• 대한원격탐사학회:학술대회논문집
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• 대한원격탐사학회 2005년도 Proceedings of ISRS 2005
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• pp.280-282
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• 2005

A ribonucleic acid (RNA) is one of the two types of nucleic acids found in living organisms. An RNA molecule represents a long chain of monomers called nucleotides. The sequence of nucleotides of an RNA molecule constitutes its primary structure, and the pattern of pairing between nucleotides determines the secondary structure of an RNA. Non-coding RNA genes produce transcripts that exert their function without ever producing proteins. Predicting the secondary structure of non-coding RNAs is very important for understanding their functions. We focus on Nussinov's algorithm as useful techniques for predicting RNA secondary structures. We introduce a new traceback matrix and scoring table to improve above algorithm. And the improved algorithm provides better levels of performance than the originals.

• Genomics & Informatics
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• 제13권4호
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• pp.94-101
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• 2015

tRNA-derived RNA fragments (tRFs) are an emerging class of non-coding RNAs (ncRNAs). A growing number of reports have shown that tRFs are not random degradation products but are functional ncRNAs made of specific tRNA cleavage. They play regulatory roles in several biological contexts such as cancer, innate immunity, stress responses, and neurological disorders. In this review, we summarize the biogenesis and functions of tRFs.

• Asian-Australasian Journal of Animal Sciences
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• 제32권7호
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• pp.1044-1051
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• 2019

Objective: Recent studies have implied that gene expression has high tissue-specificity, and therefore it is essential to investigate gene expression in a variety of tissues when performing the transcriptomic analysis. In addition, the gradual increase of long non-coding RNA (lncRNA) annotation database has increased the importance and proportion of mapped reads accordingly. Methods: We employed simple statistical models to detect the sexually biased/dimorphic genes and their conjugate lncRNAs in 40 RNA-seq samples across two factors: sex and tissue. We employed two quantification pipeline: mRNA annotation only and mRNA+lncRNA annotation. Results: As a result, the tissue-specific sexually dimorphic genes are affected by the addition of lncRNA annotation at a non-negligible level. In addition, many lncRNAs are expressed in a more tissue-specific fashion and with greater variation between tissues compared to protein-coding genes. Due to the genic region lncRNAs, the differentially expressed gene list changes, which results in certain sexually biased genes to become ambiguous across the tissues. Conclusion: In a past study, it has been reported that tissue-specific patterns can be seen throughout the differentially expressed genes between sexes in cattle. Using the same dataset, this study used a more recent reference, and the addition of conjugate lncRNA information, which revealed alterations of differentially expressed gene lists that result in an apparent distinction in the downstream analysis and interpretation. We firmly believe such misquantification of genic lncRNAs can be vital in both future and past studies.

• BMB Reports
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• 제56권2호
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• pp.49-55
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• 2023

Aging is characterized by a gradual decline in biological functions, leading to the increased probability of diseases and deaths in organisms. Previous studies have identified biological factors that modulate aging and lifespan, including non-coding RNAs (ncRNAs). Here, we review the relationship between aging and tRNA-derived small RNAs (tsRNAs), ncRNAs that are generated from the cleavage of tRNAs. We describe age-dependent changes in tsRNA levels and their functions in age-related diseases, such as cancer and neurodegenerative diseases. We also discuss the association of tsRNAs with aging-regulating processes, including mitochondrial respiration and reduced mRNA translation. We cover recent findings regarding the potential roles of tsRNAs in cellular senescence, a major cause of organismal aging. Overall, our review will provide useful information for understanding the roles of tsRNAs in aging and age-associated diseases.

• 미생물학회지
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• 제55권3호
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• pp.283-285
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• 2019

이 연구에서는 Illumina Hiseq platform을 사용하여 동해 심층 해양수로부터 분리된 Pelagicola sp. DSW4-44 (= KCTC 62762 = KCCM 43261)의 초안 유전체 염기서열 해독을 수행하였다. 그 결과, 유전체는 대략 4.85 Mbp의 길이 및 54.3%의 G + C 함량으로 구성되었고, 전체 4,566개의 단백질 암호 유전자, 3개의 rRNA 유전자, 48개의 tRNA 유전자, 3개의 non-coding RNA 유전자 및 67개의 위유전자(pseudo gene)가 확인되었다. 초안 유전체에서 균주 DSW4-44는 Pelagicola 속의 다른 균주에서 발견되지 않는 이화적 질산염의 암모늄 환원과 탈질화의 질소대사 유전자를 가지고 있었다.

• 미생물학회지
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• 제54권4호
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• pp.480-482
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• 2018

이 연구에서는 Illumina Hiseq platform을 사용하여 동해 심층 해양수로부터 분리된 Zhongshania marina $DSW25-10^T$의 유전체 염기서열 해독을 수행하였다. 그 결과, 유전체는 대략 4.08 Mbp의 길이 및 49.0%의 G + C 함량으로 구성되었고, 전체 3,702개의 단백질 암호 유전자, 3개의 rRNA 유전자, 39개의 tRNA 유전자, 4개의 non-coding RNA 유전자 및 36개의 위 유전자(pseudogenes)가 확인되었다. 또한, 지방족 및 방향족 화합물의 대사 경로가 확인되었다. 이러한 대사 경로들로 비추어 Zhongshania marina $DSW25-10^T$는 유용한 생물 정화 자원으로 사용될 수 있을 것으로 기대된다.

