• Animal Bioscience
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• 제37권6호
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• pp.1021-1030
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• 2024

Objective: R-loops are DNA:RNA triplex hybrids, and their metabolism is tightly regulated by transcriptional regulation, DNA damage response, and chromatin structure dynamics. R-loop homeostasis is dynamically regulated and closely associated with gene transcription in mouse zygotes. However, the factors responsible for regulating these dynamic changes in the R-loops of fertilized mouse eggs have not yet been investigated. This study examined the functions of candidate factors that interact with R-loops during zygotic gene activation. Methods: In this study, we used publicly available next-generation sequencing datasets, including low-input ribosome profiling analysis and polymerase II chromatin immunoprecipitation-sequencing (ChIP-seq), to identify potential regulators of R-loop dynamics in zygotes. These datasets were downloaded, reanalyzed, and compared with mass spectrometry data to identify candidate factors involved in regulating R-loop dynamics. To validate the functions of these candidate factors, we treated mouse zygotes with chemical inhibitors using in vitro fertilization. Immunofluorescence with an anti-R-loop antibody was then performed to quantify changes in R-loop metabolism. Results: We identified DEAD-box-5 (DDX5) and histone deacetylase-2 (HDAC2) as candidates that potentially regulate R-loop metabolism in oocytes, zygotes and two-cell embryos based on change of their gene translation. Our analysis revealed that the DDX5 inhibition of activity led to decreased R-loop accumulation in pronuclei, indicating its involvement in regulating R-loop dynamics. However, the inhibition of histone deacetylase-2 activity did not significantly affect R-loop levels in pronuclei. Conclusion: These findings suggest that dynamic changes in R-loops during mouse zygote development are likely regulated by RNA helicases, particularly DDX5, in conjunction with transcriptional processes. Our study provides compelling evidence for the involvement of these factors in regulating R-loop dynamics during early embryonic development.

• 대한한방내과학회지
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• 제23권2호
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• pp.181-190
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• 2002

The water extract of Omija-tang(OMJT) has been traditionally used for treatment of ischemic heart and brain damage in oriental medicine. However, little is known about the mechanism by which the water extract of OMJT protects cells from such damage. Therefore, this study was conducted to investigate the protective mechanisms of OMJT on $H_2O_2$-induced toxicity in H9c2 cardiomyoblast cells. Treatment of $H_2O_2$ markedly induced death of H9c2 cardiomyoblast cells in a dose-dependent manner. The characteristics of $H_2O_2$-induced death of H9c2 showed apparent apoptotic features, such as DNA fragmentation. However, OMJT significantly reduced both $H_2O_2$-induced cell death and chromatin fragmentation. The decrease of Bcl-XL expression by $H_2O_2$ was inhibited by OMJT. In addition, the increase of Bcl-XS and Bax expression were also inhibited by OMJT. In particular, Fas expression, which is generally recognized as cell death inducing signal by Fas/FasL interaction, was markedly increased by $H_2O_2$ in a time-dependent manner, whereas this increase was completely prevented by OMJT. The combined treatment of OMJT and $H_2O_2$ in H9c2 cells also reduced activation of caspase-9 and caspase-3 like protease. Taken together, this study indicates that the protective effects of the water extract of OMJT against oxidative damage may be mediated by the modulation of BcI-XL/S and Bax expression by way of the regulation of mitochondrial membrane potential and caspase cascades.

• 동의생리병리학회지
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• 제18권6호
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• pp.1733-1739
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• 2004

The water extract of Hwangryunhaedog-tang(HRHDT} has been traditionally used for treatment of ischemic heart and brain damage in oriental medicine. However, little is known about the mechanism by which the water extract of HRHDT rescues cells from these damages. This study was designed to investigate the protective mechanisms of HRHDT on hypoxia-induced cytotoxicity in H9c2 cardiomyoblast cells. Hypoxia, markedly decreased the viability of H9c2 cells, which was characterized with apparent apoptptic features such as chromatin condensation as well as fragmentation of genomic DNA and nuclei. However, HRHDT significantly reduced hypoxia-induced cell death and apoptotic characteristics. Also, HRHDT prevented the mitochondrial dysfunction including the disruption of mitochondria membrane permeability transition (MPT) and an increase in expression of anti-apoptotic Bcl-2 proteins in hypoxia-H9c2 cells. Taken together, this study suggests that the protective effects of the water extract of HRHDT against hypoxic damages may be mediated by the modulation of Bcl-2 and Bak expression.

