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

• Korean Journal of Veterinary Research
• /
• v.7 no.2
• /
• pp.13-18
• /
• 1967

1. Within experimental chromatin, the total protein: DNA ratio did not vary in the same organs of control and irradiated rats. However, the amount of RNA and total protein associated with the DNA varied considerably among the different types of chromatin. In particular, the content of chromatin was the control tissue. RNA and total protein ratio of chromatins from brtain, liver, testis and spleen declined with experimental I organs. 2. There was the same quantitative relationship between the amount of RNA and the amount of histone-protein associated with DNA in chromatin. 3. RNA: DNA ratio of chromatin showed 1.5-2 times increas in the irradiated organs except brain. However, RNA: DNA ratio was decreased in chromatin by irradiation. 4. Histone-protein:residual protein ratio was greatly varied among the organs. However, the effect was not found by irradiation. 5. Priming activity of chromatin showed a higher value in testis and the activity was greater in organs with higher metabolic activity: 6. Inhibition of Actinomycin D is observable in chromatin from testis, liver, spleen and brain declined without relationship between irradiated and non-irradiated conditions. Ammonium sulfate showed increased priming activity by the electrostatic dissociation of DNA and histone in chromatin on the stimulation depending on property of chromatins. 7. It is suggested that the results support a proposal that testis and spleen of highly sensitive to irradiation should an increase in the priming activity whereas brain and liver of lower sensitivity decreased in the activity.

• BMB Reports
• /
• v.54 no.10
• /
• pp.489-496
• /
• 2021

Chromatin has highly organized structures in the nucleus, and these higher-order structures are proposed to regulate gene activities and cellular processes. Sequencing-based techniques, such as Hi-C, and fluorescent in situ hybridization (FISH) have revealed a spatial segregation of active and inactive compartments of chromatin, as well as the non-random positioning of chromosomes in the nucleus, respectively. However, regardless of their efficiency in capturing target genomic sites, these techniques are limited to fixed cells. Since chromatin has dynamic structures, live cell imaging techniques are highlighted for their ability to detect conformational changes in chromatin at a specific time point, or to track various arrangements of chromatin through long-term imaging. Given that the imaging approaches to study live cells are dramatically advanced, we recapitulate methods that are widely used to visualize the dynamics of higher-order chromatin structures.

• Journal of Life Science
• /
• v.22 no.11
• /
• pp.1587-1594
• /
• 2012

3C (chromatin conformation capture) is a technique to analyze chromatin organization in nuclei of eukaryotic cells. The procedure of 3C includes the formaldehyde treatment of cells to fix interactions between proteins and between proteins and DNA in chromatin, the digestion of fixed chromatin with restriction enzyme, and the ligation of fragmented DNA. The efficiency of DNA ligation represents proximity between DNA fragments in chromatin organization. Studies in the ${\beta}$-globin locus using 3C showed that the locus control region is in close proximity to the transcriptionally-active globin genes, indicating that chromatin organization has a role in transcriptional regulation of the genes. 3C has been advanced by combining with ChIP and genome-wide sequencing. This review presents the principle and procedure of the 3C technique, the chromatin organization of the ${\beta}$-globin locus explained by 3C, and advanced techniques based on 3C.

• Proceedings of the KSAR Conference
• /
• 2001.03a
• /
• pp.41-41
• /
• 2001

Chromatin configuration and microtubule assembly were determined in porcine maturing and activated oocytes following intracytoplasmic sperm injection. Microtubule localization was confirmed using a mouse monoclonal antibody to $\alpha$-tubulin and detected using a fluorescent labeled goat anti-mouse secondary antibody. DNA was stained with propidium iodide. The image of microtubules and chromatin was captured using laser scanning confocal microscope. In germinal vesicle stage oocyte, sperm chromatin remained condensation and sperm derived microtubules were not observed at 8 to 12 h after sperm injection. At 24 h after injection, the sperm nucleus developed to the metaphase chromatin along the metaphase structure of female nucleus. In some metaphase I stage oocytes, sperm chromatin decondensed at 8 h to 12 h after injection, sperm aster was seen soon after sperm injection. At 24 h after sperm injection into metaphase I stage oocyte, male chromatin developed to the metaphase chromatin while female chromatin extruded first polar body and formed the metaphase chromatin. At 12 to 15 h after sperm injection into preactivated oocytes, condensed sperm nucleus was located in close proximity of female pronucleus. However, the condensed nucleus did not fuse with female pronucleus. In preactivated ocytes, injected sperm remained condensation, a few sperm organized small microtubular aster. Instead, maternal derived microtubules were organized near the female chromatin, which seem to move condensed male chromatin near to the female pronucleus. These results suggest that sperm nuclear decondensing activity and nucleation activity of centrosome during fertilization are cell cycle dependent. In absence of male functional centrosome, female origin centrosome takes over the role of microtubule nucleation for nuclear movement.

