• Proceedings of the Korean Information Science Society Conference
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• 2006.06a
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• pp.67-69
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• 2006

MicroRNA (miRNA)는 생체내에서 gene regulation에 관여하는 핵심 small RNA 중 하나이다. miRNA는 Primary miRNA, Precursor miRNA, mature miRNA의 과정으로 processing 된다. miRNA 최종 형태인 mature miRNA의 정확한 위치 예측은 miRNA 예측의 필수적인 부분이다. 본 논문에서는, 진화적 최적화 예측 모델 중 하나인 유전 알고리즘을 이용하여 mature miRNA의 정확한 위치 예측을 수행한다. 제시된 방법은 이미 알려진 mature miRNA 위치를 positive example로 하고 임의로 생성한 위치를 negative example로 하여 서로의 linear scoring function 적합성 함수의 값 차이가 최대한으로 되도록 예측 모델을 진화시킨다. 유전 알고리즘을 이용한 진화적 최적화 모델로부터 mature miRNA 위치 예측에서 약 1.7nt 오차를 보여 기존의 방법 보다 개선된 성능을 보인다.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.12
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• pp.6375-6378
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• 2012

Background: Small-cell lung cancer (also known as SCLC) is an aggressive form and untreated patients generally die within about 3 months. To obtain further insight into mechanism underlying malignancy with this cancer, an miRNA synergistic regulatory network was constructed and analyzed in the present study. Method: A miRNA microarray dataset was downloaded from the NCBI GEO database (GSE27435). A total of 546 miRNAs were identified to be expressed in SCLC cells. Then a miRNA synergistic network was constructed, and the included miRNAs mapped to the network. Topology analysis was also performed to analyze the properties of the synergistic network. Consequently, we could identified constitutive modules. Further, common target genes of each module were identified with CFinder. Finally, enrichment analysis was performed for target genes. Results: In this study, a miRNA synergistic network with 464 miRNAs and 2981 edges was constructed. According to the topology analysis, the topological properties between the networks constructed by LC related miRNAs and LC unrelated miRNAs were significantly different. Moreover, a module cilque0 could be identified in our network using CFinder. The module included three miRNAs (hsa-let-7c, hsa-let-7b and hsa-let-7d). In addition, several genes were found which were predicted to be common targets of cilque0. The enrichment analysis demonstrated that these target genes were enriched in MAPK signaling pathways. Conclusions: Although limitations exist in the current data, the results uncovered here are important for understanding the key roles of miRNAs in SCLC. However, further validation is required since our results were based on microarray data derived from a small sample size.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.4
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• pp.1557-1561
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• 2012

Objective: To investigate the promoter methylation status of the E-cadherin gene in non-small cell lung cancer (NSCLC) and its association with clinical pathological parameters, and to explore the relationship between downregulation of E-cadherin gene expression and the methylation status of its promoter region. Methods: Nested methylation-specific PCR was performed to examine CpG methylation within the 5' CpG island of the E-cadherin gene in lung cancer and para-cancerous tissue from 37 patients with primary non-small cell lung cancer. Quantitative real-time PCR was performed to measure the level of E-cadherin mRNA. Results: Of thirty-seven cases, 12 (32.4%) samples showed aberrant CpG methylation in tumor tissues compared with the corresponding normal tissues. In addition, a reduction in E-cadherin mRNA levels was observed in 11 of the 12 (91.7%) tumor tissues carrying a methylated E-cadherin gene. However, only 10 (43.5%) cases displayed reduced mRNA levels in tumor tissues from the remaining 23 cases (excluding 2 samples from which mRNA was unavailable) without methylation events. Downregulation of E-cadherin gene expression significantly correlated with the promoter methylation status of this gene. Conclusion: These results provide strong evidence that the methylation status of E-cadherin gene contributes to a reduction in the expression of E-cadherin mRNA, and may play a role in the development and progression of NSCLC.

• Molecules and Cells
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• v.40 no.8
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• pp.587-597
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• 2017

MicroRNAs (miRNAs) are essential small RNA molecules that regulate the expression of target mRNAs in plants and animals. Here, we aimed to identify miRNAs and their putative targets in Hibiscus syriacus, the national flower of South Korea. We employed high-throughput sequencing of small RNAs obtained from four different tissues (i.e., leaf, root, flower, and ovary) and identified 33 conserved and 30 novel miRNA families, many of which showed differential tissuespecific expressions. In addition, we computationally predicted novel targets of miRNAs and validated some of them using 5' rapid amplification of cDNA ends analysis. One of the validated novel targets of miR477 was a terpene synthase, the primary gene involved in the formation of disease-resistant terpene metabolites such as sterols and phytoalexins. In addition, a predicted target of conserved miRNAs, miR396, is SHORT VEGETATIVE PHASE, which is involved in flower initiation and is duplicated in H. syriacus. Collectively, this study provides the first reliable draft of the H. syriacus miRNA transcriptome that should constitute a basis for understanding the biological roles of miRNAs in H. syriacus.

