• Proceedings of the Korean Information Science Society Conference
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• 2005.07b
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• pp.286-288
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• 2005

MicroRNA (miRNA)는 작은 크기의 RNA분자로서 동식물의 유전자 발현 과점을 직접적으로 조절하는 인자로 알려져 있다. MiRNA는 보통 목표 유전자의 3'-UTR 영역에 상보성을 갖고 결합함으로써 작용하며 특히 miRNA의 5'부분의 8 nt 정도가 seed로서 중요하다고 알려져 있다. 반면 최근의 연구에 따르면 seed 부분의 서열의 조성 및 양상이 변화함에 따라 특이도가 결정됨을 알 수 있지만 기존의 컴퓨터를 이용한 miRNA 목표 유전자 예측 방법들은 이러한 정보를 활용하지 못한다. 본 논문에서는 열역학적인 수치와 서열의 조성뿐 아니라 miRNA:mRNA pair의 위치에 기반한 정보들을 학습에 자질로서 포함하여 목표 유전자를 예측한다. 그 결과는 위치 기반 자질이 학습 성능 향상에 중요하게 기여함을 보여준다.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.127.2-127
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• 2003

YMV-K strains were purified from D. oppostita Thunb. tv. Dung-Gun-Ma showing mosaic symptom on their leaves. YMV-K strains were filamentous particles of 780nm in length and induced cytoplasmic disorder such as inclusion body formation. Nucleotide and amino acid sequences of 5'-UTR, Pl and CP of YMV-K strains shared 80.8, 64.7 and 98.3％ identity respectively to JYMV J1 in the mean value. Purification of YMV-K strains according to JYMV purification method(S. Fuji) was conducted to product antiserum. With antiserum against YMV-K strains, the Various diagnosis methods such as IC-RT-PCR, DIBA, RIPA and indirect-ELISA were used to detect YMV-K strains in Chinese yam plant.

• BMB Reports
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• v.56 no.12
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• pp.625-632
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• 2023

Nonsense-mediated mRNA decay (NMD) is both a quality control mechanism and a gene regulation pathway. It has been studied for more than 30 years, with an accumulation of many mechanistic details that have often led to debate and hence to different models of NMD activation, particularly in higher eukaryotes. Two models seem to be opposed, since the first requires intervention of the exon junction complex (EJC) to recruit NMD factors downstream of the premature termination codon (PTC), whereas the second involves an EJC-independent mechanism in which NMD factors concentrate in the 3'UTR to initiate NMD in the presence of a PTC. In this review we describe both models, giving recent molecular details and providing experimental arguments supporting one or the other model. In the end it is certainly possible to imagine that these two mechanisms co-exist, rather than viewing them as mutually exclusive.

• Journal of Marine Life Science
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• v.3 no.1
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• pp.1-8
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• 2018

Myosin is considered as the vital motor protein in vertebrates and invertebrates. Our present study was conducted to decipher the occurrence of myosin in dog fish (Squalus mitsukurii). We isolated one clone containing 979 bp cDNA sequence, which consisted of a complete coding sequence of 453 bp and a deduced amino acid sequence of 150 amino acids from the open reading frame with molecular weight, isoelectric point and aliphatic index are 16.72 Kda, 4.49 and 78.00, respectively. It contained 428 bp long 3' UTR with single potential polyadenylation signals (AATAAA). The predicted EF CA²⁺ binding domains were identified in residue 6-41, 83-118 and 133-150. A BLAST search indicates this protein exhibits a strong similarity to whale shark (Rhincodon typus) MLC3 (91% identical) and also house mouse (Mus musculus) MLC isoform 3f (81% identical). Phylogenetic analysis revealed that this protein is a MLC 3 isoform like protein. This protein also demonstrates highly conserved region with other myosin proteins. Homology modeling of S. mitsukuri was performed using crystal structure of Gallus gallus skeletal muscle myosin II based on high similarity. Reverse transcription-polymerase chain reaction (PCR), quantitative PCR results exhibits dogfish myosin protein is highly expressed in muscle tissue.

