• Molecules and Cells
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• v.28 no.5
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• pp.407-415
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• 2009

The sirtuins are a protein family named after the first identified member, S. cerevisiae Sir2p. Sirtuins are protein deacetylases whose activity is dependent on $NAD^+$ as a cosubstrate. They are structurally defined by two central domains that together form a highly conserved catalytic center, which catalyzes the transfer of an acetyl moiety from acetyllysine to $NAD^+$, yielding nicotinamide, the unique metabolite O-acetyl-ADP-ribose and deacetylated lysine. One or more sirtuins are present in virtually all species from bacteria to mammals. Here we describe a phylogenetic analysis of sirtuins. Based on their phylogenetic relationship, sirtuins can be grouped into over a dozen classes and subclasses. Humans, like most vertebrates, have seven sirtuins: SIRT1-SIRT7. These function in diverse cellular pathways, regulating transcriptional repression, aging, metabolism, DNA damage responses and apoptosis. We show that these seven sirtuins arose early during animal evolution. Conserved residues cluster around the catalytic center of known sirtuin family members.

• Mycobiology
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• v.50 no.5
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• pp.366-373
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• 2022

Regulation of proper gene expression is important for cellular and organismal survival, maintenance, and growth. Abnormal gene expression, even for a single critical gene, can thwart cellular integrity and normal physiology to cause diseases, aging, and death. Therefore, gene expression profiling serves as a powerful tool to understand the pathology of diseases and to cure them. In this study, the difference in gene expression in Flammulina velutipes was compared between the wild type (WT) mushroom and the mutant one with clogging phenomenon. Differentially expressed transcripts were screened to identify the candidate genes responsible for the mutant phenotype using the DNA microarray analysis. A total of 88 genes including 60 upregulated and 28 downregulated genes were validated using the real-time quantitative PCR analysis. In addition, proteomic differences between the WT and mutant mushroom were analyzed using two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF). Interestingly, the genes identified by these genomic and proteomic analyses were involved in stress response, translation, and energy/sugar metabolism, including HSP70, elongation factor 2, and pyruvate kinase. Together, our data suggest that the aberrant expression of these genes attributes to the mutant clogging phenotype. We propose that these genes can be targeted to foster normal growth in F. velutipes.

• Korean Journal of Animal Reproduction
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• v.26 no.4
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• pp.347-351
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• 2002

Transgenes in HSY-TK gene driven by the lck promoter was tested for the expression in immune cells (Jurkat cells) to apply xenotransplantation of human cells into transgenic animals for the potential use of the proliferation or differentiation of human stem cells in the large animal such as an pig. Also, lck-CFP gene was used for transfection experiment into Jurkat cell to confirm the proper regulation of lck promoter for transgene expression in the T cells. Transfection of lck-GFP gene into Jurkat ceils induced CFP expression in transfected cells. The expression of Ick-TK and Ick-CFP genes was confirmed by RT-PCR using RNAs extracted from Jurkat cells, When Jurkat cells transfected with TK and CFP genes were selected against G418 or gancyclovir treatments, Jurkat cells transfected with TK gene were not proliferated in G4i8 and gancyclovir medium while intact cells or cells transfected with CFP gene could grow in gancyclovir medium. However, Jurkat cells transfected with TK or GFP gene were proliferated in G418 medium probably due to Neo$^{r}$ gene in the vector. Gancyclovir treatment destroyed Jurkat cells expressing TK gene indicating that T-cells expressing TK gene can be selectively eliminated by TK gene expression driven by lck promoter.

• Journal of Plant Biotechnology
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• v.50
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• pp.232-238
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• 2023

Histone deacetylases (HDACs) play a pivotal role in epigenetic regulation, affecting the structure of chromatin and gene expression across different stages of plant development and in response to environmental stresses. Although the role of HDACs in Arabidopsis and rice has been focused on in extensive research, the role of the HDAC gene family in various medicinal plants remains unclear. In the genome of the balloon flower (Platycodon grandiflorus), we identified 10 putative P. grandiflorus HDAC (PlgHDAC) proteins, which were classified into the three families (RPD3/HDA1, SIR2, and HD2 HDAC families) based on their domain compositions. These HDACs were predicted to be localized in various cellular compartments, indicating that they have diverse functions. In addition, the tissue-specific expression profiles of PlgHDACs differed across different plant tissues, indicating that they are involved in various developmental processes. Furthermore, the expression levels of all PlgHDACs were upregulated in leaves after waterlogging treatment, implying their potential role in coping with waterlogging-induced stress. Overall, our findings provide a comprehensive foundation for further research into the epigenetic regulation of PlgHDACs, and particularly, on their functions in response to environmental stresses such as waterlogging. Understanding the roles of these HDACs in the development and stress responses of balloon flower could have significant implications for improving crop yield and the quality of this important medicinal plant.

• BMB Reports
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• v.44 no.1
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• pp.11-21
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• 2011

During the last decade small regulatory RNA (srRNA) emerged as central players in the regulation of gene expression in all kingdoms of life. Multiple pathways for srRNA biogenesis and diverse mechanisms of gene regulation may indicate that srRNA regulation evolved independently multiple times. However, small RNA pathways share numerous properties, including the ability of a single srRNA to regulate multiple targets. Some of the mechanisms of gene regulation by srRNAs have significant effect on the abundance of free srRNAs that are ready to interact with new targets. This results in indirect interactions among seemingly unrelated genes, as well as in a crosstalk between different srRNA pathways. Here we briefly review and compare the major srRNA pathways, and argue that the impact of srRNA is always at the system level. We demonstrate how a simple mathematical model can ease the discussion of governing principles. To demonstrate these points we review a few examples from bacteria and animals.

