• BMB Reports
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• v.56 no.12
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• pp.633-644
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• 2023

Epigenetic mechanisms, primarily mediated through histone and DNA modifications, play a pivotal role in orchestrating the functional identity of a cell and its response to environmental cues. Similarly, the spatial arrangement of chromatin within the three-dimensional (3D) nucleus has been recognized as a significant factor influencing genomic function. Investigating the relationship between epigenetic regulation and 3D chromatin structure has revealed correlation and causality between these processes, from the global alignment of average chromatin structure with chromatin marks to the nuanced correlations at smaller scales. This review aims to dissect the biological significance and the interplay between the epigenome and 3D chromatin structure, while also exploring the underlying molecular mechanisms. By synthesizing insights from both experimental and modeling perspectives, we seek to provide a comprehensive understanding of cellular functions.

• Molecules and Cells
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• v.42 no.7
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• pp.512-522
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• 2019

Chromosomes located in the nucleus form discrete units of genetic material composed of DNA and protein complexes. The genetic information is encoded in linear DNA sequences, but its interpretation requires an understanding of three-dimensional (3D) structure of the chromosome, in which distant DNA sequences can be juxtaposed by highly condensed chromatin packing in the space of nucleus to precisely control gene expression. Recent technological innovations in exploring higher-order chromatin structure have uncovered organizational principles of the 3D genome and its various biological implications. Very recently, it has been reported that large-scale genomic variations may disrupt higher-order chromatin organization and as a consequence, greatly contribute to disease-specific gene regulation for a range of human diseases. Here, we review recent developments in studying the effect of structural variation in gene regulation, and the detection and the interpretation of structural variations in the context of 3D chromatin structure.

• 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.

• Journal of Microbiology and Biotechnology
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• v.32 no.12
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• pp.1515-1526
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• 2022

Eukaryotic chromatin is highly organized in the 3D nuclear space and dynamically regulated in response to environmental stimuli. This genomic organization is arranged in a hierarchical fashion to support various cellular functions, including transcriptional regulation of gene expression. Like other host cellular mechanisms, viral pathogens utilize and modulate host chromatin architecture and its regulatory machinery to control features of their life cycle, such as lytic versus latent status. Combined with previous research focusing on individual loci, recent global genomic studies employing conformational assays coupled with high-throughput sequencing technology have informed models for host and, in some cases, viral 3D chromosomal structure re-organization during infection and the contribution of these alterations to virus-mediated diseases. Here, we review recent discoveries and progress in host and viral chromatin structural dynamics during infection, focusing on a subset of DNA (human herpesviruses and HPV) as well as RNA (HIV, influenza virus and SARS-CoV-2) viruses. An understanding of how host and viral genomic structure affect gene expression in both contexts and ultimately viral pathogenesis can facilitate the development of novel therapeutic strategies.

• Journal of Microbiology and Biotechnology
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• v.17 no.12
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• pp.2056-2060
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• 2007

Transcription factor GATA-3 is the critical transcription factor for Th2 cell differentiation. In spite of its importance in Th2 cell differentiation, the molecular mechanism for its action in Th2 differentiation is poorly understood. Previous studies have suggested that GATA-3 may be involved in the chromatin remodeling in the Th2 cytokine locus. To determine whether GATA-3 exerts its effect on its target sites in the extrachromosomal status, cell transfection assay was performed. In this assay, 800 bp IL4 promoter-luciferase constructs linked with GATA-3 target sites were transfected into the M12 B cell line, D10 mouse Th2 cell lines, and human T lymphoma Jurkat cell lines with or without the GATA-3 expression vector. The GATA-3 effects on its target sites were minimal in the extrachromosomal status, supporting the previous propositions that GATA-3 functions at the chromatin level by remodeling chromatin structure.

• Molecules and Cells
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• v.46 no.2
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• pp.86-98
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• 2023

The genome is almost identical in all the cells of the body. However, the functions and morphologies of each cell are different, and the factors that determine them are the genes and proteins expressed in the cells. Over the past decades, studies on epigenetic information, such as DNA methylation, histone modifications, chromatin accessibility, and chromatin conformation have shown that these properties play a fundamental role in gene regulation. Furthermore, various diseases such as cancer have been found to be associated with epigenetic mechanisms. In this study, we summarized the biological properties of epigenetics and single-cell epigenomic profiling techniques, and discussed future challenges in the field of epigenetics.

