• Molecules and Cells
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• v.39 no.4
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• pp.281-285
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• 2016

Almost all of eukaryotic mRNAs are subjected to polyadenylation during mRNA processing. Recent discoveries showed that many of these mRNAs contain more than one polyadenylation sites in their 3' untranslated regions (UTR) and that alternative polyadenylation (APA) is prevalent among these genes. Many biological processes such as differentiation, proliferation, and tumorigenesis have been correlated to global APA events in the 3' UTR of mRNAs, suggesting that these APA events are tightly regulated and may play important physiological roles. In this review, recent discoveries in the physiological roles of APA events, as well as the known and proposed mechanisms are summarized. Perspective for future directions is also discussed.

• Proceedings of the Korea Information Processing Society Conference
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• 2012.11a
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• pp.1340-1343
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• 2012

정보의 시각화는 추상적 정보를 직관적으로 이해하기 쉽도록 시각적으로 명확하게 표현하는 방법을 말한다. 대용량의 바이오 데이터를 다루는 생물정보학(bioinformatics) 분야에서는 컴퓨터의 높은 성능을 활용하여 수많은 유전학적 데이터들을 분석하고 있다. 다양한 생물정보학 실험에서 전사체는 특정한 조건에서 발현된 RNA의 총합을 말한다. 분석된 전사체 정보는 텍스트형태로 제공이 되는데 이를 사용자가 수작업으로 비교하는 데에는 한계가 있다. 따라서 분석된 전사체 정보를 효과적으로 인지할 수 있도록 시각화하는 연구들이 진행되고 있다. 본 논문에서는 그래프 라이브러리인 yFile을 활용하여 추정된 전사체를 실시간으로 시각화하여 제공하는 방법을 제안한다. GTF파일을 입력받아서 데이터베이스에 저장하고 이 정보를 이용하여 그래프를 생성한다. 실험 결과는 전사체를 시각화 하는 방법을 통하여 다양한 전사체 정보를 알아 낼 수 있고, 최종적으로는 novel gene을 찾는 것이 가능할 것으로 기대한다.

• Proceedings of the Korea Information Processing Society Conference
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• 2020.05a
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• pp.413-416
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• 2020

COVID-19(Coronavirus Disease 2019)는 RNA 형 바이러스로써 점막감염(粘膜感染)과 비말전파(飛沫傳播)로 전염되는 급성 호흡기성 질병이다. 2019 년 12 월 중국 후베이 우한에서 처음 감염이 보고된 후 빠르게 글로벌로 확산되었고, 현재 여러 국가와 지역이 Lockdown 상태에 있다. COVID-19 의 치사율은 국가별, 연령별 차이는 있으나 사스(SARS-CoV), 메르스(MERS-CoV) 등과 비교하여 높다고 할 수 없다. 그러나 COVID-19 는 신종 코로나바이러스로써 아직 백신(Vaccine)과 항바이러스제가 개발되지 않았고 다른 질병과 비교하여 빠른 감염 속도때문에 의료 공백, 사회적 혼란, 경제적 손실을 크게 일으키고 있다. 따라서 바이러스의 확산 양상을 데이터 분석을 통하여 예측할 수 있다면 사회·경제적인 폐해를 줄일 수 있어 Bass 모델과 R 패키지를 이용하여 COVID-19 확산 예측 모형을 계량적으로 제시하였다.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.174-174
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• 2017

To cope with phosphate (Pi) deficient stress, plants modulate various physiological and developmental processes, such as gene expression, Pi uptake and translocation, and root architecture changes. Here, we report the identification and characterization of novel activation-tagged mutant involved in Pi starvation signaling in Arabidopsis. The hpd (${\underline{h}ypersensitive}$ to ${\underline{P}i}$ $ {\underline{d}eficiency}$) mutant exhibits enhanced phosphate uptake and altered root architectural change under Pi starvation compared to wild type. Expression analysis of auxin-responsive DR5::GUS reporter gene in hpd mutant indicated that auxin translocation in roots under Pi starvation are suppressed in hpd mutant plants. Impaired auxin translocation in roots of hpd mutant was attributable to abnormal root architecture changes in Pi starvation conditions. Our results indicated that abnormal auxin translocation in hpd mutant might be due to mis-regulation of auxin efflux carrier proteins, PIN-FORMED (PIN) 1, and 2 under Pi starvation conditions. Not only expression levels but also expression domains of PIN proteins were altered in hpd mutant in response to Pi starvation. Molecular genetic analysis of hpd mutant revealed that the mutant phenotype is caused by the lesion in ENHANCED SILENCING PHENOTYPE4 (ESP4) gene whose function is proposed in mRNA 3'-end processing. The results suggest that mRNA processing plays crucial roles in Pi homeostasis as well as developmental reprograming in response to Pi deprivation in Arabidopsis.