• The Plant Pathology Journal
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• v.24 no.2
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• pp.152-158
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• 2008

A peculiar virus-like disease of tomato showing yellow mosaic and necrotic spots on leaves and necrosis on veins, petioles and stems was observed at the Tomato Experimental Station (TES), Buyeo, Chungcheongnamdo, Korea. The disease incidence at TES fields ranged from 21 to 35% infecting different tomato cultivars. For this reason, to identify the virus infecting tomato and to characterize the virus based on biology, serology, cytology and at molecular level. Here, leaf samples were randomly collected from different infected tomato cultivars at TES fields and greenhouses and tested by ELISA using Pepper mottle virus (PePMoV) and Tomato mosaic virus (ToMV) antisera. Infected saps were mechanically inoculated in different host plants to test for pathogenicity, symptomatology and host ranges. Infected tissues and ultrathin sections were examined by electron microscopy. Finally, putative coat protein and 3'-untranslated region (CP/3'-UTR) fragment was amplified and cloned for sequence determination and analyzed its genetic relationship to existing PepMoV and PVY sequences at the Genbank. Results showed 69% of the samples were positive with PepMoV, 13% with ToMV and 19 % were doubly infected with PepMoV and ToMV. Symptoms greatly varied from different host plants inoculated with tomato leaf sap infected with PepMoV alone and discussed in detailed in this paper. Electron microscopy from infected tissues showed filamentous particles of 720-750nm in length, a typical morphology and size of PepMoV. In addition, cylindrical inclusion bodies, pinwheels, scrolls and laminates with masses of fibrillar inclusions were also found in ultrathin sections. Alignment of the sequences of the CP/3'-UTR revealed >96% sequence identity with PepMoV and only <61% with PVY. Taken together, all these evidences presented clearly indicated that the causal agent infecting tomato at TES was PepMoV and we designated this PepMoV infecting tomato as Tom-sd2 strain in this study.

• Nutrition Research and Practice
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• v.12 no.1
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• pp.61-68
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• 2018

BACKGROUND/OBJECTIVES: This study aimed to test the association between APOA5 3'-UTR variants (rs662799) and cardiometabolic traits in Koreans. SUBJECTS/METHODS: For this study, epidemiological data, Apolipoprotein A5 (APOA5) genotype information, and lymphoblastoid cell line (LCL) biospecimens from a subset of the Ansung-Ansan cohort within the Korean Genome and Epidemiology study (KoGES-ASAS; n = 7,704) as well as epidemiological data along with genomic DNA biospecimens of participants from a subset of the Korea National Health and Nutrition Examination Survey (KNHANES 2011-12; n = 2,235) were obtained. APOA5 mRNA expression was also measured. RESULTS: APOA5 rs662799 genotype distributions in both the KoGES-ASAS and KNHANES groups were 50.6% for TT, 41.3% for TC, and 8.1% for CC, which are similar to those in previous reports. In both groups, minor C allele carriers, particularly subjects with CC homozygosity, had lower high-density lipoprotein (HDL) cholesterol and higher triglyceride levels than TT homozygotes. Linear regression analysis showed that the minor C allele significantly contributed to reduction of circulating HDL cholesterol levels [${\beta}=-2.048$, P < 0.001; ${\beta}=-2.199$, P < 0.001] as well as elevation of circulating triglyceride levels [${\beta}=0.053$, P < 0.001; ${\beta}=0.066$, P < 0.001] in both the KoGES-ASAS and KNHANES groups. In addition, higher expression levels of APOA5 in LCLs of 64 healthy individuals were negatively associated with body mass index (r = -0.277, P = 0.027) and circulating triglyceride level (r = -0.340, P = 0.006) but not significantly correlated with circulating HDL cholesterol level. On the other hand, we observed no significant difference in the mRNA level of APOA5 according to APOA5 rs662799 polymorphisms. CONCLUSIONS: The C allele of APOA5 rs662799 was found to be significantly associated with cardiometabolic traits in a large Korean population from the KoGES-ASAS and KNHANES. The effect of this genotype may be associated with post-transcriptional regulation, which deserves further experimental confirmation.

• Animal Bioscience
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• v.34 no.2
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• pp.172-184
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• 2021

