• 생명과학회지
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• 제27권12호
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• pp.1494-1499
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• 2017

Candida albicans에 의한 구강 감염(캔디다증)은 구강 점막에 빈번하게 발생하며 잘 알려진 질병이다. 구강 캔디다증은 생명을 위협하는 정도의 곰팡이 감염증은 아니나, 특정상황에서 개인에게 심각한 위험을 초래할 수도 있다. 마이크로 RNA는 세포 내에서 다른 타겟 유전자를 저해하는 작은 크기의 RNA 분자이며 단백질을 코딩하지는 않고 번역과정을 억제하는 조절자로서의 역할을 하고 있다. 본 연구는 C. albicans의 마이크로RNA를 처음으로 동정하고 그러한 마이크로RNA가 지닌 기능을 조사하기 위함이다. 이를 위하여 C. albicans의 small RNA를 차세대 염기분석법을 통하여 분석하고 그러한 RNA들의 2차 구조를 생물정보학적 방법으로 조사하였다. 분석한 small RNA들은 마이크로 RNA라고 불리울 수 있는 특징들을 가지고 있었으며, 특별히 높게 발현되고 있는 두개의 마이크로 RNA 정도 크기의 RNA가 CBP1 유전자의 3' 말단 비번역구역(UTR)에서 반대방향으로 발현하는 것을 밝혀 내었다. 우리는 이러한 C. albicans의 RNA가 CBP1 유전자를 타겟으로 하여 조절하는지 알아보기 위해 RNA를 인위적으로 합성한 후 세포 내로 주입하고, 형광형미경으로 도입 사실을 확인하였다. 하지만 4시간과 8시간 후에 CBP1의 발현 변화는 관찰되지 않았다. 따라서, 이러한 결과는 C. albicans가 마이크로RNA에 의한 RNA 간섭(RNAi) 작용이 다른 진핵세포와는 다르게 작용하는 것을 알 수 있다.

• Molecules and Cells
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• 제42권5호
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• pp.379-385
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• 2019

Non-coding RNAs (ncRNAs) comprise various RNA species, including small ncRNAs and long ncRNAs (lncRNAs). ncRNAs regulate various cellular processes, including transcription and translation of target messenger RNAs. Recent studies also indicate that ncRNAs affect organismal aging and conversely aging influences ncRNA levels. In this review, we discuss our current understanding of the roles of ncRNAs in aging and longevity, focusing on recent advances using the roundworm Caenorhabditis elegans. Expression of various ncRNAs, including microRNA (miRNA), tRNA-derived small RNA (tsRNA), ribosomal RNA (rRNA), PIWI-interacting RNA (piRNA), circular RNA (circRNA), and lncRNA, is altered during aging in C. elegans. Genetic modulation of specific ncRNAs affects longevity and aging rates by modulating established aging-regulating protein factors. Because many aging-regulating mechanisms in C. elegans are evolutionarily conserved, these studies will provide key information regarding how ncRNAs modulate aging and lifespan in complex organisms, including mammals.

• The Plant Pathology Journal
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• 제16권5호
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• pp.252-256
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• 2000

The 16S-23S rRNA intergenic spacer regions (ISRs) were sequenced and analyzed to design specific primer for identification of Pectobacterium chrysanthemi. Two types ISRs, large and small ISRs, were identified from three strains (ATCC 11663, KACC 10163 and KACC 10165) of P. chrysanthemi and Pectobacterium carotovorum subsp. carotovorum ATCC 15713.Large ISRs contained transfer RNA-Ile(tRNA$^{Ile}$)and tRNA$^{Ala}$, and small ISRs contained tRNA$^{Glu}$. Size of the small ISRs of P. chrysanthemi ranged on 354-356 bp, while it was 451 bp in small ISR of P. carotovorum subsp. carotovorum ATCC 15713. From hypervariable region of small ISRs, species-specific primer for P. chrysanthemi with 20 bp length (CHPG) was designed from hypervariable region of small ISRs, which was used as forward promer to detect P. chrysanthemi strains with R23-1R produced PCR product of about 260bp size (CHSF) only from P. chrysanthemi strains, not from other Pectobacterium spp. and Erwinia spp. Direct PCR from bacterial cell without extracting DNA successfully amplified a specific fragment, CHSF, from P. chrysanthemi ATCC 11663. The limit of PCR detection was 1${\pm}10^2$ cfu/ml.

