• Proceedings of the Botanical Society of Korea Conference
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• 1987.07a
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• pp.283-307
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• 1987

Glycinin and $\beta$-conglycinin are the most abundant storage protein in soybean. These proteins are known to be synthesized predominantly during germination and cell expansion phase of seed development for short period, and synthesized not in other tissues. Genes encoding these storage proteins are useful system to study the mechanism of development stage and tissue specific gene expression in eukaryotes, especially plants, at the molecular level. The cDNA and genomic clones coding for glycinin have been isolated and regulation mechanism of the gene expression has been studied. Initially, development and tissue-specific expression of the glycinin gene is regulated at the level of transcription. Post-transcriptional processing is also responsible for delayed accumulation of the mRNA. Translational control of the storage protein gene has not been reported. Post-translational modification is another strategic point to regulate the expression of the gene. It is possible to identify positive and/or negative reguratory clements in vivo by producing transgenic plants agter gene manipulation. Elucidation of activation and repression mechanism of soybean storage protein genes will contribute to the understanding of the other plant and eukaryotic genes at molecular level.

• BMB Reports
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• v.28 no.6
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• pp.509-514
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• 1995

A putative secondary structure of the mRNA for the human hepatitis B virus (HBV) X gene is proposed based on not only chemical and enzymatic determination of its single- and double-stranded regions but also selection by the computer program MFOLD for energy minimum conformation under the constraints that the experimentally determined nucleotides were forced or prohibited to base pair. An RNA of 536 nucleotides including the 461-nucleotide HBV X mRNA sequence was synthesized in vitro by the phage T7 RNA polymerase transcription. The thermally renatured transcripts were subjected to chemical modifications with dimethylsulfate and kethoxal and enzymatic hydrolysis with single strand-specific RNase T1 and double strand-specific RNase V1, separately. The sites of modification and cleavage were detected by reverse transcriptase extension of 4 different primers. Many nucleotides could be assigned with high confidence, twenty in double-stranded and thirty-seven in Single-stranded regions. These nucleotides were forced and prohibited, respectively, to base pair in running the recursive RNA folding program MFOLD. The results suggest that 6 different regions (5 within X mRNA) of 14~23 nucleotides are Single-stranded. This putative structure provides a good working model and suggests potential target sites for antisense and ribozyme inhibitors and hybridization probes for the HBV X mRNA.

• BMB Reports
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• v.50 no.4
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• pp.162-163
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• 2017

RNA polymerase II-interacting the Set2 methyltransferase co-transcriptionally methylates histone H3 at lysine 36 within the body of genes. This modification facilitates histone deacetylation by Rpd3S HDAC in 3' transcribed regions to suppress cryptic initiation and slow elongation. Although this pathway is important for global deacetylation, no strong effects have been seen on genome-wide transcription under optimized laboratory conditions. In contrast, this pathway slows the kinetics of mRNA induction when target genes are induced upon environmental changes. Interestingly, a majority of Set2-repressed genes are overlapped by a lncRNA transcription that targets H3K36 methylation and deacetylation by Rpd3S HDAC to mRNA promoters. Furthermore, this pathway delays the induction of many cryptic transcripts upon environmental changes. Therefore, the Set2-Rpd3S HDAC pathway functions to fine-tune expression dynamics of mRNAs and ncRNAs.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.2
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• pp.275-281
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• 2009

Modification of thyroid hormone levels has a profound effect on skeletal muscle differentiation, predominantly through direct regulation involving thyroid hormone receptors. Nevertheless, little is known about the regulation of myostatin gene expression in skeletal muscle due to altered concentrations of thyroid hormone. Thus, the goal of our study was to find out whether altered thyroid states could change the gene expression of myostatin, the most powerful inhibitor of skeletal muscle development. A hyperthyroid state was induced in rats by daily injections of L-thyroxine 20 mg/100 g body weight for 14 days, while a hypothyroid state was induced in another group of rats by administering methimazole (0.04%) in drinking water for 14 days. After a period of 14 days of L-thyroxine treatment we observed a significant increase of myostatin expression both in mRNA and protein level. However, decreased expression of myostatin mRNA and protein were observed in hypothyroid rats. Furthermore, our studies demonstrated that the upregulation of myostatin gene expression might be responsible for the loss of body weight induced by altered thyroid hormone levels. We concluded that myostatin played a role in a metabolic process in muscle that was regulated by thyroid hormone.

• Mycobiology
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• v.50 no.1
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• pp.1-11
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• 2022

The ascomycete fungus Cordyceps militaris infects lepidopteran larvae and pupae and forms characteristic fruiting bodies. Owing to its immune-enhancing effects, the fungus has been used as a medicine. For industrial application, this fungus can be grown on geminated soybeans as an alternative protein source. In our study, we performed a comprehensive transcriptomic analysis to identify core gene sets during C. militaris cultivation on germinated soybeans. RNA-Seq technology was applied to the fungal cultures at seven-time points (2, 4, and 7-day and 2, 3, 5, 7-week old cultures) to investigate the global transcriptomic change. We conducted a time-series analysis using a two-step regression strategy and chose 1460 significant genes and assigned them into five clusters. Characterization of each cluster based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases revealed that transcription profiles changed after two weeks of incubation. Gene mapping of cordycepin biosynthesis and isoflavone modification pathways also confirmed that gene expression in the early stage of GSC cultivation is important for these metabolic pathways. Our transcriptomic analysis and selected genes provided a comprehensive molecular basis for the cultivation of C. militaris on germinated soybeans.

