• Bulletin of the Korean Chemical Society
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• v.30 no.12
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• pp.2867-2868
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• 2009

• Biomedical Science Letters
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• v.10 no.1
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• pp.55-63
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• 2004

Bovine leukemia virus (BLV) is a causative agent for lymphoma disease in cattle including cows worldwide. BLV shares similar virion structure and characteristics with other retroviruses. The pol gene of the BLV genome produced reverse transcriptase (RT) and integrase (IN) for important roles for BLV genome integration into host cell chromosomes that is known to be coded in the 3' side of the BLV pol gene (one third portion). In this study, we have sequenced 978 bp in the 3' side of the BLV pol gene from BLV 10C3 in order to determine the BLV IN region of it. And we compared it to the nucleotide sequences of an Australian BLV isolate. As a result, nucleotide sequences of the IN region of the Korean-type BLV pol gene were mutated at a rate of 3.7%. We can confirm that the typical mutations are such as Arg (AGG) $\rightarrow$ Lys (AAG), Thr (ACG) $\rightarrow$ Met (ATG), Ile (ATT) $\rightarrow$ Val (GTT), Asn (ACC) $\rightarrow$ His (CAC), Phe (TTT) $\rightarrow$ Leu (TTG) and Asn (ACC) $\rightarrow$ Asp (GAC). From the analysis of the sequencing data, we were able to determine the zinc-finger-like "HHCC" motif in the amino terminus of BLV IN, that was H-$X_3$-H-$X_{25}-C-X_2$-C. It was also found the DD35E motif in the IN catalytic domain as D-$X_{56}$-D-$X_{35}$-E. It fits very well to the consensus sequences of retroviral IN as well as HHCC motif.

• BMB Reports
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• v.44 no.4
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• pp.267-272
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• 2011

ZAS3 is a large zinc finger transcription repressor that binds the ${\kappa}B$-motif via two signature domains of ZASN and ZASC. A loss-of-function study showed that lack of ZAS3 protein induced accelerated cell proliferation and tumorigenesis. Conversely, gain-of-function studies showed that ZAS3 repressed $NF{\kappa}B$-activated transcription by competing with $NF{\kappa}B$ for the ${\kappa}B$-motif. Based on these observations, we hypothesize that ZAS3 promotes apoptosis by interrupting anti-apoptotic activity of $NF{\kappa}B$. Here, we present evidence that upon $TNF{\alpha}$ stimulation, ZAS3 inhibits $NF{\kappa}B$-mediated cell survival and promotes caspase-mediated apoptosis. The inhibitory effect of ZAS3 on $NF{\kappa}B$ activity is mediated by neither direct association with $NF{\kappa}B$ nor disrupting nuclear localization of $NF{\kappa}B$. Instead, ZAS3 repressed the expression of two key anti-apoptotic genes of $NF{\kappa}B$, TRAF1 and TRAF2, thereby sensitizing cells to $TNF{\alpha}$-induced cell death. Taken together, our data suggest that ZAS3 is a tumor suppressor gene and therefore serves as a novel therapeutic target for developing anti-cancer drugs.

• BMB Reports
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• v.41 no.7
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• pp.511-515
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• 2008

The nucleocapsid (NC) protein of the Human Immunodeficiency Virus-1 plays a key role in viral genomic packaging by specifically recognizing the Psi($\Psi$) RNA sequence within the HIV-1 genome RNA. Recently, a novel cell-based assay was developed to probe the specific interactions in vivo between the NC and $\Psi$-RNA using E.coli cells (J. Virol. 81: 6151-55, 2007). In order to examine the extendibility of this cell-based assay to RNAs other than $\Psi$-RNA, this study tested the RNA aptamers isolated in vitro using the SELEX method, but whose specific binding ability to NC in a living cellular environment has not been established. The results demonstrate for the first time that each of those aptamer RNAs can bind specifically to NC in a NC zinc finger motif dependent manner within the cell. This confirms that the cell-based assay developed for NC-$\Psi$interaction can be further extended and applied to NC-binding RNAs other than $\Psi$-RNA.

• Journal of Radiation Industry
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• v.10 no.1
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• pp.7-12
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• 2016

Ikaros, a transcription factor containing zinc-finger motif, has known as a critical regulator of hematopoiesis in immune system. Ikaros protein modulates the transcription of target genes via binding to the regulatory elements of the genes promoters. However the regulatory function of Ikaros in other organelle except nuclear remains to be determined. This study explored radiation-induced modulatory function of Ikaros in cytoplasm. The results showed that Ikaros protein lost its DNA binding ability after LDIR (low-dose ionizing radiation) exposure. Cell fractionation and Western blot analysis showed that Ikaros protein was translocated into cytoplasm from nuclear by LDIR. This was confirmed by immunofluorescence assay. We identified Autotaxin as a novel protein which potentially interacts with Ikaros through in vitro protein-binding screening. Co-immunoprecipitation assay revealed that Ikaros and Autotaxin are able to bind each other. Autotaxin is a crucial enzyme generating lysophosphatidic acid (LPA), a phospholipid mediator, which has potential regulatory effects on immune cell growth and motility. Our results indicate that LDIR potentially regulates immune system via protein-protein interaction of Ikaros and Autotaxin.