• Molecules and Cells
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• v.43 no.7
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• pp.662-670
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• 2020

We have investigated the involvement of the pre-mRNA processing factor 4B (PRP4) kinase domain in mediating drug resistance. HCT116 cells were treated with curcumin, and apoptosis was assessed based on flow cytometry and the generation of reactive oxygen species (ROS). Cells were then transfected with PRP4 or pre-mRNA-processing-splicing factor 8 (PRP8), and drug resistance was analyzed both in vitro and in vivo. Furthermore, we deleted the kinase domain in PRP4 using Gateway™ technology. Curcumin induced cell death through the production of ROS and decreased the activation of survival signals, but PRP4 overexpression reversed the curcumin-induced oxidative stress and apoptosis. PRP8 failed to reverse the curcumin-induced apoptosis in the HCT116 colon cancer cell line. In xenograft mouse model experiments, curcumin effectively reduced tumour size whereas PRP4 conferred resistance to curcumin, which was evident from increasing tumour size, while PRP8 failed to regulate the curcumin action. PRP4 overexpression altered the morphology, rearranged the actin cytoskeleton, triggered epithelial-mesenchymal transition (EMT), and decreased the invasiveness of HCT116 cells. The loss of E-cadherin, a hallmark of EMT, was observed in HCT116 cells overexpressing PRP4. Moreover, we observed that the EMT-inducing potential of PRP4 was aborted after the deletion of its kinase domain. Collectively, our investigations suggest that the PRP4 kinase domain is responsible for promoting drug resistance to curcumin by inducing EMT. Further evaluation of PRP4-induced inhibition of cell death and PRP4 kinase domain interactions with various other proteins might lead to the development of novel approaches for overcoming drug resistance in patients with colon cancer.

• The Korean Journal of Physiology and Pharmacology
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• v.17 no.3
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• pp.189-195
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• 2013

Amyloid-${\beta}$ peptide ($A{\beta}$), generated by proteolytic cleavage of the amyloid precursor protein (APP), plays a pivotal role in the pathogenesis of Alzheimer's disease (AD). The key step in the generation of $A{\beta}$ is cleavage of APP by beta-site APP-cleaving enzyme 1 (BACE1). Levels of BACE1 are increased in vulnerable regions of the AD brain, but the underlying mechanism is unknown. In the present study, we reported the effects of ferrous ions at subtoxic concentrations on the mRNA levels of BACE1 and a-disintegrin-and-metalloproteinase 10 (ADAM10) in PC12 cells and the cell responses to ferrous ions. The cell survival in PC12 cells significantly decreased with 0 to 0.3 mM $FeCl_2$, with 0.6 mM $FeCl_2$ treatment resulting in significant reductions by about 75%. 4,6-diamidino-2-phenylindole (DAPI) staining showed that the nuclei appeared fragmented in 0.2 and 0.3 mM $FeCl_2$. APP-${\alpha}$-carboxyl terminal fragment (APP-${\alpha}$-CTF) associations with ADAM10 and APP-${\beta}$-CTF with BACE1 were increased. Levels of ADAM10 and BACE1 mRNA increased in response to the concentrations of 0.25 mM, respectively. In addition, p-ERK and p-Bad (S112, S155) expressions were increased, suggesting that APP-CTF formation is related to ADAM10/ BACE1 expression. Levels of Bcl-2 protein were increased, but significant changes were not observed in the expression of Bax. These data suggest that ion-induced enhanced expression of AMDA10/BACE1 could be one of the causes for APP-${\alpha}/{\beta}$-CTF activation.

• Microbiology and Biotechnology Letters
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• v.42 no.2
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• pp.184-189
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• 2014

Yeast strains demonstrating fibrinolytic activity were isolated from traditional fermented soybean in Gangwon province, Korea. The AFY-1 strain isolated from fermented soybean paste showed the highest fibrinolytic activity (3.5 U/mg protein) corresponding to a 1.75 fold higher fibrinolytic activity compared with the plasmin (2.0 U/mg protein). The optimum temperature for the growth of AFY-1 strain was $32^{\circ}C$. Analysis of 18S rRNA gene sequence and carbon source utilization pattern indicated that the AFY-1 strain shares the highest homology (99%) with Saccharomycetales sp.

• Nutrition Research and Practice
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• v.10 no.2
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• pp.131-138
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• 2016