• Korean Journal of Clinical Laboratory Science
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• v.56 no.1
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• pp.10-20
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• 2024

RNA-sequencing (RNA-seq) is a technique used for providing global patterns of transcriptomes in samples. However, it can only provide the average gene expression across cells and does not address the heterogeneity within the samples. The advances in single-cell RNA sequencing (scRNA-seq) technology have revolutionized our understanding of heterogeneity and the dynamics of gene expression at the single-cell level. For example, scRNA-seq allows us to identify the cell types in complex tissues, which can provide information regarding the alteration of the cell population by perturbations, such as genetic modification. Since its initial introduction, scRNA-seq has rapidly become popular, leading to the development of a huge number of bioinformatic tools. However, the analysis of the big dataset generated from scRNA-seq requires a general understanding of the preprocessing of the dataset and a variety of analytical techniques. Here, we present an overview of the workflow involved in analyzing the scRNA-seq dataset. First, we describe the preprocessing of the dataset, including quality control, normalization, and dimensionality reduction. Then, we introduce the downstream analysis provided with the most commonly used computational packages. This review aims to provide a workflow guideline for new researchers interested in this field.

• Reproductive and Developmental Biology
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• v.32 no.3
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• pp.183-191
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• 2008

This study was conducted to investigate the development and gene expression in miniature pig nuclear transfer (mNT) embryos produced under different osmolarity culture conditions. Control group of mNT embryos was cultured in PZM-3 for 6 days. Treatment group of mNT embryos was cultured in modified PZM-3 with NaCl (mPZM-3, 320 mOsmol) for 2 days, and then cultured in PZM-3 (270 mOsmol) for 4 days. Blastocyst formation rate of the treatment group was significantly higher than the control and the apoptosis rate was significantly lower in treatment group. Bax-$\alpha$ and caspase-3 mRNA expression were significantly higher in the control than the treatment group. Also, the majority of imprinting genes were expressed aberrantly in in vitro produced mNT blastocysts compared to in vivo derived blastocyst H19 and Xist mRNA expression were significantly lower in the control than the treatment group or in vivo. IGF2 mRNA expression was significantly higher in the control than the treatment group or in vivo. IGF2r mRNA expression was significantly lower in the control. Methylation profiles of individual DNA strands in H19 upstream T-DMR sequences showed a similar methylation status between treatment group and in vivo. These results indicate that the modification of osmolarity in culture medium at early culture stage could provide more beneficial culture environments for mNT embryos.

• BMB Reports
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• v.53 no.11
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• pp.551-564
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• 2020

Proper development of the nervous system is critical for its function, and deficits in neural development have been implicated in many brain disorders. A precise and predictable developmental schedule requires highly coordinated gene expression programs that orchestrate the dynamics of the developing brain. Especially, recent discoveries have been showing that various mRNA chemical modifications can affect RNA metabolism including decay, transport, splicing, and translation in cell type- and tissue-specific manner, leading to the emergence of the field of epitranscriptomics. Moreover, accumulating evidences showed that certain types of RNA modifications are predominantly found in the developing brain and their dysregulation disrupts not only the developmental processes, but also neuronal activities, suggesting that epitranscriptomic mechanisms play critical post-transcriptional regulatory roles in development of the brain and etiology of brain disorders. Here, we review recent advances in our understanding of molecular regulation on transcriptome plasticity by RNA modifications in neurodevelopment and how alterations in these RNA regulatory programs lead to human brain disorders.

• Plant Biotechnology Reports
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• v.5 no.3
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• pp.289-295
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• 2011

The SpoU family of proteins catalyzes the methylation of transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs). We characterized a putative tRNA/rRNA methyltransferase, VaSpoU1 of the SpoU family, from Viscum album (mistletoe). VaSpoU1 and other plant SpoU1s exhibit motifs of the SpoU methylase domain that are conserved with bacterial and yeast SpoU methyltransferases. VaSpoU1 transcripts were detected in the leaves and stems of V. album. VaSpoU1-GFP fusion proteins localized to both chloroplasts and mitochondria in Arabidopsis protoplasts. Sequence analysis similarly predicted that the plant SpoU1 proteins would localize to chloroplasts and mitochondria. Interestingly, mitochondrial localization of VaSpoU1 was inhibited by the deletion of a putative N-terminal presequence in Arabidopsis protoplasts. Therefore, VaSpoU1 may be involved in tRNA and/or rRNA methylation in both chloroplasts and mitochondria.

• Mycobiology
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• v.50 no.5
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• pp.357-365
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• 2022

Schizophyllum commune has emerged as the most promising model mushroom to study developmental stages (mycelium, primordium), which are two primary processes of fruit body development. Long non-coding RNA (lncRNA) has been proved to participate in fruit development and sex differentiation in fungi. However, potential lncRNAs have not been identified in S. commune from mycelium to primordium developmental stages. In this study, lncRNA-seq was performed in S. commune and 61.56 Gb clean data were generated from mycelium and primordium developmental stages. Furthermore, 191 lncRNAs had been obtained and a total of 49 lncRNAs were classified as differently expressed lncRNAs. Additionally, 26 up-regulated differently expressed lncRNAs and 23 down-regulated between mycelium and primordia libraries were detected. Further, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that differentially expressed lncRNAs target genes from the MAPK pathway, phosphatidylinositol signal, ubiquitin-mediated proteolysis, autophagy, and cell cycle. This study provides a new resource for further research on the relationship between lncRNA and two developmental stages (mycelium, primordium) in S. commune.