• 자연과학논문집
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• 제18권1호
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• pp.47-53
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• 2007

바실러스 서브틸리스 유전체에서 여러 환경의 적응에 이용할 것으로 보이는 새로운 small RNA를 찾는 시도로 다음과 같은 방식으로 유전체를 검색하였다. 첫째로 유전자들 사이에 존재하는 DNA 서열을 대상으로 전사인자들인 PerR, OhrR, Fur, Zur의 인식서열을 조사하였고, 둘째로 인자 비의존성 전사종결 부위를 조사하였다. 이들 조사에서 전사인자의 위치와 전사종결부위가 300 bp 내외에서 가까이 존재하는 후보 DNA 서열을 대상으로 전사인자 부위에서 전사촉진자의 서열이 발견되는지를 조사하였다. 이 결과 PerR 5개, Fur 2개, OhrR, Zur에서 각각 1개의 새로운 small RNA로 추정되는 부위가 발견되었다.

• Tissue Engineering and Regenerative Medicine
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• 제15권6호
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• pp.711-719
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• 2018

BACKGROUND: Collagen organization within tissues has a critical role in wound regeneration. Collagen fibril diameter, arrangements and maturity between connective tissue growth factor (CTGF) small interfering RNA (siRNA) and mismatch scrambled siRNA-treated wound were compared to evaluate the efficacy of CTGF siRNA as a future implement for scar preventive medicine. METHODS: Nanocomplexes of CTGF small interfering RNA (CTGF siRNA) with cell penetrating peptides (KALA and $MPG^{{\Delta}NLS}$) were formulated and their effects on CTGF downregulation, collagen fibril diameter and arrangement were investigated. Various ratios of CTGF siRNA and peptide complexes were prepared and down-regulation were evaluated by immunoblot analysis. Control and CTGF siRNA modified cells-populated collagen lattices were prepared and rates of contraction measured. Collagen organization in rabbit ear 8 mm biopsy punch wound at 1 day to 8 wks post injury time were investigated by transmission electron microscopy and histology was investigated with Olympus System and TS-Auto software. CONCLUSION: CTGF expression was down-regulated to 40% of control by CTGF siRNA/KALA (1:24) complexes (p<0.01) and collagen lattice contraction was inhibited. However, down-regulated of CTGF by CTGF $siRNA/MPG^{{\Delta}NLS}$ complexes was not statistically significant. CTGF KALA-treated wound appeared with well formed-basket weave pattern of collagen fibrils with mean diameter of $128{\pm}22nm$ (n = 821). Mismatch siRNA/KALA-treated wound showed a high frequency of parallel small diameter fibrils (mean $90{\pm}20nm$, n = 563). CONCLUSION: Controlling over-expression of CTGF by peptide-mediated siRNA delivery could improve the collagen orientation and tissue remodeling in full thickness rabbit ear wound.

• BMB Reports
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• 제48권3호
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• pp.147-152
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• 2015

Small interfering RNA (siRNA) functions through pairing with specific mRNA sequences and results in the mRNA's degradation. It is a potential therapeutic approach for many diseases caused by altered gene expression. The delivery of siRNA is still a major problem due to its rapid degradation in the circulation. Various strategies have been proposed to help with the cellular uptake of siRNA and short or small hairpin RNA (shRNA). Here, we reviewed recently published data regarding local applications of siRNA. Compared with systemic delivery methods, local delivery of siRNA/shRNA has many advantages, such as targeting the specific tissues or organs, mimicking a gene knockout effect, or developing certain diseases models. The eye, brain, and tumor tissues are 'hot' target tissues/organs for local siRNA delivery. The siRNA can be delivered locally, in naked form, with chemical modifications, or in formulations with viral or non-viral vectors, such as liposomes and nanoparticles. This review provides a comprehensive overview of RNAi local administration and potential future applications in clinical treatment.