• Biomolecules & Therapeutics
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• 제18권4호
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• pp.454-462
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• 2010

The present study investigated the neuroprotective effect of Carpinus tschonoskii MAX and its intracellular protective mechanism on 6-hydroxydopamine (6-OHDA)-induced oxidative damage in PC12 cells. We found that pretreatment of PC12 cells with C. tschonoskii extract significantly inhibited the cell death induced by 6-OHDA in a dose dependent manner. C. tschonoskii extract decreased 6-OHDA-induced apoptotic events such as chromatin condensation, DNA fragmentation, the decrease of Bcl-2/Bax ratio, caspase-3 activation and PARP cleavage. C. tschonoskii extract also reduced generation of 6-OHDA-induced reactive oxygen species and nitric oxide. Furthermore, C. tschonoskii extract up-regulated the myocyte enhancer factor 2 D (MEF2D), a critical transcription factor for neuronal survival, and Akt activity, whereas it inhibited the activity of ERK1/2 and JNK. The results suggest that C. tschonoskii extract decreases 6-OHDA-induced oxidative stress and could prevent PC12 cell apoptosis induced by 6-OHDA via the up-regulation of MEF2D and Akt activity, and thus may have application in developing therapeutic agents for Parkinson's disease.

• 대한한의학회지
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• 제22권4호
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• pp.58-68
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• 2001

Objectives : This study was designed to investigate the protective mechanisms of Samul-tang (SMT) on $H_2O_2$-induced toxicity in H9c2 cardiomyoblast cells. Methods : The cultured cells were pretreated with SMT and exposed to $H_2O_2$. The cell damage was assessed by using MTT assay. Also, we used Hoechst staining, Western blotting analysis. Results : SMT significantly reduced both $H_2O_2$-induced cell death and chromatin fragmentation. The decrease of Bcl2 expression by $H_2O_2$ was inhibited by SMT. In addition, the increase of Bax expression was also inhibited by SMT. In particular, Fas expression, which is generally recognized as cell death inducing signal by Fas/FasL interaction, was markedly decreased by $H_2O_2$ in a time-dependent manner, whereas this decrease was completely prevented by SMT. The cotreatment of SMT and $H_2O_2$ in H9c2 cells also induced the phosphorylation of ERK in a time-dependent manner. Moreover, PD098059, a specific inhibitor of ERKl/2, attenuated the protective effect of SMT on $H_2O_2$-induced toxicity in H9c2 cardiomyoblast cells. Furthermore, the protective effect of SMT was significantly blocked by treatment of SB203580, a specific inhibitor of p38. Conclusions : Taken together, this study suggests that the protective effects of the water extract of SMT against oxidative damages may be mediated by the modulation of Bel2 and Bax expression via the regulation of ERK and p38 signaling pathway.

• The Plant Pathology Journal
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• 제32권2호
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• pp.85-94
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• 2016

Studies were conducted to determine the role of 3-methylthioproprionic acid (MTPA) in the pathogenicity of potato stem canker, Rhizoctonia solani, and the concentrations required to inhibit growth of R. solani under laboratory and plant house-based conditions. The experiments were laid out in a completely randomized design with five treatments and five replications. The treatments were 0, 1, 2, 4, and 8 mM concentrations of MTPA. The purified toxin exhibited maximal activity at pH 2.5 and $30^{\circ}C$. MTPA at 1, 2, 4, and 8 mM levels reduced plant height, chlorophyll content, haulm fresh weight, number of stolons, canopy development, and tuber weight of potato plants, as compared to the control. MTPA significantly affected mycelial growth with 8 mM causing the highest infection. The potato seedlings treated with MTPA concentrations of 1.0-8.0 mM induced necrosis of up to 80% of root system area. Cankers were resulted from the injection of potato seedling stems with 8.0 mM MTPA. The results showed the disappearance of cell membrane, rough mitochondrial and cell walls, change of the shape of chloroplasts, and swollen endoplasmic reticulum. Seventy-six (76) hours after toxin treatment, cell contents were completely broken, cytoplasm dissolved, and more chromatin were seen in the nucleus. The results suggested that high levels of the toxin concentration caused cell membrane and cytoplasm fracture. The integrity of cellular structure was destroyed by the phytotoxin. The concentrations of the phytotoxin were significantly correlated with pathogenicity and caused damage to the cell membrane of potato stem base tissue.

• Preventive Nutrition and Food Science
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• 제8권2호
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• pp.113-118
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• 2003

We recently extracted lignans such as matairesinol and 2-hydroxyarctigenin from safflower seeds and found that they exhibit a potent cytotoxic effect on human promyleocytic leukemia HL-60 cells. In this study, we investigated whether mechanisms of the matairesinol-induced cell death are associated with the programmed cell death, apoptosis. Matairesinol dose-dependently reduced viability of HL-60 cells with an IC/sun 50/ value of 60 $\mu$M. Staining of cells with Hoechst 33342 revealed distinct morphological features of apoptosis, such as the nuclei broken into chromatin containing fragments of various sizes in the cells exposed to 100 $\mu$M matairesinol for 24 hr. Agarose gel electrophoresis of DNA from the cells treated with matairesinol showed internucleosomal DNA degradation into oligonucleosomal sizes. DNA ladder like patterns were easily detected after treatment with matairesinol concentrations ranging from 10 to 100 $\mu$M after 24 hr. In cells treated with 100 $\mu$M matairesinol for differing time periods, the DNA ladder was detectable from 6 hr onward. A time course histogram of the DNA content analyzed by flow cytometry revealed a rapid increase in subdiploid cells and a concomitant decrease in diploid cells exposed to 100 $\mu$M matairesinol. These results indicate that matairesinol-induced HL-60 cell death was due to the DNA damage and apoptosis.

