학회지
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• 제27권3호
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• pp.220-224
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• 2010

소 바이러스성 설사 바이러스는 전세계 축산업에서 중요한 질병이다. 대한민국의 최대 소 사육지역인 경북지방에서 유행하고 있는 소 바이러스 설사 바이러스를 조사하기 위해, 소 바이러스성 설사 바이러스의 임상증상을 보이는 한우 송아지로부터 365개의 분변을 채취하였다. 가검물을 채취한 365 마리 송아지 가운데 50 마리가 소 바이러스성 설사 바이러스에 양성반응을 보였다. 5'-UTR을 이용한 계통발생 분석에서 48두 송아지가 BDVD-2a에 속했고, 2두에서만 각각 BVDV-1a와 BVDV-1b로 분류되었다. 이들 결과는 BVDV-2a가 경북지역의 한우 송아지에서 유행하고 있음을 제시하고 있다.

• 생명과학회지
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• 제26권11호
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• pp.1232-1236
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• 2016

Mitochondrial calcium uptake 1 (MICU1)은 2개의 canonical EF hands를 가지고 미토콘드리아 내막에 위치하여, 미토콘드리아의 칼슘 섭취에 중요한 기능을 하는 것으로 알려져 있다. 근육 세포의 미토콘드리아 칼슘 섭취는 사후에 급속냉각 또는 냉장 시, 근육 내 칼슘 방출로 인한 강직과 관련되어 있으므로 궁극적으로는 육질 형성에 관련이 있을 것으로 판단된다. 따라서 본 연구에서는 돼지 MICU1 유전자의 exon영역의 변이를 탐색하고, 발굴된 변이에 대해 육질 형질과의 연관성 분석을 실시하였다. 이를 위해 버크셔 667두(암퇘지 347두, 거세수퇘지 320두)가 이용되었으며, MICU1 유전자의 cDNA를 염기서열 해독하여 비교함으로써 exon 영역의 변이를 발굴하였다. 그 결과 MICU1의 3' 비해독 영역(untranslated region, UTR)에서 3개의 단일염기다형성(single-nucleotide polymorphism, SNP)를 발견했다. 그리고 이들 SNP에 대해 공시돈의 육질형질(근육 pH, 육즙 손실, 육색, 근내지방함량)과 연관성 분석을 실시했다. SNP1 (c.*136G>A)에서는 육즙 손실(p=0.017), 근내지방함량(p=0.039)과 연관되어 있었고, SNP2 (c.*222G>A)와 SNP3 (c.*485G>A)에서는 각각 육즙 손실(p=0.018)과 근내지방함량(p<0.001)과 연관되어 있는 것을 확인하였다. 따라서 본 결과를 바탕으로, 돼지에서 육질과 관련된 후보 유전자로 추정된 MICU1 유전자로부터 3' 비해독 영역의 변이가 유의적으로 육질 형질과 관련되어있다는 것이 확인되었다. 향후 MICU1 유전자의 3' 비해독 영역의 변이들에 기능적 역할을 정확히 파악하기 위한 분자생물학적 특성 연구가 필요할 것으로 판단된다.

• Journal of Microbiology and Biotechnology
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• 제29권1호
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• pp.127-140
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• 2019