• Genomics & Informatics
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• 제16권4호
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• pp.18.1-18.9
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• 2018

Long non-coding RNAs (lncRNAs) are classified as RNAs that are longer than 200 nucleotides and cannot be translated into protein. Several studies have demonstrated that lncRNAs are directly or indirectly involved in a variety of biological processes and in the regulation of gene expression. In addition, lncRNAs have important roles in many diseases including cancer. It has been shown that abnormal expression of lncRNAs is observed in several human solid tumors. Several studies have shown that many lncRNAs can function as oncogenes in cancer development through the induction of cell cycle progression, cell proliferation and invasion, anti-apoptosis, and metastasis. Oncogenic lncRNAs have the potential to become promising biomarkers and might be potent prognostic targets in cancer therapy. However, the biological and molecular mechanisms of lncRNA involvement in tumorigenesis have not yet been fully elucidated. This review summarizes studies on the regulatory and functional roles of oncogenic lncRNAs in the development and progression of various types of cancer.

• Asian Pacific Journal of Cancer Prevention
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• 제14권2호
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• pp.1077-1082
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• 2013

Background: Renal cell carcinoma (RCC) is a malignancy with a poor prognosis. We aimed to explore whether the expression of Long Non-Coding RNA (LncRNA) growth arrest-specific transcript 5 (GAS5) is associated with RCC genesis. Methods: We selected twelve clinical samples diagnosed for renal clear cell carcinoma and found that the LncRNA GAS5 transcript levels were significantly reduced relative to those in adjacent unaffected normal renal tissues. Results: In addition, expression of GAS5 was lower in the RCC cell line A498 than that in normal renal cell line HK-2. Furthermore, using functional expression cloning, we found that overexpression of GAS5 in A498 cells inhibited cell proliferation, induced cell apoptosis and arrested cell cycling. At the same time, the migration and invasion potential of A498 cells were inhibited compared to control groups. Conclusion: Our study provided the first evidence that a decrease in GAS5 expression is associated with RCC genesis and progression and overexpression of GAS5 can act as a tumor suppressor for RCC, providing a potential attractive therapeutic approach for this malignancy.

• Asian Pacific Journal of Cancer Prevention
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• 제15권23호
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• pp.10513-10524
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• 2015

Background: Metastasis is a major reason for poor prognosis in patients with cancer, including hepatocellular carcinoma (HCC). A salient feature is the ability of cancer cells to colonize different organs. Long non-coding RNAs (lncRNAs) play important roles in numerous cellular processes, including metastasis. Materials and Methods: In this study, the lncRNA expression profiles of two HCC cell lines, one with high potential for metastasis to the lung (HCCLM3) and the other to lymph nodes (HCCLYM-H2) were assessed using the Arraystar Human LncRNA Array v2.0, which contains 33,045 lncRNAs and 30,215 mRNAs. Coding-non-coding gene co-expression (CNC) networks were constructed and gene set enrichment analysis (GSEA) was performed to identify lncRNAs with potential functions in organ-specific metastasis. Levels of two representative lncRNAs and one representative mRNA, RP5-1014O16.1, lincRNA-TSPAN8 and TSPAN8, were further detected in HCC cell lines with differing metastasis potential by qRT-PCR. Results: Using microarray data, we identified 1,482 lncRNAs and 1,629 mRNAs that were differentially expressed (${\geq}1.5$ fold-change) between the two HCC cell lines. The most upregulated lncRNAs in H2 were RP11-672F9.1, RP5-1014O16.1, and RP11-501G6.1, while the most downregulated ones were lincRNA-TSPAN8, lincRNA-CALCA, C14orf132, NCRNA00173, and CR613944. The most upregulated mRNAs in H2 were C15orf48, PSG2, and PSG8, while the most downregulated ones were CALCB, CD81, CD24, TSPAN8, and SOST. Among them, lincRNA-TSPAN8 and TSPAN8 were found highly expressed in high lung metastatic potential HCC cells, while lowly expressed in no or low lung metastatic potential HCC cells. RP5-1014O16.1 was highly expressed in high lymphatic metastatic potential HCC cell lines, while lowly expressed in no lymphatic metastatic potential HCC cell lines. Conclusions: We provide the first detailed description of lncRNA expression profiles related to organ-specific metastasis in HCC. We demonstrated that a large number of lncRNAs may play important roles in driving HCC cells to metastasize to different sites; these lncRNAs may provide novel molecular biomarkers and offer a new basis for combating metastasis in HCC cases.

• 대한의생명과학회지
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• 제25권2호
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• pp.113-122
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• 2019

Long-non coding RNAs (LncRNAs) constitute a wide and extremely diverse family of RNA transcripts that are greater than 200 base pairs in length and are not translated into proteins. X-inactive specific transcript (XIST) was the first long non-coding RNA to be discovered, back in 1991. Its function in X-chromosome inactivation has been extensively studied for three decades, though other functional roles of XIST that involve a variety of fascinating mechanisms remain to be elucidated. Here, we review the emerging oncogenic role of XIST in various human cancers.