• BMB Reports
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• 제41권4호
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• pp.310-315
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• 2008

BirA ligase is a prokaryotic ortholog of holocarboxylase synthetase (HCS) that can biotinylate proteins. This study tested the hypothesis that BirA ligase catalyzes the biotinylation of eukaryotic histones. If so, this would mean that recombinant BirA ligase is a useful surrogate for HCS in studies of histone biotinylation. The biological activity of recombinant BirA ligase was confirmed by enzymatic biotinylation of p67. In particular, it was found that BirA ligase biotinylated both calf thymus histone H1 and human bulk histone extracts. Incubation of recombinant BirA ligase with H3-based synthetic peptides showed that lysines 4, 9, 18, and 23 in histone H3 are the targets for the biotinylation by BirA ligase. Modification of the peptides (e.g., serine phosphorylation) affected the subsequent biotinylation by BirA ligase, suggesting crosstalk between modifications. In conclusion, this study suggests that prokaryotic BirA ligase is a promiscuous enzyme and biotinylates eukaryotic histones. Moreover the biotinylation of histones by BirA ligase is consistent with the proposed role of human HCS in chromatin.

• Asian Pacific Journal of Cancer Prevention
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• 제16권12호
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• pp.4803-4812
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• 2015

Chronic alcohol and tobacco abuse plays a crucial role in the development of different liver associated disorders. Intake promotes the generation of reactive oxygen species within hepatic cells exposing their DNA to continuous oxidative stress which finally leads to DNA damage. However in response to such damage an entangled protective repair machinery comprising different repair proteins like ATM, ATR, H2AX, MRN complex becomes activated. Under abnormal conditions the excessive reactive oxygen species generation results in genetic predisposition of various genes (as ADH, ALDH, CYP2E1, GSTT1, GSTP1 and GSTM1) involved in xenobiotic metabolic pathways, associated with susceptibility to different liver related diseases such as fibrosis, cirrhosis and hepatocellular carcinoma. There is increasing evidence that the inflammatory process is inherently associated with many different cancer types, including hepatocellular carcinomas. The generated reactive oxygen species can also activate or repress epigenetic elements such as chromatin remodeling, non-coding RNAs (micro-RNAs), DNA (de) methylation and histone modification that affect gene expression, hence leading to various disorders. The present review provides comprehensive knowledge of different molecular mechanisms involved in gene polymorphism and their possible association with alcohol and tobacco consumption. The article also showcases the necessity of identifying novel diagnostic biomarkers for early cancer risk assessment among alcohol and tobacco users.

• Molecules and Cells
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• 제38권4호
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• pp.362-372
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• 2015

Setdb1, an H3-K9 specific histone methyltransferase, is associated with transcriptional silencing of euchromatic genes through chromatin modification. Functions of Setdb1 during development have been extensively studied in embryonic and mesenchymal stem cells as well as neurogenic progenitor cells. But the role of Sedtdb1 in myogenic differentiation remains unknown. In this study, we report that Setdb1 is required for myogenic potential of C2C12 myoblast cells through maintaining the expressions of MyoD and muscle-specific genes. We find that reduced Setdb1 expression in C2C12 myoblast cells severely delayed differentiation of C2C12 myoblast cells, whereas exogenous Setdb1 expression had little effect on. Gene expression profiling analysis using oligonucleotide microarray and RNA-Seq technologies demonstrated that depletion of Setdb1 results in downregulation of MyoD as well as the components of muscle fiber in proliferating C2C12 cells. In addition, exogenous expression of MyoD reversed transcriptional repression of MyoD promoter-driven luciferase reporter by Setdb1 shRNA and rescued myogenic differentiation of C2C12 myoblast cells depleted of endogenous Setdb1. Taken together, these results provide new insights into how levels of key myogenic regulators are maintained prior to induction of differentiation.

• Applied Microscopy
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• 제28권4호
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• pp.591-601
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• 1998

The neurotoxic effects of radiation have been studied in NSC-34 hybrid cells derived from embryonic mouse spinal cord cells. NSC-34 cells irradiated at 25Gy were decreased the cell viability in a time and dose dependent manner. The decrease in cell viability induced by the irradiation was blocked by catalase. Antagonists of the N-methyl-D-aspartate (NMDA) receptor, including D-2-amino-5-phosphonovaleric acid (APV) and chlorokynurenic acid (CKA), similarly blocked radiational induced in cell viability. We performed morphological analysis of light and electron microscope. NSC-34 cells irradiated at 25Gy were decreased the cell density and increased lysosomes and vacuoles in the cytoplasm. Especially chromatin modification was observed. These results indicated that radiation was involved in the oxidant-initiated neurotoxicity and the compounds catalase, APV and CKA were shown to be neuroprotective against radiation.

