• Molecules and Cells
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• v.45 no.7
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• pp.435-443
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• 2022

In response to environmental changes, signaling pathways rewire gene expression programs through transcription factors. Epigenetic modification of the transcribed RNA can be another layer of gene expression regulation. N⁶-adenosine methylation (m⁶A) is one of the most common modifications on mRNA. It is a reversible chemical mark catalyzed by the enzymes that deposit and remove methyl groups. m⁶A recruits effector proteins that determine the fate of mRNAs through changes in splicing, cellular localization, stability, and translation efficiency. Emerging evidence shows that key signal transduction pathways including TGFβ (transforming growth factor-β), ERK (extracellular signal-regulated kinase), and mTORC1 (mechanistic target of rapamycin complex 1) regulate downstream gene expression through m⁶A processing. Conversely, m⁶A can modulate the activity of signal transduction networks via m⁶A modification of signaling pathway genes or by acting as a ligand for receptors. In this review, we discuss the current understanding of the crosstalk between m⁶A and signaling pathways and its implication for biological systems.

• Genomics & Informatics
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• v.20 no.1
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• pp.2.1-2.11
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• 2022

The method of single-cell RNA sequencing has been rapidly developed, and numerous experiments have been conducted over the past decade. Their results allow us to recognize various subpopulations and rare cell states in tissues, tumors, and immune systems that are previously unidentified, and guide us to understand fundamental biological processes that determine cell identity based on single-cell gene expression profiles. However, it is still challenging to understand the principle of comprehensive gene regulation that determines the cell fate only with transcriptome, a consequential output of the gene expression program. To elucidate the mechanisms related to the origin and maintenance of comprehensive single-cell transcriptome, we require a corresponding single-cell epigenome, which is a differentiated information of each cell with an identical genome. This review deals with the current development of single-cell epigenomic library construction methods, including multi-omics tools with crucial factors and additional requirements in the future focusing on DNA methylation, chromatin accessibility, and histone post-translational modifications. The study of cellular differentiation and the disease occurrence at a single-cell level has taken the first step with single-cell transcriptome and is now taking the next step with single-cell epigenome.

• Proceedings of the Korean Society of Applied Pharmacology
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• 1998.11a
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• pp.141-141
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• 1998

In order to study the effect of nitric oxide on the regulation of mouse cyplal expression, 5' flanking DNA of mouse cytochrome P450 lal was cloned into pGL3 basic vector encoding luciferase gene. pcyplal-Luc was transfected into Hepa I cells and various chemicals were treated. Luciferase activity was stimulated 1000 folds over that of control by TCDD (2,3,7,8-tetrachloro-p-dioxin) treatment and this stimulation was dose dependent. When SNP (sodium nitroprusside) which donates nitric oxide was administrated, this stimulatory effect of TCDD on luciferase activity was decreased. And LPS (lipopolysaccharide) which is an iNOS (inducible nitric oxide synthase) inducer also decreased the stimulatory effect of TCDD on luciferase. And iNOS inhibitor N$\^$G/-nitro-ι-arginine + TCDD treatment increased the stimulation effect of TCDD and this effect was abolished when ι-arginine was added to N$\^$G/-nitro-ι-arginine + TCDD treatment. When N$\^$G/-nitro-ι-arginine was concomitantly administrated with SNP or LPS to confirm the effect of nitric oxide, the inhibitory effect of SNP or LPS was abolished. These data strongly suggest that nitric oxide might be an inhibitory regulator on the cytochrome P450 lal gene expression in Hepa cells.

• Molecules and Cells
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• v.46 no.1
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• pp.33-40
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• 2023

RNAs are versatile molecules that are primarily involved in gene regulation and can thus be widely used to advance the fields of therapeutics and diagnostics. In particular, circular RNAs which are highly stable, have emerged as strong candidates for use on next-generation therapeutic platforms. Endogenous circular RNAs control gene regulatory networks by interacting with other biomolecules or through translation into polypeptides. Circular RNAs exhibit cell-type specific expression patterns, which can be altered in tissues and body fluids depending on pathophysiological conditions. Circular RNAs that are aberrantly expressed in diseases can function as biomarkers or therapeutic targets. Moreover, exogenous circular RNAs synthesized in vitro can be introduced into cells as therapeutic molecules to modulate gene expression networks in vivo. Depending on the purpose, synthetic circular RNA sequences can either be identical to endogenous circular RNA sequences or artificially designed. In this review, we introduce the life cycle and known functions of intracellular circular RNAs. The current stage of endogenous circular RNAs as biomarkers and therapeutic targets is also described. Finally, approaches and considerations that are important for applying the available knowledge on endogenous circular RNAs to design exogenous circular RNAs for therapeutic purposes are presented.

