• BMB Reports
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• 제56권12호
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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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• 제42권7호
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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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• 제54권5호
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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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• 제32권12호
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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.

• BMB Reports
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• 제57권9호
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• pp.381-387
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• 2024

The nucleus, a highly organized and dynamic organelle, plays a crucial role in regulating cellular processes. During cell differentiation, profound changes occur in gene expression, chromatin organization, and nuclear morphology. This review explores the intricate relationship between nuclear architecture and cellular function, focusing on the roles of the nuclear lamina, nuclear pore complexes (NPCs), sub-nuclear bodies, and the nuclear scaffold. These components collectively maintain nuclear integrity, organize chromatin, and interact with key regulatory factors. The dynamic remodeling of chromatin, its interactions with nuclear structures, and epigenetic modifications work in concert to modulate gene accessibility and ensure precise spatiotemporal control of gene expression. The nuclear lamina stabilizes nuclear shape and is associated with inactive chromatin regions, while NPCs facilitate selective transport. Sub-nuclear bodies contribute to genome organization and gene regulation, often by influencing RNA processing. The nuclear scaffold provides structural support, impacting 3D genome organization, which is crucial for proper gene expression during differentiation. This review underscores the significance of nuclear architecture in regulating gene expression and guiding cell differentiation. Further investigation into nuclear structure and 3D genome organization will deepen our understanding of the mechanisms governing cell fate determination.

• Journal of Microbiology and Biotechnology
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• 제17권12호
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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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• 제46권2호
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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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• 제48권6호
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• pp.777-784
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• 2006

본 연구는 돼지에서 정자 SCSA와 정자 운동성 및 인공수정을 이용한 분만율과의 상관관계를 조사하기 위해 인공수정센터에서 정액 생산용으로 이용되고 있는 종모돈 중 개체별 정액을 이용한 인공수정 번식성적을 가지고 있는 종모돈 26두의 정액 성상 기록과 번식성적을 분석 하였고, 액상정액을 공시하여 정자운동성 분석과 SCSA를 실시하였다. 종모돈의 정액 채취 횟수에 따른 SCSA 분석은 종모돈 26두를 공시하여 정액을 8주간 6회 채취하여 공시하였다. 종모돈은 인공수정 분만율(80% 이상 ; 종모돈 7두, AI 256복, 8070% ; 종모돈 9두, AI 745복 및 70% 미만 ; 종모돈 10두, AI 293 복)에 따라 3개 군으로 구분 하였다. 액상 정액의 CASA 분석 결과는 분만율에 따른 종모돈 군 간에 유의적인 차이는 인정되지 않았다. 종모돈의 SCSA 결과는 분만율이 높을수록 COMP αt, %Red, %Peak R 및 %Mean R 값은 낮게 나타났고, 분만율이 가장 낮은 종모돈 군과 다른 두 군간에 유의적인 차이를 보였다(P<0.05). 종모돈 정액을 채취 차수에 따른 정액의 성상과 SCSA를 조사한 결과에서 채취 차수에 따른 차이는 나타나지 않았다. 종모돈의 인공수정 분만율과 SCSA 결과와의 상관관계는 COMP αt, SD αt, %Red, %Peak R, Mean R는 모두 부의 상관관계를 나타냈다. 이상의 결과에서 SCSA는 종모돈 정액의 수정 능력을 평가하고 예측하는데 유용한 방법으로 사료된다.

• 한국동물번식학회:학술대회논문집
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• 한국동물번식학회 2002년도 춘계학술발표대회 발표논문초록집
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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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• 제13권1호
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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.