• Korean Journal of Plant Tissue Culture
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• v.24 no.1
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• pp.1-35
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• 1997

Fertilized egg, by successive cell divisions, differentiates into different tissues and organs with various structures and functions. Different cells and tissues contain different proteins, products of selective gene expression. Not all the genes in any genomes are equally active, temporal and spatial gene expression being the general rule. Present paper attempts to review the tanscriptional mechanisms or the initiations of transcription from several angles. In some of the organisms the genes in the process of transcription or the genes in the inactive state can be seen under the light microscope. Some bands of Drosophila polytene chromosomes may exhibit a swollen or puff appearance under certain conditions. A puff, unfolded or decondensed form of chromomere, represents sets of intense transcriptional activity or RNA synthesis. The heterochromatic X chromosome whose genes remain inactive in the female mammals can be visualized as a dark staining structure called Barr body, Configuration of chromatin differs between transcribed and nontranscribed chromatin. Modification to the chromatin facilitates RNA synthesis. The movement of large polymerase molecule along the DNA would probably be facilitated if some modifications of the chromatin configuration is effected. Methylation of cytosines in CG sequences is associated with inactive genes. Methylation can play a role in determination of mammalian cells during embryogenesis. Demethylation is necessary for the gene to be expressed during development A histone modification that is also known to be correlated with transcriptional capacity of chromatin is acetylation of the lysine residues of the core histones. Chromatin containing a high level of histone acetylation is very sensitive to DNase 1. For the transcription to occur TBP must first bind to the TATA box. Another TF, TF IIB, then binds to the promoter-TBP complex, facilitating the access of RNA polymerase to the transcription initiation site. As recently as eight years ago researchers assumed that histones were irrelevant to the regulation of gene expression. Histones combine with the DNA to form nucleosome of the chromatin. Histones are vital participant in gene regulation. Histone and basal factors compete for access to TATA box. When DNA is exposed to basal factors before histones are introduced, the basal factors assemble on TATA boxes preventing the access of histones, allowing transcription to occur, for transcription to begin, activator protein at the upstream activation sequence or enhancer must interact with the tail of histone H4 at TATA box and cause the histone role particle to dissociate from the TATA box leading to partial breakup of the histone core particle and allowing the basal factors to bind to the TATA box. New concept of genomic flux in contrast to the old concept of static genome has been developed based on the powerful new molecular techniques. Genomic changes such as repetitive DNAs and transposable elements, it is assumed but not yet proved, may affect some of the developmental patterns that characterize particular cells, tissues, organs, and organisms. In the last decade or so remarkable achievement have been made in the researches of the structures and functions of TFs and the specific target sequences located in promoters or enhancers where these TFs bind. TFs have independent domains that bind DNA and that activate transcription. DNA binding domain of TFs serves to bring the protein into the right location. There are many types of DNA binding domains. Common types of motifs can be found that are responsible for binding to DNA. The motifs are usually quite short and comprise only a small part of the protein structure. Steroid receptors have domains for hormone binding, DNA binding, and activating transcription. The zinc finger motif comprises a DNA binding domain. Leucine zipper consist of a stretch of amino acids with a leucine residue in every seventh position Two proteins form a dimer because they interact by means of leucine zippers on similar α-helical domain. This positions their DNA binding basic domains for interaction with the two halves of a DNA sequence with dyad symmetry of TGACTCA, ACTGAGT.

• Journal of Plant Biotechnology
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• v.42 no.3
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• pp.204-214
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• 2015

SHI-RELATED SEQUENCE (SRS) genes are plant-specific transcription factors that contain a zinc-binding RING finger motif, which play a critical role in plant growth and development. Among Brassica rapa SRS genes, BrSRS7 and BrLRP1 genes, isolated from shoot apical regions are important regulators of plant growth and development. In order to explore the function of BrSRS genes in horticultural plant growth and development, two constructs containing BrSRS7 and BrLRP1 under the control of a cauliflower mosaic virus 35S promoter were introduced into petunia by Agrobacterium-mediated transformation. The resulting transgenic plants were dwarf and compact plants with reduced plant height and diameter. Additionally, these transgenic plants had upward-curled leaves of narrow width and short internodes. Interestingly, the flower shapes of petunia were different among transgenic plants harboring different kinds of SRS genes. These phenotypes were stably inherited through generations $T_2$ and $T_3$. Semi-quantitative RT-PCR analyses of transgenic plants revealed that BrSRS7 and BrLRP1 regulate expression of gibberellin (GA)- and auxinrelated genes, PtAGL15- and PtIAMT1-related, involved in shoot morphogenesis. These results indicate that the overexpression of BrSRS7 and BrLRP1 genes suppressed the growth and development of petunia by regulating expression of GA- and auxin-related genes. From these data, we deduce that BrSRS7 and BrLRP1 genes play an important role in the regulation of plant growth and development in petunia. These findings suggest that transformation with the BrSRS genes can be applied to other species as a tool for growth retardation and modification of plant forms.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.11
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• pp.1529-1539
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• 2017