• Journal of Microbiology and Biotechnology
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• 제11권3호
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• pp.515-523
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• 2001

The dinoflagellates have some primitive nuclear features and are evolutionarily intermediate between prokaryotes and eukaryotes. The small subunit ribosomal RAN gene, the 5.8S ribosomal RNA gene, and the internal transcribed spacer (ITS) of Gonyaulax polyedra were cloned, and their sequences were analyzed to better understand their evolutionary position. The small subunit ribosomal RNA gene was 1,794 nt long, the large subunit ribosomal RNA gene was approximately 3,500 nt long, and the 5.8S ribosomal RNA gene was 159 nt long. The first internal transcribed spacer (ITS1) was 191 nt long, and the second internal transcribed spacer (ITS2) was 185 nt long. The intergenic spacer of the ribosomal RNA gene (IGS) was about 2,200 nt long, indicating that 5,800 nt of transcribed sequences were separated by roughly 2,200 nt of intergenic spacer. The ribosomal RNA genes were repeated many times and arranged in a head-to-tail, tandemly repeated manner. The repeating unit of ribosomal RNA gene of G. polyedra was proposed to be 8,000 nt long. Based on the lengths of ribosomal RNA, sequence alignments with representative organisms, and phylogenetic analysis on ribosomal RNA, G. polyedra appears to be one of the alveolates branched from the eukaryotic crown and, among dinoflagellates, it seems to not have emerged early.

• Genomics & Informatics
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• 제9권1호
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• pp.39-43
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• 2011

MicroRNAs (miRNAs) are recently discovered small RNA molecules usually resulting in translational repression and gene silencing. Despite the fact that specific cloning of small RNA's is a method in practice, computational identification of miRNA's has been a major focus recent days, since is a rapid process following AB initio and sequence alignment methods. Here we developed new software called MiRPI that aims to identify the highly conserved miRNAs without any mismatches from given fasta formatted gene sequences by using non-repeated miRNA dataset of the user's interest. The new window embedded with the software is used to identify the targets for inputted mature miRNAs in the mRNA sequences. Also MiRPI is designed to measure the precursor miRNA statistics, majorly focusing the Adjusted Minimum Folding free Energy (AMFE) and Minimum Folding free Energy Index (MFEI), the most important parameters in miRNA confirmation. MiRPI is developed by PERL (Practical Extraction and Report Language) and Tk (Tool kit widgets) scripting languages. It is user friendly, portable offline software that works in all windows OS, sized to 3 MB.

• The Plant Pathology Journal
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• 제16권2호
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• pp.98-104
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• 2000

For the taxonomic evaluaition, 15 strains of the genus Pectobacterium and Erwinia were analyzed for 16S-23S rDNA intergenic spacer regions (ISRs). These species contained two types of ISRs, large and small ISRs. Large ISRs were on the range of 474-569 bp size, and coding transfer $\textrm{RNA}^{11e}$($\textrm{tRNA}^{11e}$) and $\textrm{tRNA}^{Ala}$. Small ISRs were 354-459 bp in length and coding $\textrm{tRNA}^{Glu}$. The sequence variations of two ISRs among species and strains were very high as compared with 16S rRNA gene sequences. By phylogenetic trees on the basis of two ISRs, Pectobacterium ere differentiated into P. carotovorum-P. cactiaidum group and P. chrysanthemi group. However, the taxonomic position of E. cypripedii and E. rhapontici, which were not clear on taxonomic delineation between Pectobacterium and Erwinia, were not clearly resolved on the basis of ISRs.

• BMB Reports
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• 제47권11호
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• pp.619-624
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• 2014

Antisense RNA is a type of noncoding RNA (ncRNA) that binds to complementary mRNA sequences and induces gene repression by inhibiting translation or degrading mRNA. Recently, several small ncRNAs (sRNAs) have been identified in Escherichia coli that act as antisense RNA mainly via base pairing with mRNA. The base pairing predominantly leads to gene repression, and in some cases, gene activation. In the current study, we examined how the location of target sites affects sRNA-mediated gene regulation. An efficient antisense RNA expression system was developed, and the effects of antisense RNAs on various target sites in a model mRNA were examined. The target sites of antisense RNAs suppressing gene expression were identified, not only in the translation initiation region (TIR) of mRNA, but also at the junction between the coding region and 3' untranslated region. Surprisingly, an antisense RNA recognizing the upstream region of TIR enhanced gene expression through increasing mRNA stability.