BACKGROUND/OBJECTIVES: Citrus and its peels have been used in Asian folk medicine due to abundant flavonoids and usage of citrus peels, which are byproducts from juice and/or jam processing, may be a good strategy. Therefore, the aim of this study was to examine antioxidant and anti-inflammatory effects of bioconversion of Jeju Hallabong tangor (Citrus kiyomi ${\times}$ ponkan; CKP) peels with cytolase (CKP-C) in RAW 264.7 cells. MATERIALS/METHODS: Glycosides of CKP were converted into aglycosides with cytolase treatment. RAW 264.7 cells were pre-treated with 0, 100, or $200{\mu}g/ml$ of citrus peel extracts for 4 h, followed by stimulation with $1{\mu}g/ml$ lipopolysaccharide (LPS) for 8 h. Cell viability, DPPH radical scavenging activity, nitric oxide (NO), and prostagladin $E_2$ ($PGE_2$) production were examined. Real time-PCR and western immunoblotting assay were performed for detection of mRNA and/or protein expression of pro-inflammatory mediators and cytokines, respectively. RESULTS: HPLC analysis showed that treatment of CKP with cytolase resulted in decreased flavanone rutinoside forms (narirutin and hesperidin) and increased flavanone aglycoside forms (naringenin and hesperetin). DPPH scavenging activities were observed in a dose-dependent manner for all of the citrus peel extracts and CKP-C was more potent than intact CKP. All of the citrus peel extracts decreased NO production by inducible nitric oxide synthase (iNOS) activity and $PGE_2$ production by COX-2. Higher dose of CKP and all CKP-C groups significantly decreased mRNA and protein expression of LPS-stimulated iNOS. Only $200{\mu}g/ml$ of CKP-C markedly decreased mRNA and protein expression of cyclooxygenase-2 in LPS-stimulated RAW 264.7 cells. Both 100 and $200{\mu}g/ml$ of CKP-C notably inhibited mRNA levels of $interleukin-1{\beta}$ ($IL-1{\beta}$) and IL-6, whereas $200{\mu}g/ml$ CKP-C significantly inhibited mRNA levels of $TNF-{\alpha}$. CONCLUSIONS: This result suggests that bioconversion of citrus peels with cytolase may enrich aglycoside flavanones of citrus peels and provide more potent functional food materials for prevention of chronic diseases attributable to oxidation and inflammation by increasing radical scavenging activity and suppressing pro-inflammatory mediators and cytokines.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.11
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• pp.1824-1836
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• 2020

Objective: On the hypothesis that grazing of cattle prompts organs to secrete or internalize circulating microRNAs (c-miRNAs) in parallel with changes in energy metabolism, we aimed to clarify biological events in adipose, skeletal muscle, and liver tissues in grazing Japanese Shorthorn (JSH) steers by a transcriptomic approach. Methods: The subcutaneous fat (SCF), biceps femoris muscle (BFM), and liver in JSH steers after three months of grazing or housing were analyzed using microarray and quantitative polymerase chain reaction (qPCR), followed by gene ontology (GO) and functional annotation analyses. Results: The results of transcriptomics indicated that SCF was highly responsive to grazing compared to BFM and liver tissues. The 'Exosome', 'Carbohydrate metabolism' and 'Lipid metabolism' were extracted as the relevant GO terms in SCF and BFM, and/or liver from the >1.5-fold-altered mRNAs in grazing steers. The qPCR analyses showed a trend of upregulated gene expression related to exosome secretion and internalization (charged multivesicular body protein 4A, vacuolar protein sorting-associated protein 4B, vesicle associated membrane protein 7, caveolin 1) in the BFM and SCF, as well as upregulation of lipolysis-associated mRNAs (carnitine palmitoyltransferase 1A, hormone-sensitive lipase, perilipin 1, adipose triglyceride lipase, fatty acid binding protein 4) and most of the microRNAs (miRNAs) in SCF. Moreover, gene expression related to fatty acid uptake and inter-organ signaling (solute carrier family 27 member 4 and angiopoietin-like 4) was upregulated in BFM, suggesting activation of SCF-BFM organ crosstalk for energy metabolism. Meanwhile, expression of plasma exosomal miR-16a, miR-19b, miR-21-5p, and miR-142-5p was reduced. According to bioinformatic analyses, the c-miRNA target genes are associated with the terms 'Endosome', 'Caveola', 'Endocytosis', 'Carbohydrate metabolism', and with pathways related to environmental information processing and the endocrine system. Conclusion: Exosome and fatty acid metabolism-related gene expression was altered in SCF of grazing cattle, which could be regulated by miRNA such as miR-142-5p. These changes occurred coordinately in both the SCF and BFM, suggesting involvement of exosome in the SCF-BFM organ crosstalk to modulate energy metabolism.

• Experimental and Molecular Medicine
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• v.50 no.12
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• pp.7.1-7.14
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• 2018

Dysregulation of long noncoding RNA (lncRNA) expression is linked to the development of various diseases. Recently, an emerging body of evidence has indicated that lncRNAs play important roles in the pathogenesis of inflammatory bowel diseases (IBDs), including Crohn's disease (CD) and ulcerative Colitis (UC). In IBD, lncRNAs have been shown to be involved in diverse processes, including the regulation of intestinal epithelial cell apoptosis, association with lipid metabolism, and cell-cell interactions, thereby enhancing inflammation and the functional regulation of regulatory T cells. In this review, we aim to summarize the current knowledge regarding the role of lncRNAs in IBD and highlight potential avenues for future investigation. We also collate potentially immune-relevant, IBD-associated lncRNAs identified through a built-by association analysis with respect to their neighboring protein-coding genes within IBD-susceptible loci. We further underscore their importance by highlighting their enrichment for various aspects of immune system regulation, including antigen processing/presentation, immune cell proliferation and differentiation, and chronic inflammatory responses. Finally, we summarize the potential of lncRNAs as diagnostic biomarkers in IBD.