Objective: The objective of this study was to compare the DNA methylation profile in the longissimus dorsi muscle between Small Tailed Han and Dorper${\times}$Small Tailed Han crossbred sheep which were known to exhibit significant difference in meat-production. Methods: Six samples (three in each group) were subjected to the methylated DNA immunoprecipitation sequencing (MeDIP-seq) and subsequent bioinformatics analyses to detect differentially methylated regions (DMRs) between the two groups. Results: 23.08 Gb clean data from six samples were generated and 808 DMRs were identified in gene body or their neighboring up/downstream regions. Compared with Small Tailed Han sheep, we observed a tendency toward a global loss of DNA methylation in these DMRs in the crossbred group. Gene ontology enrichment analysis found several gene sets which were hypomethylated in gene-body region, including nucleoside binding, motor activity, phospholipid binding and cell junction. Numerous genes were found to be differentially methylated between the two groups with several genes significantly differentially methylated, including transforming growth factor beta 3 (TGFB3), acyl-CoA synthetase long chain family member 1 (ACSL1), ryanodine receptor 1 (RYR1), acyl-CoA oxidase 2 (ACOX2), peroxisome proliferator activated receptor-gamma2 (PPARG2), netrin 1 (NTN1), ras and rab interactor 2 (RIN2), microtubule associated protein RP/EB family member 1 (MAPRE1), ADAM metallopeptidase with thrombospondin type 1 motif 2 (ADAMTS2), myomesin 1 (MYOM1), zinc finger, DHHC type containing 13 (ZDHHC13), and SH3 and PX domains 2B (SH3PXD2B). The real-time quantitative polymerase chain reaction validation showed that the 12 genes are differentially expressed between the two groups. Conclusion: In the current study, a tendency to a global loss of DNA methylation in these DMRs in the crossbred group was found. Twelve genes, TGFB3, ACSL1, RYR1, ACOX2, PPARG2, NTN1, RIN2, MAPRE1, ADAMTS2, MYOM1, ZDHHC13, and SH3PXD2B, were found to be differentially methylated between the two groups by gene ontology enrichment analysis. There are differences in the expression of 12 genes, of which ACSL1, RIN2, and ADAMTS2 have a negative correlation with methylation levels and the data suggest that DNA methylation levels in DMRs of the 3 genes may have an influence on the expression. These results will serve as a valuable resource for DNA methylation investigations on screening candidate genes which might be related to meat production in sheep.

• Development and Reproduction
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• v.4 no.1
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• pp.67-77
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• 2000

Snailfish usually lives at the bottom of the sea and showed typical retrogressive change with specialized tissue structures of skin and skeletons. In order to obtain the specific genes of snailfish, highly expressed in the body, we made subtracted cDNA library and analyzed 200 clones. Totally 200 clones were obtained and sequenced, and among them 62 clones were turned out to be homologous to the known gene, i.e., thioesterase (9), myosin (8), creatine kinase (7), skeletal alpha-actin (6), parvalbumin b (5), ribosomal protein (5), type I collagen (3), muscle troponin (3), dopamine receptor (2), histatin (2), and heat shock protein (2), cystatin (1), lectin (1), statherin (1), secretory carrier membrane protein (1), keratin type I (1), desmin (1), chloroplast (1), muscle tropomyosin (1), reticulum calcium ATPase (1), ribonucleoprotein (1). The remaining 138 clones were low homologous or non-redundant genes through Genbank search. Especially 5 clones were novel and specifically expressed in the body tissues of Snailfish by in situ hybridization. Therefore, we analysed these 5 clones to identify the C-terminal protein structures and motifs, and partly defined the roles of these proteins in comparison with the expression patterns by in situ hybridization. C9O-77, about 5000 bp, was supposed to be a matrix protein expressed strongly positive in epithelium, myxoid tissue, fibrous tissue and collagenous tissue. C9O-116, about 1500 bp, was supposed to be a transmembrane protein which was weakly expressed in the fibrous tissue, epithelium tissue, and myxoid tissue, but strong in muscle tissue. C9O-130, about 1200 bp, was supposed to be an intracytoplasmic molecule usually in the epithelial cells. C9O-161, about 2000 bp, was weakly expressed in epithelium, muscle tissue and myxoid tissue, but specially strong in epithelium. C9O-171, about 1000 bp, was supposed to be a transcription factor containing zinc finger like domain, which was intensely expressed in the epithelium, muscle tissue, fibrous tissue, and in collagenous tissue.