• BMB Reports
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• 제54권10호
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• pp.522-527
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• 2021

Lysine-specific demethylase 1 (LSD1) is an epigenetic regulator that modulates the chromatin status, contributing to gene activation or repression. The post-translational modification of LSD1 is critical for the regulation of many of its biological processes. Phosphorylation of serine 112 of LSD1 by protein kinase C alpha (PKCα) is crucial for regulating inflammation, but its physiological significance is not fully understood. This study aimed to investigate the role of Lsd1-S112A, a phosphorylation defective mutant, in the cigarette smoke extract/LPS-induced chronic obstructive pulmonary disease (COPD) model using Lsd1^SA/SA mice and to explore the potential mechanism underpinning the development of COPD. We found that Lsd1^SA/SA mice exhibited increased susceptibility to CSE/LPS-induced COPD, including high inflammatory cell influx into the bronchoalveolar lavage fluid and airspace enlargement. Additionally, the high gene expression associated with the inflammatory response and oxidative stress was observed in cells and mice containing Lsd1-S112A. Similar results were obtained from the mouse embryonic fibroblasts exposed to a PKCα inhibitor, Go6976. Thus, the lack of LSD1 phosphorylation exacerbates CSE/LPS-induced COPD by elevating inflammation and oxidative stress.

• 생명과학회지
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• 제25권6호
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• pp.703-708
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• 2015

Hox 유전자는 호메오도메인을 포함한 전사인자로써, 발생 과정 중 전후축을 따라 몸의 형태 형성을 조절하는 역할을 한다. 레티노산(RA)은 발생 과정에서 필수적인 형태형성인자이며 세포의 특성을 결정하는데 중요한 조절자이다. 특히, RA는 생쥐나 인간으로부터 만들어진 배아암종(EC)세포에서 Hox 유전자의 발현을 조절한다고 밝혀져 있다. 또한 RA에 의한 세포 분화와 유전자 조절 과정에 히스톤 변이가 중요한 역할을 하는 것으로 보고되어 있다. 히스톤 변이가 RA에 의해 유도되는 Hox 유전자의 발현에 특이적인 역할을 할 것으로 유추되기 때문에, 이 연구의 목적은 F9 생쥐배아 기형암종세포에서 RA에 의해 유도되는 Hoxc 유전자의 순차적인 발현이 히스톤 변이에 의해 일어나는 것인지를 조사하는 것이다. Hox 유전자의 발현 양상과 히스톤 변이는 semi-quantitative RT-PCR, RNA-sequencing과 chromatin immuno-precipitation (ChIP)-PCR 기법을 이용하여 관찰하였다. RA 처리 후(0일(D0), 1일(D1), 3일(D3)), Hoxc4 유전자의 발현(D1)은 Hoxc5부터 –c10 유전자(D3)보다 먼저 시작되었다. Hox가 발현하지 않는 D0 샘플은 전사 억제 마커인 H3K27me3이 모든 Hoxc 좌위에 강하게 표지 되어 있었으나 D1과 D3 샘플에서는 모든 좌위의 H3K27me3 표지가 확연히 줄어들어 있었다. 전사 발현 마커인 H3K4me3가 Hoxc 유전자의 순차적인 발현과 더 연관성이 있는 것으로 보이는데 D1에서 Hoxc4 발현과 함께 H3K4me3이 표지 되어 있었고, D3에서는 Hoxc 유전자 발현과 함께 모든 좌위에서 H3K4me3 마커가 존재했기 때문이다. 모든 결과를 종합해 보았을 때 F9 세포에서 RA에 의해 유도된 Hoxc 유전자의 순차적인 발현은 Hoxc 좌위에서 H3K27me3가 사라지고, H3K4me3가 표지 되는 히스톤 메틸화의 변이에 의해 결정되는 것으로 사료된다.

• Molecules and Cells
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• 제41권11호
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• pp.953-963
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• 2018