• BMB Reports
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• 제53권6호
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• pp.299-310
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• 2020

Chronic liver disease progresses through several stages, fatty liver, steatohepatitis, cirrhosis, and eventually, it leads to hepatocellular carcinoma (HCC) over a long period of time. Since a large proportion of patients with HCC are accompanied by cirrhosis, it is considered to be an important factor in the diagnosis of liver cancer. This is because cirrhosis leads to an irreversible harmful effect, but the early stages of chronic liver disease could be reversed to a healthy state. Therefore, the discovery of biomarkers that could identify the early stages of chronic liver disease is important to prevent serious liver damage. Biomarker discovery at liver cancer and cirrhosis has enhanced the development of sequencing technology. Next generation sequencing (NGS) is one of the representative technical innovations in the biological field in the recent decades and it is the most important thing to design for research on what type of sequencing methods are suitable and how to handle the analysis steps for data integration. In this review, we comprehensively summarized NGS techniques for identifying genome, transcriptome, DNA methylome and 3D/4D chromatin structure, and introduced framework of processing data set and integrating multi-omics data for uncovering biomarkers.

• Molecules and Cells
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• 제41권8호
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• pp.799-807
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• 2018

Emerging evidence has suggested that cellular crosstalk between RNF168 and poly(ADP-ribose) polymerase 1 (PARP1) contributes to the precise control of the DNA damage response (DDR). However, the direct and reciprocal functional link between them remains unclear. In this report, we identified that RNF168 ubiquitinates PARP1 via direct interaction and accelerates PARP1 degradation in the presence of poly (ADP-ribose) (PAR) chains, metabolites of activated PARP1. Through mass spectrometric analysis, we revealed that RNF168 ubiquitinated multiple lysine residues on PARP1 via K48-linked ubiquitin chain formation. Consistent with this, micro-irradiation-induced PARP1 accumulation at damaged chromatin was significantly increased by knockdown of endogenous RNF168. In addition, it was confirmed that abnormal changes of HR and HNEJ due to knockdown of RNF168 were restored by overexpression of WT RNF168 but not by reintroduction of mutants lacking E3 ligase activity or PAR binding ability. The comet assay also revealed that both PAR-binding and ubiquitin-conjugation activities are indispensable for the RNF168-mediated DNA repair process. Taken together, our results suggest that RNF168 acts as a counterpart of PARP1 in DDR and regulates the HR/NHEJ repair processes through the ubiquitination of PARP1.

• Applied Microscopy
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• 제28권2호
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• pp.225-236
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• 1998

Adriamycin is a one of anthracyclin antibiotics isolated from the culture media of Streptomyces peucetius var casius. The formation of reactive oxygen metabolite by redox cycling during the metabolism and the inhibition of DNA synthesis results in antineoplastic effects of adriamycin. The authors have demonstrated the effects of SOD(superoxide dismutase) or DMTU (dimethyl thiourea), which are used as an antioxidant, on the ultrastructural changes of the gastric chief cells after the administration of adriamycin in the rat. Adriamycin (30 mg/kg) was administered intraperitoneally to the Sprague-Dawley rats weighing about 220 gm and SOD (15000 unit/kg) or DMTU (500 mg/kg) were administered intraperitoneally to the rats 30 minutes after the administration of adriamycin. The gastric chief cells 24, 48 and 72 hours after the administration of adriamycin were observed with Hitachi-600 electron microscope. The results were as follows. 1. SOD or DMTU alone did not affect the ultra structures of the gastric chief cells in the rat. 2. Dilation, sacculation and segmentation of the cisternae of rough endoplasmic reticulum, dilation of the saccules of Golgi complex and dilated mitochondria with electron lucent matrix were seen in the adriamycin treated rats. In the course of time, the ultrastructures of the chief cell changed markedly. 72 hours after drug administration, severely dilated cisternae of rough endoplasmic reticulum, with clumping of chromatin around the nuclear envelope and mitochondria with electron lucent matrix and dilated cristae were seen in the chief cell. 3. The treatment of SOD is more effective than DMTU to attenuated the ultrastructural changes of the chief cells in the adriamycin administered rat. Consequently it is suggested that adriamycin would induce the degenerative changes of the organelles of the chief cell. The treatment of SOD is more effective than DMTU to attenuate the adriamycin induced damage.