• BMB Reports
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• v.38 no.4
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• pp.457-467
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• 2005

Open reading frame (ORF) 3 on the Choristoneura fumiferana granulovirus (ChfuGV), located in the 11 kb fragment of the BamHI genomic bank encodes a predicted 32-kDa putative kinase protein. Bioinformatics analysis on the predicted amino acid sequence of ChfuGV PK-1 revealed the existence of 11 catalytic subdomains. Sequence analysis within the 5'-untranslated region (5'-UTR) of ChfuGV pk-1 indicates the presence of both putative early and late promoter motifs, indicating that pk-1 may be expressed throughout the infection cycle. Promoter sequence analysis reveals that pk-1 is deprived of a TATA box and appears instead to be regulated by other cis-acting transcriptional regulatory elements. Temporal transcription analysis by RT-PCR confirms the appearance of transcripts detected from 2 h p.i. until 72 h p.i. Northern blot hybridization characterizes pk-1 transcription as a 1.2 kb transcript. Homology comparisons reveal that ChfuGV PK-1 protein is most closely related to Phthorimaea operculalla granulovirus (PoGV) with 80% amino acid identity.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.2
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• pp.917-923
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• 2014

Chondrosarcomas are malignant cartilage-forming tumors of bone which exhibit resistance to both chemotherapy and radiation treatment. miRNAs have been well demonstrated to regulate gene expression and play essential roles in a variety of biological processes, including proliferation, differentiation, migration, cell cycling and apoptosis. In this study, we obtained evidence that miR-100 acts as a tumor suppressor in human chondrosarcomas. Interestingly, cisplatin resistant chondrosarcoma cells exhibit decreased expression of miR-100 compared with parental cells. In addition, we identified mTOR as a direct target of miR-100. Overexpression of miR-100 complementary pairs to the 3' untranslated region (UTR) of mTOR, resulted in sensitization of cisplatin resistant cells to cisplatin. Moreover, recovery of the mTOR pathway by overexpression of S6K desensitized the chondrosarcoma cells to cisplatin, suggesting the miR-100-mediated sensitization to cisplatin dependent on inhibition of mTOR. In summary, the present studies highlight miR-100 as a tumor suppressor in chondrosarcoma contributing to anti-chemoresistance. Overexpression of miR-100 might be exploited as a therapeutic strategy along with cisplatin-based combined chemotherapy for the treatment of clinical chondrosarcoma patients.

• Proceedings of the Korean Information Science Society Conference
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• 2006.06a
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• pp.13-15
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• 2006

microRNA는 유전자의 전사 후 과정에서 negative regulation을 담당하는 small noncoding RNA의 한 증류이다. 최근까지 330여개의 인간 microRNA가 발견되었지만 그들의 기능이 밝혀진 것은 소수에 불과하다. microRNA의 기능은 3'UTR에 불완전 상보결합을 통해 negative regulation을 받게 되는 유전자의 기능으로부터 유추되는 것이 일반적이다. 특별히 유전체상에 군집화 된 microRNA들은 하나의 전사체로부터 발현되는 것으로 판단되며, 같은 또는 관련된 기능을 하거나 같은 목표 유전자를 조절하기 위한 functional family일 가능성이 높다. 또한 이러한 functional family는 하나의 전사체로부터 발현되기 때문에, 조직별로 조건별로 같은 발현 패턴을 보여야 한다. 본 연구에서는 발현데이터로부터 microRNA functional family를 탐색하기 위해, 5개의 연구 그룹에서 공개한 조직별 microRNA 발현데이터를 표준화 작업을 거친 후 통합하고 k-nearest neighbor 알고리즘을 이용해 결측치를 보정한 후 microRNA 발현사이의 correlation을 계산한다. 이때 데이터 통합에서 생기는 문제에 robust한 결과를 얻기 위해 실제 발현데이터가 아닌 rank 데이터부터 correlation을 측정한다. 계산된 spearman ranked correlation 결과와 microRNA의 genomic coordination 정보로부터 34개의 functional family를 정의할 수 있었다.

