• BMB Reports
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• v.57 no.5
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• pp.216-231
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• 2024

Mammalian genomes are intricately compacted to form sophisticated 3-dimensional structures within the tiny nucleus, so called 3D genome folding. Despite their shapes reminiscent of an entangled yarn, the rapid development of molecular and next-generation sequencing technologies (NGS) has revealed that mammalian genomes are highly organized in a hierarchical order that delicately affects transcription activities. An increasing amount of evidence suggests that 3D genome folding is implicated in diseases, giving us a clue on how to identify novel therapeutic approaches. In this review, we will study what 3D genome folding means in epigenetics, what types of 3D genome structures there are, how they are formed, and how the technologies have developed to explore them. We will also discuss the pathological implications of 3D genome folding. Finally, we will discuss how to leverage 3D genome folding and engineering for future studies.

• Bulletin of the Korean Chemical Society
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• v.32 no.spc8
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• pp.3051-3056
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• 2011

We calculate the free energy surfaces for two small proteins and a protein-RNA complex system by using a lattice model approach. In particular, we employ the Munoz-Eaton model, which is a native-structure based statistical mechanical model for studying protein folding problem. The model can provide very useful insights into the folding mechanisms by allowing one to calculate the free energy surfaces efficiently. We first calculate the free energy surfaces of ubiquitin and BBL, using both approximate and recently developed exact solutions of the model. Ubiquitin exhibits a typical two-state folding behavior, while BBL downhill folding in our study. We then extend the method to study of a protein-RNA complex. In particular, we focus on PAZ-siRNA complex. In order to elucidate the interplay between folding and binding kinetics for this system we perform comparative studies of PAZ only, PAZ-siRNA complex and two mutated complexes. We find that folding and binding are strongly coupled with each other and the bound PAZ is more stable than the unbound PAZ. Our results also suggest that the binding sites of the siRNA may serve act as a nucleus in the folding process.

• Journal of the Korean Chemical Society
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• v.63 no.6
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• pp.427-434
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• 2019

The role of hydrophobic residues on protein folding reaction was studied by folding kinetics measurements in conjunction with protein engineering. The HubWA, which was derived from human ubiquitin by mutating the residues at 45 (Phe to Trp) and 26 (Val to Ala), was used as a mutational background. Fourteen hydrophobic residues were mutated to alanine. Among fourteen variants generated, only four variant proteins (V5A, I13A, V17A, and I36A) were suitable for folding study. The folding kinetics of these variants was measured by stopped-flow fluorescence spectroscopy. The folding kinetics of HubWA and V17A was observed to follow a three-state on-pathway mechanism. On the other hand, folding kinetics of V5A, I13A, and I36A was observed to follow a two-state mechanism. Based on these observations, transition of protein folding reaction from collision-diffusion mechanism to nucleation-condensation mechanism was discussed.

• BMB Reports
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• v.54 no.5
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• pp.233-245
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• 2021

In eukaryotes, the genome is hierarchically packed inside the nucleus, which facilitates physical contact between cis-regulatory elements (CREs), such as enhancers and promoters. Accumulating evidence highlights the critical role of higher-order chromatin structure in precise regulation of spatiotemporal gene expression under diverse biological contexts including lineage commitment and cell activation by external stimulus. Genomics and imaging-based technologies, such as Hi-C and DNA fluorescence in situ hybridization (FISH), have revealed the key principles of genome folding, while newly developed tools focus on improvement in resolution, throughput and modality at single-cell and population levels, and challenge the knowledge obtained through conventional approaches. In this review, we discuss recent advances in our understanding of principles of higher-order chromosome conformation and technologies to investigate 4D chromatin interactions.

• BMB Reports
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• v.40 no.4
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• pp.453-458
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• 2007

Bacterial luciferase is a heterodimeric enzyme, which catalyzes the light emission reaction, utilizing reduced FMN (FMNH2), a long chain aliphatic aldehyde and $O_2$, to produce green-blue light. This enzyme can be readily classed as slow or fast decay based on their rate of luminescence decay in a single turnover. Mutation of Glu175 in $\alpha$ subunit to Gly converted slow decay Xenorhabdus Luminescence luciferase to fast decay one. The following studies revealed that changing the luciferase flexibility and lake of Glu-flavin interactions are responsible for the unusual kinetic properties of mutant enzyme. Optical and thermodynamics studies have caused a decrease in free energy and anisotropy of mutant enzyme. Moreover, the role of Glu175 in transition state of folding pathway by use of stopped-flow fluorescence technique has been studied which suggesting that Glu175 is not involved in transition state of folding and appears as surface residue of the nucleus or as a member of one of a few alternative folding nuclei. These results suggest that mutation of Glu175 to Gly extended the structure of Xenorhabdus Luminescence luciferase, locally.

• Journal of Life Science
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• v.13 no.5
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• pp.596-603
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• 2003

Cells respond to an accumulation of unfolded proteins in the endoplasmic reticulum (ER) by increasing transcription of genes encoding molecular chaperones and folding enzymes. The information is transmitted from the ER lumen to the nucleus by intracellular signaling pathway, called the unfolded protein response (UPR). To obtain genes related to UPR from B. mori, the cDNA library was constructed with mRNA isolated from Bm5 cell lines in which N-glycosylation was inhibited by tunicamycin treatment. From the cDNA library, we selected 40 clones that differentially expressed when cells were treated with tunicamycin. Among these clones, we have isolated ATFC gene showing similarity with Hac1p, encoding a bZIP transcription factor of 5. cerevisiae. Basic-leucine zipper (bZIP) domain in amino acid sequences of ATFC shared homology with yeast Hac1p. Also, ATFC is up-regulated by accumulation of unfolded proteins in the ER through the treatment of ER stress drugs. Therefore we suggest that ATFC represents a major component of the putative transcription factor responsible for the UPR leading to the induction of ER-localized stress proteins.