• Animal cells and systems
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• v.8 no.3
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• pp.213-220
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• 2004

MicroRNA and siRNA (small interfering RNA), representative members of small RNA, exert their effects on target gene expression through association with protein complexes called miRNP (microRNA associated ribonucleoproteins) and RISC (RNA induced silencing complex), respectively. Although the protein complexes are yet to be fully characterized, human EIF2C2 protein has been identified as a component of both miRNP and RISC. In this report, we raised antiserum against EIF2C2 in order to begin understanding the protein complexes. An immunoblot result indicates that EIF2C2 protein is ubiquitously expressed in a variety of cell lines from human and mouse. EIF2C2 protein exists in both cellular compartments, as indicated by an immunoblot assay with a nuclear extract and a cytosolic fraction (S100 fraction) from HeLa S3 lysate. Depletion of EIF2C1 or EIF2C2 protein resulted in a decrease of microRNA, suggesting a possible role of these proteins in microRNA stability or biogenesis. We also prepared antiserum against dsRNA binding protein PACT, whose homologs in C. elegans and Drosophila are known to have a role in the RNAi (RNA interference) pathway. The expression of PACT protein was also observed in a wide range of cell lines.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.34 no.1
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• pp.21-26
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• 2001

To examine functionality of depolymerized alginate obtained by hydrolysis of alginate through a heating process at $121^{\circ}C$ on gastrointestinal physiology, the changes of body weight, organ weight and length, pancreatic and small intestinal composition, and light microscopy (LM) observation of small intestinal microvilli's appearances were checked in the rats. Rats were fed diets containing $1\%, 5\%, and 10\%$ of each depolymerized alginate (HAG-10, HAG-50, HAG-100) and alginate for 35 days, The feeding of 5 and $10\%$ HAG-50 and $10\%$ alginate diets for 35 days significantly depressed the body weight gain, but increased the length and weight of the small intestine and cecum in rats (p<0.01). Pancreatic protease activity was decreased significantly (p<0.01) in all groups except lo/o of HAG-10 diets, but the protein content increased in all groups, However, pancreatic amylase and lipase activities as well as DNA and RNA content were not significantly different. The small intestinal protein and the DNA content were the highest in diets fed $5\%$ HAG-50; RNA content increased significantly (p<0.01) in all groups except in the fiber-free diets. Light microscopy (LM) observation showed growth of small intestinal microvilli with numerous ridges; the multiplication of the convolution goblet cells in rats fed with diets containing $5\%$ of HAG-50 were more than others group.

• Bulletin of the Korean Chemical Society
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• v.32 no.spc8
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• pp.3051-3056
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• 2011

We calculate the free energy surfaces for two small proteins and a protein-RNA complex system by using a lattice model approach. In particular, we employ the Munoz-Eaton model, which is a native-structure based statistical mechanical model for studying protein folding problem. The model can provide very useful insights into the folding mechanisms by allowing one to calculate the free energy surfaces efficiently. We first calculate the free energy surfaces of ubiquitin and BBL, using both approximate and recently developed exact solutions of the model. Ubiquitin exhibits a typical two-state folding behavior, while BBL downhill folding in our study. We then extend the method to study of a protein-RNA complex. In particular, we focus on PAZ-siRNA complex. In order to elucidate the interplay between folding and binding kinetics for this system we perform comparative studies of PAZ only, PAZ-siRNA complex and two mutated complexes. We find that folding and binding are strongly coupled with each other and the bound PAZ is more stable than the unbound PAZ. Our results also suggest that the binding sites of the siRNA may serve act as a nucleus in the folding process.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.139.1-139
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• 2003

Tissues from woody plant contain higher amount of phenolic compounds and polysaccharides, which give inhibitory effects on reverse transcriptase and/or Taq ploymerase. The common multiple-step protocols using several additives to inhibit polyphenoic compounds during nucleic acid extraction are time consuming and laborious. Sodium sulfite (Na$_2$SO$_3$) was used as inhibitor of polyphenolic oxidases in extraction buffer and compare it's effect between commercial RNA extraction kit and small-scale double-stranded RNA (dsRNA) extraction by RT-PCR. During nucleic acid extraction procedure, addition of 0.5％-1.5％ (w/v) sodium sulfite to Iysis buffer or STE buffer resulted in lighter color change than extracts without sodium sulfite and improve the RT-PCR detection. When commercial RNA extraction kit used, optimal concentration of sodium sulfite were variable according to the host plant. However, using dsRNA as RT-PCR template, 1.5％ sodium sulfite in STE buffer improves the detection of both viruses and unspecific amplifications were reduced significantly, Furthermore, when viruses existed at low titers in host plant, small-scale dsRNA extractions were very reliable.

• BMB Reports
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• v.43 no.4
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• pp.291-296
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• 2010

Cyclin-dependent kinase 2 (CDK2) is a member of serine/threonine protein kinases, which initiates the principal transitions of the eukaryotic cell cycle and is a promising target for cancer therapy. The present study was designed to inhibit cdk2 gene expression to induce cell cycle arrest and cell proliferation suppression. Here, we constructed a series of RNA interference (RNAi) plasmids which can successfully express small interference RNA (siRNA) in the transfected human cells. The results showed that the RNAi plasmids containing the coding sequences for siRNAs down-regulated the cdk2 gene expression in human cancer cells at the mRNA and the protein levels. Furthermore, we found that the cell cycle was arrested at G0G1 phases and the cell proliferation was inhibited by different siRNAs. These results demonstrate that suppression of CDK2 activity by RNAi may be an effective strategy for gene therapy in human cancers.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.22
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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.