• Korean Journal of Veterinary Research
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• v.39 no.4
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• pp.772-777
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• 1999

The uncaped genomic RNA of bovine viral diarrhea virus (BVDV) initiates translation by recruitment of eukaryotic translation initiation factors at the internal ribosome entry site (IRES). N-terminal protease ($N^{pro}$) is the first translation product of the open reading frame (ORF). By using the vaccinia virus SP6 RNA polymerase transient expression system, we showed previously that deletion of $N^{pro}$ region reduced translation by 21%. To better understand the biological significance of $N^{pro}$ for translation, we carried out a mutational analysis of the $N^{pro}$ region of BVDV cloned in the intercistronic region of a bicistronic reporter plasmid. We constructed a bicistronic expression vector in which the entire 5 UTR and the mutated $N^{pro}$ region (${\Delta}386-901$, ${\Delta}415-901$ and ${\Delta}657-901$) was cloned between two reporter genes, chloramphenicol acetyltransferase (CAT) and luciferase (LUC). In vivo translation analyses showed that $N^{pro}$ region was dispensible for efficient translation. The results indicate that the $N^{pro}$ region is not essential for BVDV RNA translation and the 3' boundary of BVDV IRES is expanded into $N^{pro}$ region, suggesting that $N^{pro}$ may not play a major role in BVDV replication.

• Food Science of Animal Resources
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• v.32 no.6
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• pp.776-782
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• 2012

Marbling (intramuscular fat) is the most economically important meat quality trait in Hanwoo (Korean cattle). The endothelial differentiation G-protein coupled receptor 1 (EDG1) gene, involved in blood vessel formation, is located within the genomic region of a quantitative trait locus (QTL) for marbling on bovine chromosome 3. Thus, the EDG1 gene can be considered as a positional and functional candidate gene for meat quality in beef cattle. This study aimed to identify single nucleotide polymorphisms (SNPs) in the EDG1 gene and to evaluate their associations with carcass traits in Hanwoo population. We have sequenced a fragment of 5'-UTR of the EDG1 gene and identified one SNP. Genotyping of the g.166A>G SNP marker was carried out using PCR-RFLP analysis in 309 Hanwoo steers in order to evaluate their association with carcass traits. The g.166A>G SNP marker showed a significant effect on the marbling score. Animals with the GG genotype had higher marbling score compared with AA and AG genotypes (p<0.05). This SNP marker also showed a significant additive effects for the marbling score (p<0.05). These results suggest that the EDG1 gene can be used as a molecular marker for DNA marker-assisted selection in order to increase the levels of the marbling score in Hanwoo.

• Plant Resources
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• v.1 no.1
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• pp.13-21
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• 1998

A cDNA Fragment encoding iron storage protrin generated by polymerase chain reaction(PCR) using highly conserved regions of ferritin related genes were used to sereen a red pepper cDNA library. cDNA clone was designated as Fp1. Fp1 clone contatines a 5' nontranslated region of 51dp containing stop conds. Down stream from 5' UTP. an open reading frame of 750bp was observed. followed by a 3' UTR of 272bp. The deduces amino acid sequence of red pepper protein(Fp1) showed 84%, 48% and 36% identity with soybean(SolC). human(HuL H) and horse spleen(HoS-L) ferritin mRNA accumulation in response to iron. Ferritin mRNA accumulation was transient and particularly abundant in leaves. reaching a maxmum at 12h. The level of ferritin mRNA in roots was affected to a lesser extent than in leaves.

• The Plant Pathology Journal
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• v.27 no.1
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• pp.33-36
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• 2011

The genome of a potyvirus isolate associated with chlorotic spots and vein banding symptoms on Spathiphyllum spp., in Andhra Pradesh state, India was amplified by RT-PCR using degenerate potyvirus primers, amplicons cloned, and sequence (1.6 kb) analyzed. This virus isolate shared maximum identity of 74.8% and 80.2% at coat protein (CP) gene nucleotide (906 nucleotides) and amino acid (302 amino acids) levels, respectively with Dasheen mosaic virus (DsMV)-M13 isolate reported from China. But its 3'-UTR (258 nucleotides) had maximum identity of 62.5% with DsMV-Vietnam isolate. The deduced molecular weight of CP is 33.57 kDa and it contained DAG triplet in its N-terminal region. In CP amino acid based phylogenetic analysis, this virus isolate represented a separate branch but closer to DsMV isolates cluster. Based on the molecular criteria set for the discrimination of species and genus in the Potyviridae family, the present virus isolate was identified as a distinct virus species in the genus Potyvirus and proposed the name Spathiphyllum chlorotic vein banding virus (SCVbV).