Objective: Vanin1 (VNN1) is a pantetheinase that can catalyze the hydrolysis of pantetheine to produce pantothenic acid and cysteamine. Our previous studies showed that VNN1 is specifically expressed in chicken liver. In this study, we aimed to investigate the roles of peroxisome proliferators activated receptor α (PPARα) and miRNA-181a-5p in regulating VNN1 gene expression in chicken liver. Methods: 5'-RACE was performed to identify the transcription start site of chicken VNN1. JASPAR and TFSEARCH were used to analyze the potential transcription factor binding sites in the promoter region of chicken VNN1 and miRanda was used to search miRNA binding sites in 3' untranslated region (3'UTR) of chicken VNN1. We used a knock-down strategy to manipulate PPARα (or miRNA-181a-5p) expression levels in vitro to further investigate its effect on VNN1 gene transcription. Luciferase reporter assays were used to explore the specific regions of VNN1 targeted by PPARα and miRNA-181a-5p. Results: Sequence analysis of the VNN1 promoter region revealed several transcription factor-binding sites, including hepatocyte nuclear factor 1α (HNF1α), PPARα, and CCAAT/enhancer binding protein α. GW7647 (a specific agonist of PPARα) increased the expression level of VNN1 mRNA in chicken primary hepatocytes, whereas knockdown of PPARα with siRNA increased VNN1 mRNA expression. Moreover, the predicted PPARα-binding site was confirmed to be necessary for PPARα regulation of VNN1 gene expression. In addition, the VNN1 3'UTR contains a sequence that is completely complementary to nucleotides 1 to 7 of miRNA-181a-5p. Overexpression of miR-181a-5p significantly decreased the expression level of VNN1 mRNA. Conclusion: This study demonstrates that PPARα is an important transcriptional activator of VNN1 gene expression and that miRNA-181a-5p acts as a negative regulator of VNN1 expression in chicken hepatocytes.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.6
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• pp.3499-3502
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• 2013

MicroRNAs (miRNAs) are a class of endogenously expressed small, non-coding, single-stranded RNAs that negatively regulate gene expression, mainly by binding to 3'- untranslated regions (3'UTR) of their target messenger RNAs (mRNAs), which cause blocks of translation and/or mRNA cleavage. Recently, miRNAprofiling studies demonstrated the microRNA-497 (miR-497) level to be down-regulated in all prostate carcinomas compared with BPH samples. The purpose of this study was to investigate the potential role of miR-497 in human prostate cancer. Proliferation, cell cycle and apoptosis assays were conducted to explore the potential function of miR-497 in human prostate cancer cells. Results showed that miR-497 suppressed cellular growth and initiated G0/G1 phase arrest of LNCaP and PC-3 cells. We also observed that miR-497 increased the percentage of apoptotic cells by increasing caspase-3/7 activity. Taken together, our results demonstrated that miR-497 can inhibit growth and induce apoptosis by caspase-3 activation in prostate cancer cells, which suggest its use as a potential therapeutic target in the future.

• Molecules and Cells
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• v.46 no.1
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• pp.57-64
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• 2023

In eukaryotic cells, a key RNA processing step to generate mature mRNA is the coupled reaction for cleavage and polyadenylation (CPA) at the 3' end of individual transcripts. Many transcripts are alternatively polyadenylated (APA) to produce mRNAs with different 3' ends that may either alter protein coding sequence (CDS-APA) or create different lengths of 3'UTR (tandem-APA). As the CPA reaction is intimately associated with transcriptional termination, it has been widely assumed that APA is regulated cotranscriptionally. Isoforms terminated at different regions may have distinct RNA stability under different conditions, thus altering the ratio of APA isoforms. Such differential impacts on different isoforms have been considered as post-transcriptional APA, but strictly speaking, this can only be considered "apparent" APA, as the choice is not made during the CPA reaction. Interestingly, a recent study reveals sequential APA as a new mechanism for post-transcriptional APA. This minireview will focus on this new mechanism to provide insights into various documented regulatory paradigms.

• Journal of the Korean Magnetic Resonance Society
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• v.21 no.3
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• pp.109-113
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• 2017

The hepatitis C virus (HCV) internal ribosome entry site (IRES) is an RNA structure located in the 5'-UTR of the HCV RNA genome. The HCV IRES consists of four domains I, II, III, and IV, where domains II - IV are recognized by 40S ribosomal subunit and the domain III is bound to eukaryotic initiation factor 3 (eIF3) for translation initiation. Here, we have characterized the tertiary interaction between an L-/K- rich peptide and the HCV IRES domain IV. To probe the peptide binding interface in RNA, we synthesized $^{13}C$- and $^{15}N$-double labeled RNA and the binding site was identified by using the chemical shift perturbation (CSP) NMR methods. Our results showed that the peptide binds to the upper stem of the IRES domain IV, indicating that the tertiary interaction between the IRES domain IV and the peptide would disrupt the initiation of translation of HCV mRNA by blocking the start codon exposure. This study will provide an insight into the new peptide-based anti-viral drug design targeting HCV IRES RNA.