• Journal of Animal Science and Technology
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• v.48 no.6
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• pp.777-784
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• 2006

This study was designed to investigate between the semen characteristics and sperm chromatin structure in boar with different farrowing rates and relationship between fertility by AI and results of sperm chromatin structure assay (SCSA). The CASA (computer-aided sperm analysis) and SCSA were performed with liquid semen in boars. The all SCSA parameters based on the farrowing rates by AI were significantly differ (P<0.05). The significant negative correlations (P<0.05) were observed between all SCSA parameters and farrowing rate obtained by AI in the field. In conclusion, these results suggest that the sperm parameters evaluated in these studies may be useful indicators to predict the fertility by AI.

• Proceedings of the KSAR Conference
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• 2002.06a
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• pp.6-6
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• 2002

This study was conducted to investigate the effect of recipient activation time on the nuclear remodeling, chromatin structure, pronuclear formation and in vitro development of bovine nuclear transfer embryos derived from adult ear skin cells. Somatic cells were transferred to enucleated oocytes after quiescent treatments by serum starvation or culture to confluency. Nuclear transfer embryos were activated with a combination of Ca/sup 2+/-ionophore and cycloheximide at 1, 1.5, 2, 2.5, 3, and 5 h after electrofusion. (omitted)

• Asian-Australasian Journal of Animal Sciences
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• v.13 no.1
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• pp.10-18
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• 2000

This paper describes the magnetic orientation of the intact and demembranated bull sperm treated by DTT or heparin in a 5,400 G static field. Semen samples collected from four bulls (Japanese Black) were mixed to the same sperm density. One percentage triton X-100 was used to extract the plasma membrane. The intact and demembranated sperm suspensions were treated with 20, 200, 2,000 mM DTT, 100, 1,000 or 10,000 units heparin solutions at $4{^{\circ}C}$ for 6 days. The decondensation of the sperm nuclei treated by DTT or heparin was examined by measuring the sperm head area at 1, 3, and 6 days. After measuring the area, each sperm sample was exposed to a 5,400 G static magnetic field generated by Nd-Fe-B permanent magnets for 24 hours at room temperature. Results showed that the decondensation of bull sperm nuclei was not induced by the heparin treatment, however, incomplete decondensation was induced by the DTT treatment. During the magnetic orientation, bull sperms treated by DTT or heparin had low percentages of long axis perpendicular to the magnetic lines of force. However, different aspects were obtained for long axis perpendicular orientations following treatment of DTT or heparin. Through the DTT treatment, the decline of long axis perpendicularly oriented percentages was due to the increase of long axis parallel orientation with the head of the flat plane perpendicular to the magnetic lines of force, whereas, using the heparin treatment, the decline of long axis perpendicular orientation was due to the increment of long axis parallel orientation with the head of the flat plane parallel to the magnetic lines of force. Also, percentages of the head of the flat plane perpendicular were decreased by the heparin treatment. These findings suggest that maintaining the structure of protamine in the chromatin is necessary for the sperm head to orient with its flat plane perpendicular, and maintaining the disulfide bond in the chromatin is necessary for the long axis of sperm to orient perpendicularly.

• Development and Reproduction
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• v.1 no.1
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• pp.9-24
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• 1997

To investigate the process of spermiogenesis of the Korean eastern Daubenton's bat, Myotis daubentonii ussuriensis, the testis obtained from mature male bats was studied by transmission electron microscope and were based on the variety and diagnostic characters of cell organells. The results obtained from the present study are as follows. According to the differentiation of the cell organells, the spermiogenesis of the Korean eastern Daubenton's bat, M. d. ussuriensis, was divided into Golg, cap, acrosome, maturation and spermiation phases. Besides, these Golgi, cap, acrosome, and maturation phase were subdivided into the steps of early and late phases repectively and matruation phase was subdivided into step of early, mid and late phases. Therfore, the spermiogenesisof M. d. ussuriensis has been divided into a total of 11 phases. The chromatin granules began to condense at the early cap phase, regularized at the acrosome phase, and a perfect nucleus of sperm was formed at the maturation phase. The chromatoid body was occurred in the upper cytoplasm of nucleus at the early Golgi phase, and it was accurred the posterior cytoplasm of the nucleus at the early maturatio phase. The formation of sperm tail began to be develop in the early golgi phase, and completed at the spermiation phase. The fiber structure of middle piece was consisted of nine outer doublets and two central singlet microtubules and Nos. 1, 5, 6 and 9 in the outer dense were larger than the others(2, 3, 4, 7, 8).