The stepwise development of T cells from a multipotent precursor is guided by diverse mechanisms, including interactions among lineage-specific transcription factors (TFs) and epigenetic changes, such as DNA methylation and hydroxymethylation, which play crucial roles in mammalian development and lineage commitment. To elucidate the transcriptional networks and epigenetic mechanisms underlying T-cell lineage commitment, we investigated genome-wide changes in gene expression, DNA methylation and hydroxymethylation among populations representing five successive stages of T-cell development (DN3, DN4, DP, $CD4^+$, and $CD8^+$) by performing RNA-seq, MBD-seq and hMeDIP-seq, respectively. The most significant changes in the transcriptomes and epigenomes occurred during the DN4 to DP transition. During the DP stage, many genes involved in chromatin modification were up-regulated and exhibited dramatic changes in DNA hydroxymethylation. We also observed 436 alternative splicing events, and approximately 57% (252) of these events occurred during the DP stage. Many stage-specific, differentially methylated regions were observed near the stage-specific, differentially expressed genes. The dynamic changes in DNA methylation and hydroxymethylation were associated with the recruitment of stage-specific TFs. We elucidated interactive networks comprising TFs, chromatin modifiers, and DNA methylation and hope that this study provides a framework for the understanding of the molecular networks underlying T-cell lineage commitment.

• 농업과학연구
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• 제43권1호
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• pp.72-79
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• 2016

It has long been known that nutritional and environmental influences during the early developmental period affect the biological mechanisms which determine animal metabolism. This phenomenon, termed 'metabolic imprinting', can cause subtle but long-lasting responses to prenatal and postnatal nutrition and even be passed onto the next generation. A large amount of research data shows that nutrient availability, in terms of quantity as well as quality, during the early developing stages can decrease the number of newborn piglets and their body weight and increase their susceptibility to death before weaning. However, investigation of potential mechanisms of 'the metabolic imprinting' effect have been scant. Therefore, it remains unknown which factors are responsible for embryonic and early postnatal nutrition and which factors are major determinants of body weight and number of new born piglets. Intrauterine undernutrition, for example, was studied using a rat model providing dams 50% restricted nutrients during pregnancy and the results showed significant decreases in birth weight of newborns. This response may be a characteristic of a subset of modulations in embryonic development which is caused by the metabolic imprinting. Underlying mechanisms of intrauterine undernutrition and growth retardation can be explained in part by epigenetics. Epigenetics modulate animal phenotypes without changes in DNA sequences. Epigenetic modifications include DNA methylation, chromatin modification and small non-coding RNA-associated gene silencing. Precise mechanisms must be identified at the morphologic, cellular, and molecular levels by using interdisciplinary nutrigenomics approaches to increase pig production. Experimental approaches for explaining these potential mechanisms will be discussed in this review.

• 대한예방한의학회지
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• 제14권2호
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• pp.1-12
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• 2010

The individual differences in disease development and susceptibility have been researched primarily on the subject of genes, environment or the interaction between genes and the environment respectively. However, there have been limitations in explaining complex diseases, and the differences in health and diseases in monozygotic and dizygotic twins. Fortunately, thanks to active research on the relationship between genes and the environment, and epigenetics, there has been much progress in the understanding of body's reactions and changes. Epigenetics is referred to as a study of gene expression through the interactions of DNA methylation, chromatin's histone and the change of structure in tail, RNA editing without any change in DNA sequence. In this paper, we introduce the basic concepts and mechanisms of epigenetics. The result of the epigenetics is heritable ; can regulate gene expressions ; is reversible ; and has many variable forms depending on cell types. The influences of epigenetics occur throughout life, but it is mainly determined in utero during early pregnancies. Diseases occur or the risk rises if these influences continue after birth until adult life when problems occur in excess/lack of nutrition, environmental plasticity, or already inputted data. Therefore, there is a need for change and innovation, especially in interest and investment in health education for young women near pregnancies and correct treatment of epigenetic-related diseases.

• Genomics & Informatics
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• 제14권3호
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• pp.78-84
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• 2016

Extranodal natural killer (NK)/T-cell lymphoma, nasal type (NKTCL), is a malignant disorder of cytotoxic lymphocytes of NK or T cells. It is an aggressive neoplasm with a very poor prognosis. Although extranodal NKTCL reportedly has a strong association with Epstein-Barr virus, the molecular pathogenesis of NKTCL has been unexplored. The recent technological advancements in next-generation sequencing (NGS) have made DNA sequencing cost- and time-effective, with more reliable results. Using the Ion Proton Comprehensive Cancer Panel, we sequenced 409 cancer-related genes to identify somatic mutations in five NKTCL tissue samples. The sequencing analysis detected 25 mutations in 21 genes. Among them, KMT2D, a histone modification-related gene, was the most frequently mutated gene (four of the five cases). This result was consistent with recent NGS studies that have suggested KMT2D as a novel driver gene in NKTCL. Mutations were also found in ARID1A, a chromatin remodeling gene, and TP53, which also recurred in recent NGS studies. We also found mutations in 18 novel candidate genes, with molecular functions that were potentially implicated in cancer development. We suggest that these genes may result in multiple oncogenic events and may be used as potential bio-markers of NKTCL in the future.