• Korean Journal of Veterinary Research
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• v.48 no.3
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• pp.305-310
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• 2008

A 10-year-old female Yorkshire terrier with the clinical signs of nasal swelling, epistaxis and nasal discharge was presented to the Veterinary Teaching Hospital in the Cheju National University. Abnormal nasal mass was detected in physical examination and radiographic findings. After surgical excision, the sample of nasal mass was referred to Pathology Department of Veterinary Medicine. Grossly, the mass was soft, friable, and $2.5{\times}4cm$ cm in size. Histopathologically, the mass was composed of mediumsized non-keratinizing columnar to polyhedral cells arranged in anastomosing ribbon and large nest. It has complex in-folding of thick epithelial layers separated by fibrovascular septa. Tumor cells showed characteristic palisading arrangement of columnar cells, and perpendicularly distributed to the basement membrane. The cells had pale basophilic cytoplasm, oval nucleus and one or more nucleoli, and indistinct cellular border. Many tumor cell emboli were presented in lymphatics. Immunohistochemistry revealed that tumor cells were cytokeratin (CK) 19 and CK clone MNF116 positive and but CK7 and CK high molecular weight negative. Based on the gross, histopathologic, and immunohistochemical findings, the mass was diagnosed as transitional carcinoma in nasal cavity. In our best knowledge, this is the first report of transitional carcinoma originated from transitional zone of canine nasal cavity in Korea.

• International Journal of Industrial Entomology and Biomaterials
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• v.7 no.2
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• pp.133-137
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• 2003

Cells respond to an accumulation of unfolded proteins in the endoplasmic reticulum (ER) by increasing transcription of genes encoding molecular chaperones and folding enzymes. The information is transmitted from the ER lumen to the nucleus by intracellular signaling pathway, called the unfolded protein response (UPR). In Saccharomyces cerevisiae, such induction is mediated by the cis-acting unfolded response element (UPRE) which has been thought to be recognized by Hac1p transcription factor. We cloned the ATFC gene showing similarity with Hac1p, and then examined to determine whether ATFC gene product specifically binds to UPRE by electrophoretic mobility shift assays. ATFC gene product displayed appreciable binding ${to ^{32}}P-labelled$ UPRE. Therefore, we concluded that ATFC represents a major component of the putative transcription factor responsible for the UPR leading to the induction of ER-localized stress proteins.

• Biomedical Science Letters
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• v.4 no.2
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• pp.77-86
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• 1998

Age-related changes in the lens capsule and epithelium of cataractous patients, ranging from 20 to 7o years old, were studied by means or LM, immunohistochemistry, and TEM. The lens capsule was divided into four zones; the anterior, subanterior, middle, and basal zone. The van Gieson staining reaction for collagen was prominent at the anterior and subanterior parts of the lens capsule. The reaction was more decreased in the elder group than the younger group. The collagen type IV reaction was prominent at the anterior zone of the lens capsule and around the cell. The reaction was more decreased in the elder group than the younger group. 3. The Periodic Acid Shiff-Alcian Blue reaction for mucopolysaccharide was prominent at the anterior zone of the lens capsule. The reaction was more decreased in the elder group than the younger group. The Apoptotic reaction was prominent at the nucleus of the lens epithelial cell. In the elder the cataractous group, the number of the apoptotic cells was more decreased. The electron microscopic change of lens epithelial cells were characterized by the increase of lateral fold and the cytoplasm with various vacuoles and Golgi complex. In the basal part, lens epithelial cell protruded toward the lens capsule in the 20-year-old group. The basal part of the 40-year-old group was flattened and covered with the cytoplasmic processes of adjacent cells. In the 60-year-old group, the mass of rough filaments separated lens capsule and the basal part of the lens epithelial cell. The electron microscopic change of the middle part of lens capsule was characterized by the aggregation of electron dense materials in the 40-year-old group, and the appearance of filamentous materials and the decrease of electron dense granules in the 60-year-old group.

• The Korean Journal of Zoology
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• v.18 no.2
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• pp.87-101
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• 1975

Electron microscopic studies on the ultrastructure of the mouse oocyte were made to investigate the inhibition of germinal vesicle breakdown by dibutyryl cAMP. The nuclear membrane of the dibutyryl cAMP-treated oocyte is characterized by a decreased degree of folding, maintains the normal double membrane structure, and shows an increased occurrence of the nuclear pore. It is suggested that these may be related to the suppression of the maturation of oocytes at the germinal vesicle. Mitochondria in the control cell were shown to be spread evenly throughout the cytoplasm and structurally underdeveloped or transitionary having little cristae development. On the contrary, mitochondria in the treated oocyte were found to be localized mainly around the nucleus and to show a greater extent of cristae development. The oocyte treated with dibutyryl cAMP appears to have fewer and structurally simpler lysosomes as compared to the control. The Golgi complex in the control oocyte exhibits the typical granular and lamellar structure, whereas that in the treated cell is poorly developed. Many multivesicular bodies, tonofilaments, and free ribosomes were observed in the control as well as in treated cells. The microvilli become structurally irregular, and a development of the perivitelline space is apparent in the treated oocyte. It is concluded that there is no basic difference in the ultrastructure between the oocytes treated with dibutyryl cAMP for 24 hours in the medium and those collected directly from the follicle. However, the finding that dibutyryl cAMP induces a development of more pores along the nuclear membrane strongly suggests the possibility that this compound inhibits the maturation of oocytes by influencing the permeability of the nuclear membrane.