• Journal of Plant Biotechnology
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• v.49 no.4
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• pp.292-2999
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• 2022

Anthocyanin, an important component in the grape berry skin, strongly affects grape quality. The transcription factors VvMYBA1 and VvMYBA2 (VvMYBA1/2) control anthocyanin biosynthesis. In addition, cultivation and environmental factors, such as light, influence anthocyanin accumulation. The present study aimed to clarify the effect of shading (reduced light condition) on the transcriptomic regulation of anthocyanin biosynthesis using a red-wine grape cultivar, Vitis vinifera 'Pinot Noir', and its white mutant, 'Pinot Blanc', caused by the deletion of the red allele of VvMYBA1/2. The grape berry skins were analyzed for anthocyanin content and global gene transcription accumulation. The microarray data were later validated by quantitative real-time PCR. A decisive influence of VvMYBA1/2 on the expression of an anthocyanin-specific gene, UDP glucose: flavonoid 3-O-glucosyltransferase, was observed as expected. In contrast, upstream genes of the pathway, which are shared by other flavonoids, were also expressed in 'Pinot Blanc', and the mRNA levels of some of these genes decreased in both cultivars on shading. Thus, the involvement of light-sensitive transcription factor(s) other than VvMYBA1/2 was suggested for the expression control of the upstream genes of the anthocyanin biosynthetic pathway. Furthermore, it was suggested that the effects of these factors are different among isogenes.

• The Plant Pathology Journal
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• v.17 no.2
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• pp.77-82
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• 2001

Erwinia amylovora causes a devastating disease called fire blight in rosaceous trees and shrubs such as apple, pear, and raspberry. To successfully infect its hosts, the pathogen requires a set of clustered genes termed hrp. Studies on the hrp system of E. amylovora indicated that it consists of three functional classes of genes. Regulation genes including hrpS, hrpS, hrpXY, and hrpL produce proteins that control the expression of other genes in the cluster. Secretion genes, many of which named hrc, encode proteins that may form a transmembrane complex, which is devoted to type III protein secretion. Finally, several genes encode the proteins that are delivered by the protein secretion apparatus. They include harpins, DspE, and other potential effector proteins that may contribute to proliferation of E. amylovora inside the hosts. Harpins are glycine-rich heat-stable elicitors of the hypersensitive response, and induce systemic acquired resistance. The pathogenicity protein DseE is homologous and functionally similar to an avirulence protein of Pseudomonas syringae. The region encompassing the hrpldsp gene cluster of E. amylovora shows features characteristic of a genomic island : a cryptic recombinase/integrase gene and a tRNA gene are present at one end and genes corresponding to those of the Escherichia coli K-12 chromosome are found beyond the region. This island, designated the Hrp pathogenicity island, is more than 60 kilobases in size and carries as many as 60 genes.

• Oncology Letters
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• v.41 no.1
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• pp.361-368
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• 2019

Gliomas, the most highly malignant central nervous system tumors, are associated with an extremely poor patient survival rate. Given that gliomas are derived from mutations in glial precursor cells, a considerable number of them strongly react with glial precursor cell-specific markers. Thus, we investigated whether malignant gliomas can be converted to glial cells through the regulation of endogenous gene expression implicated in glial precursor cells. In the present study, we used three small-molecule compounds, [cyclic adenosine monophosphate (cAMP) enhancer, a mammalian target of rapamycin (mTOR) inhibitor, and a bromodomain and extra-terminal motif (BET) inhibitor] for glial reprogramming. Small-molecule-induced gliomas (SMiGs) were not only transformed into exhibiting a glial-specific morphology, but also showed positive reactions with glial-specific markers such as glial fibrillary acidic protein (GFAP), 2',3'-cyclic nucleotide 3'-phosphohydrolase (CNP) and anti-oligodendrocyte (RIP). A microarray analysis indicated that SMiGs exhibited a marked increase in specific gene levels, whereas that of a malignant cancer-specific gene was greatly decreased. Moreover, proliferation of the cells was markedly suppressed after the conversion of malignant glioma cells into glial cells. Our findings confirmed that malignant gliomas can be reprogrammed to non-proliferating glial cells, using a combination of small molecules, and their proliferation can be regulated by their differentiation. We suggest that our small-molecule combination (with forskolin, rapamycin and I-BET151) may be the next generation of anticancer agents that act by reprogramming malignant gliomas to differentiate into glial cells.

• Proceedings of the Korean Society of Applied Entomolohy Conference
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• 2004.05a
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• pp.53-53
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• 2004

• Biomolecules & Therapeutics
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• v.17 no.4
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• pp.335-347
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• 2009

This review covers current developments in molecular-based studies of the structure and function of carboxylesterases. To allay the confusion of the classic classification of carboxylesterase isozymes, we have proposed a novel nomenclature and classification of mammalian carboxylesterases on the basis of molecular properties. In addition, mechanisms of regulation of gene expression of carboxylesterases by xenobiotics, and involvement of carboxylesterase in drug metabolism are also described.

• Proceedings of the Korea Environmental Mutagen Society Conference
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• 2003.10a
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• pp.136-136
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• 2003