Since 1990, many nucleic acid expression platforms consisting of DNA or RNA have been developed. However, although RNA expression platforms have been relatively neglected, several such platforms capped at the 5' end of RNA by an anti-reverse cap analog have now been developed. At the same time, the capping reaction is a bottleneck in the production of such platforms, with high cost and low efficiency. Here, we investigated several viral and eukaryotic internal ribosome entry sites (IRESs) to develop an optimal RNA expression platform, because IRES-dependent translation does not require a capping step. RNA expression platforms constructed with IRESs from the 5' untranslated regions of the encephalomyocarditis virus (EMCV) and the intergenic region of the cricket paralysis virus (CrPV) showed sufficient expression efficiency compared with cap-dependent RNA expression platforms. However, eukaryotic IRESs exhibited a lower viral IRES expression efficiency. Interestingly, the addition of a poly(A) sequence to the 5' end of the coxsackievirus B3 (CVB3) IRES (pMA-CVB3) increased the expression level compared with the CVB3 IRES without poly(A) (pCVB3). Therefore, we developed two multiexpression platforms (termed pMA-CVB3-EMCV and pCrPV-EMCV) by combining the IRESs of CVB3, CrPV, and EMCV in a single-RNA backbone. The pMA-CVB3-EMCV-derived RNA platform showed the highest expression level. Moreover, it clearly exhibited expression in mouse muscles in vivo. These RNA expression platforms prepared using viral IRESs will be useful in developing potential RNA-based prophylactic or therapeutic vaccines, because they have better expression efficiency and do not need a capping step.

• The Plant Pathology Journal
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• 제15권5호
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• pp.270-279
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• 1999

cDNAs complementary to the 3'-terminal regions of two potyvirus genomes were cloned and sequenced. The clone G7 contains one open reading frame (ORF) of 1,338 nucleotides and a 3' untranslated region (3'-UTR) of 403 nucleotides at the 3'-end excluding the 3'end poly(A) tail. The putative viral coat protein (CP) shows 55%-92% amino acid sequence homology to those of Allium potyviruses. The genome size of the virus was analyzed to be about 9.0 kb by Northern blot analysis. Five cDNA clones were screened out using GPV2 oligonucleotide as a probe. One of these clones, DEA72, which has a longest cDNA insert, contains one ORF of 1,459 nucleotides and a 3'-UTR of 590 nucleotides at the 3'-end excluding the 3'-end poly(A) tail. The putative viral CP shows 57%-88% amino acid sequence homologies to those of Allium potyviruses. The genome size of the virus was analyzed to be about 9.6 kb by Northern blot analysis. The results of immunoblot and Northern blot analyses suggest that almost all of the tested garlic plants showing mosaic or streak symptoms are infected with DEA72-potyvirus in variable degrees but rarely infected with G7-potyvirus in variable degrees but rarely infected with DEA72-potyvirus in variable degrees but rarely infected with G7-potyvirus. Immunoelectron microscopy using anti-DEA72 CP antibody shows that this potyvirus is about 750 nm long and flexuous rod shaped.

• Genomics & Informatics
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• 제19권2호
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• pp.17.1-17.13
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• 2021

Breast cancer is one of the leading causes of cancer in women all over the world and accounts for ~25% of newly observed cancers in women. Epigenetic modifications influence differential expression of genes through non-coding RNA and play a crucial role in cancer regulation. In the present study, epigenetic regulation of gene expression by in-silico analysis of histone modifications using chromatin immunoprecipitation sequencing (ChIP-Seq) has been carried out. Histone modification data of H3K4me3 from one normal-like and four breast cancer cell lines were used to predict miRNA expression at the promoter level. Predicted miRNA promoters (based on ChIP-Seq) were used as a probe to identify gene targets. Five triple-negative breast cancer (TNBC)-specific miRNAs (miR153-1, miR4767, miR4487, miR6720, and miR-LET7I) were identified and corresponding 13 gene targets were predicted. Eight miRNA promoter peaks were predicted to be differentially expressed in at least three breast cancer cell lines (miR4512, miR6791, miR330, miR3180-3, miR6080, miR5787, miR6733, and miR3613). A total of 44 gene targets were identified based on the 3'-untranslated regions of downregulated mRNA genes that contain putative binding targets to these eight miRNAs. These include 17 and 15 genes in luminal-A type and TNBC respectively, that have been reported to be associated with breast cancer regulation. Of the remaining 12 genes, seven (A4GALT, C2ORF74, HRCT1, ZC4H2, ZNF512, ZNF655, and ZNF608) show similar relative expression profiles in large patient samples and other breast cancer cell lines thereby giving insight into predicted role of H3K4me3 mediated gene regulation via the miRNA-mRNA axis.

• 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.