• Journal of Microbiology and Biotechnology
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• v.33 no.3
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• pp.410-418
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• 2023

Bacilysin is a dipeptide antibiotic composed of L-alanine and L-anticapsin produced by certain strains of Bacillus subtilis. Bacilysin is gaining increasing attention in industrial agriculture and pharmaceutical industries due to its potent antagonistic effects on various bacterial, fungal, and algal pathogens. However, its use in industrial applications is hindered by its low production in the native producer. The biosynthesis of bacilysin is mainly based on the bacABCDEF operon. Examination of the sequence surrounding the upstream of the bac operon did not reveal a clear, strong ribosome binding site (RBS). Therefore, in this study, we aimed to investigate the impact of RBS as a potential route to improve bacilysin production. For this, the 5' untranslated region (5'UTR) of the bac operon was edited using the CRISPR/Cas9 approach by introducing a strong ribosome binding sequence carrying the canonical Shine-Dalgarno sequence (TAAGGAGG) with an 8 nt spacing from the AUG start codon. Strong RBS substitution resulted in a 2.87-fold increase in bacilysin production without affecting growth. Strong RBS substitution also improved the mRNA stability of the bac operon. All these data revealed that extensive RBS engineering is a promising key option for enhancing bacilysin production in its native producers.

• The Korean Journal of Physiology and Pharmacology
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• v.27 no.2
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• pp.131-141
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• 2023

Compelling evidence has demonstrated the critical role of circular RNAs (circRNAs) during lung adenocarcinoma (LUAD) progression. Herein, we explored a novel circRNA, circ_0129047, and detailed its mechanism of action. The expression of circ 0129047, microRNA-665 (miR-665), and protein tyrosine phosphatase receptor type B (PTPRB) in LUAD tissues and cells was determined using reverse transcription quantitative polymerase chain reaction and Western blotting. Cell Counting Kit8 and colony formation assays were conducted to detect LUAD cell proliferation, and western blotting was performed to quantify apoptosis-related proteins (Bcl2 and Bax). Luciferase reporter and RNA immunoprecipitation assays were used to validate the predicted interaction between miR-665 and circ_0129047 or PTPRB. A xenograft assay was used for the in vivo experiments. Circ_0129047 and PTPRB were downregulated in LUAD tissues and cells, whereas miR-665 expression was upregulated. Overexpression of circ_0129047 suppresses LUAD growth in vivo and in vitro. Circ_0129047 is the target of miR-665, and the miR-665 mimic ablated the antiproliferative and pro-apoptotic phenotypes of LUAD cells by circ_0129047 augmentation. MiR-665 targets the 3'UTR of PTPRB and downregulates PTPRB expression. PTPRB overexpression offsets the pro-proliferative potential of miR-665 in LUAD cells. Circ_0129047 sequestered miR-665 and upregulated PTPRB expression, thereby reducing LUAD progression, suggesting a promising approach for preventing LUAD.

• BMB Reports
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• v.53 no.5
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• pp.278-283
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• 2020

Muscle fibers are generally formed as multinucleated fibers that are differentiated from myoblasts. Several reports have identified transcription factors and proteins involved in the process of muscle differentiation, but the roles of microRNAs (miRNAs) in myogenesis remain unclear. Here, comparative analysis of the miRNA expression profiles in mouse myoblasts and gastrocnemius (GA) muscle uncovered miR-3074-3p as a novel miRNA showing markedly reduced expression in fully differentiated adult skeletal muscle. Interestingly, elevating miR-3074-3p promoted myogenesis in C2C12 cells, primary myoblasts, and HSMMs, resulting in increased mRNA expression of myogenic makers such as Myog and MyHC. Using a target prediction program, we identified Caveolin-1 (Cav1) as a target mRNA of miR-3074-3p and verified that miR-3074-3p directly interacts with the 3' untranslated region (UTR) of Cav1 mRNA. Consistent with the findings in miR-3074-3p-overexpressing myoblasts, knockdown of Cav1 promoted myogenesis in C2C12 cells and HSMMs. Taken together, our results suggest that miR-3074-3p acts a positive regulator of myogenic differentiation by targeting Cav1.