• BMB Reports
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• v.43 no.1
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• pp.29-33
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• 2010

It is well known that PR/SET family members participate in transcriptional regulation via chromatin remodeling. PRDM10 might play an essential role in gene expression, but no such evidence has been observed so far. To assess PRDM10 expression at various stages of mouse development, we performed immunohistochemistry using available PRDM10 antibody. Embryos were obtained from three distinct developmental stages. At E8.5, PRDM10 expression was concentrated in the mesodermal and neural crest populations. As embryogenesis proceeded further to E13.5, PRMD10 expression was mainly in mesoderm-derived tissues such as somites and neural crest-derived populations such as the facial skeleton. This expression pattern was consistently maintained to the fetal growth period E16.5 and adult mouse, suggesting that PRDM10 may function in tissue differentiation. Our study revealed that PRDM10 might be a transcriptional regulator for normal tissue differentiation during mouse embryonic development.

• BMB Reports
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• v.49 no.10
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• pp.578-583
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• 2016

Special AT-rich sequence binding protein 1 (SATB1) is a nuclear matrix-associated DNA-binding protein that functions as a chromatin organizer. SATB1 is highly expressed in aggressive breast cancer cells and promotes growth and metastasis by reprograming gene expression. Through genome-wide cross-examination of gene expression and histone methylation, we identified SATB1 target genes for which expression is associated with altered epigenetic marks. Among the identified genes, long noncoding RNA urothelial carcinoma-associated 1 (UCA1) was upregulated by SATB1 depletion. Upregulation of UCA1 coincided with increased H3K4 trimethylation (H3K4me3) levels and decreased H3K27 trimethylation (H3K27me3) levels. Our study showed that SATB1 binds to the upstream region of UCA1 in vivo, and that its promoter activity increases with SATB1 depletion. Furthermore, simultaneous depletion of SATB1 and UCA1 potentiated suppression of tumor growth and cell survival. Thus, SATB1 repressed the expression of oncogenic UCA1, suppressing growth and survival of breast cancer cells.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.2
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• pp.591-598
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• 2012

Aim and background: MicroRNAs (miRNAs) are a class of naturally occurring small noncoding RNAs that regulate gene expression, cell growth, differentiation and apoptosis by targeting mRNAs for translational repression or cleavage. The present study was conducted to study miRNAs in Egyptian breast cancer (BC) and their relation to metastasis, tumor invasion and apoptosis in addition to their association with the ER and PR statuses. Methods: Real Time RT-PCR was performed to identify the miRNA expression level of eight miRNAs and eight metastatic-related genes in 40 breast cancer samples and their adjacent non-neoplastic tissues. The expression levels of each miRNA relative to U6 RNA were determined using the $^{2-{\Delta}}CT$ method. Also, miRNA expression profiles of the BC and their corresponding ANT were evaluated. Results: The BC patients showed an up-regulation in miRNAs (mir-155, mir-10, mir-21 and mir-373) with an upregulation in MMP2, MMp9 and VEGF genes. We found down regulation in mir-17p, mir-126, mir-335, mir-30b and also TIMP3, TMP1 and PDCD4 genes in the cancer tissue compared to the adjacent non-neoplastic tissues. Mir -10b, mir -21, mir-155 and mir373 and the metastatic genes MMP2, MMP9 and VEGF were significantly associated with an increase in tumor size (P < 0.05). No significant difference was observed between any of the studied miRNAs regarding lymph node metastasis. Mir-21 was significantly over-expressed in ER-/PR-cases. Conclusion: Specific miRNAs (mir-10, mir-21, mir-155, mir-373, mir-30b, mir-126, mir-17p, mir-335) are associated with tumor metastasis and other clinical characteristics for BC, facilitating identification of individuals who are at risk.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.20
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• pp.8931-8936
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• 2014

Background: Herbal compounds such as curcumin which decrease telomerase and gene expression have been considered as beneficial tools for lung cancer treatment. In this article, we compared the effects of pure curcumin and curcumin-loaded NIPAAm-MAA nanoparticles on telomerase and PinX1 gene expression in a lung cancer cell line. Materials and Methods: A tetrazolium-based assay was used for determination of cytotoxic effects of curcumin on the Calu-6 lung cancer cell line and telomerase and pinX1 gene expression was measured with real-time PCR. Results: MTT assay showed that Curcumin-loaded NIPAAm-MAA inhibited the growth of the Calu-6 lung cancer cell line in a time and dose-dependent manner. Our q-PCR results showed that the expression of telomerase gene was effectively reduced as the concentration of curcumin-loaded NIPAAm-MAA increased while expression of the PinX1 gene became elevated. Conclusions: The results showed that curcumin-loaded-NIPAAm-MAA exerted cytotoxic effects on the Calu-6 cell line through down-regulation of telomerase and stimulation of pinX1 gene expression. NIPPAm-MAA could be good carrier for such kinds of hydrophobic agent.

• Journal of the Korean Magnetic Resonance Society
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• v.2 no.2
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• pp.152-157
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• 1998

The diversity of RNA functions ranges from storage and propagation of genetic information to enzymatic activity during RNA processing and protein synthesis. This diversity of functions requires an equally diverse arrays of structures, and, very often, the formation of functional RNA-protein complexes. Recognition of specific RNA signals by RNA-binding proteins is central to all aspects of post-transcriptional regulation of gene expression. We will describe how NMR is being used to understand at the atomic level how these important biological processes occur.