• Journal of Microbiology
• /
• v.34 no.1
• /
• pp.54-60
• /
• 1996

Taking advantage of the heat inducible HSP82 gene in yeast, chromatin structure after transcription cessation was investigated. Alteration of chromating conformation within the HSP82 gene transcription unit into an active state has been shown to correlate with its transcriptional induction. It was thus of interest to examine whether the active chromatin state within the HSP82 mRNA analysis, the gene ceased its transcription within a few hours of cultivation at a normal condition after heat induction. In this condition, an active chromatin conformation in the HSP82 gene body was changed into an inactie state which was revealed by DNase I resistance and by typical nucleosomal cutting periodicity in the corresponding chromatin. These results thus ruled out the possibility of a long-term maintenance of the DNase I sensitive chromatin after transcription cessation. DNA replication may be a critical event for the chromatin reprogramming.

• Genomics & Informatics
• /
• v.15 no.4
• /
• pp.114-122
• /
• 2017

It is becoming increasingly clear that eukaryotic genomes are subjected to higher-order chromatin organization by the CCCTC-binding factor/cohesin complex. Their dynamic interactions in three dimensions within the nucleus regulate gene transcription by changing the chromatin architecture. Such spatial genomic organization is functionally important for the spatial disposition of chromosomes to control cell fate during development and differentiation. Thus, the dysregulation of proper long-range chromatin interactions may influence the development of tumorigenesis and cancer progression.

• Clinical and Experimental Reproductive Medicine
• /
• v.38 no.3
• /
• pp.142-147
• /
• 2011

Objective: This study was performed to evaluate testicular sperm chromatin condensation using aniline blue-eosin (AB-E) staining and its effects on IVF-ET. Methods: Chromatin condensation was analyzed using AB-E staining in 27 cases of testicular sperm extraction. There were 19 cases of obstructive azoospermia (OA) and 8 cases of non-obstructive azoospermia (NOA) in IVF-ET. Mature sperm heads were stained red-pink whereas immature sperm heads were stained dark blue. The percentage of sperm chromatin condensation was calculated from the ratio of the number of red-pink sperm to the total number of sperm analyzed. Results: The overall percentages of chromatin condensation in OA and NOA were $31.1{\pm}11.2%$ and $26.3{\pm}14.4%$, respectively. The fertilization rate was significant higher in OA than NOA ($p$ <0.05); however, the rates of good embryos and clinical pregnancy did not show statistical differences. In OA and NOA, statistical differences were not observed in the rate of chromatin condensation, fertilization, good embryos, and clinical pregnancy between the pregnant group and non-pregnant group. Conclusion: Chromatin condensation is less stable than OA and showed a low fertilization rate in NOA. While there were no significant differences in chromatin condensation results between NOA and OA, we propose that a pattern of decreased chromatin condensation in NOA is one of the factors of low fertilization results requiring further study.

• Genes and Genomics
• /
• v.40 no.12
• /
• pp.1301-1308
• /
• 2018

Background Adipocyte differentiation is completed by changing gene expression. Chromatin is closely related to gene expression. Therefore, its structure might be changed for adipocyte differentiation. Mouse 3T3-L1 preadipocytes have been used as a cell model to study molecular mechanisms of adipogenesis. Objective To examine changes of chromatin modification and expression of histone modifying enzymes during adipocyte differentiation. Methods Microscopic analysis and Oil Red O staining were performed to determine distinct phenotype of adipocyte differentiation. RT-PCR and Western blot analysis were used to examine expression levels of histone modifying enzymes during adipocyte differentiation. Histone modifications were examined by immunostaining analysis. Results Expression levels of P300 and cbp were increased during adipocyte differentiation. However, acetylation of histones was not quantitatively changed postdifferentiation of 3T3-L1 cells compared to that at pre-differentiation. RT-PCR and Western blot analyses showed that expression levels of hdac2 and hdac3 were increased during adipocyte differentiation, suggesting histone acetylation at chromatin level was homeostatically controlled by increased expression of both HATs and HDACs. Tri-methylation level of H3K9 (H3K9me3), but not that of H3K27me3, was significantly decreased during adipocyte differentiation. Decreased expression of setdb1 was consistent with reduced pattern of H3K9me3. Knock-down of setdb1 induced adipocyte differentiation. This suggests that setdb1 is a key chromatin modifier that modulates repressive chromatin. Conclusion These results suggest that there exist extensive mechanisms of chromatin modifications for homeostatic balance of chromatin acetylation and deconstruction of repressive chromatin during adipocyte differentiation.

• The Korean Journal of Nuclear Medicine
• /
• v.1 no.2
• /
• pp.27-34
• /
• 1967

1. Within experimental chromatin, the total protein: DNA ratio did not vary in the same organs of control and irradiated rats. However, the amount of RNA and total protein associated with the DNA varied considerably among the different types of chromatin. In particular, the content of chromatin was the highest in the irradiated tissue, and the lowest in the chromatin control tissue. RNA and total protein ratio of chromatins from brain, liver, testis and spleen declined with experimental organs. 2. There was the same quantitative relationship between the amount of RNA and the amount histone-protein associated with DNA in each chromatin. 3. RNA:DNA ratio of chromatin showed a $1.5{\sim}2$ times increase in the irradiated organs except brain. However, RNA:DNA ratio was decreased in chromatin by irradiation. 4. Histone-protein:Residual protein ratio was greatly varied among the organs. However, the effect was not found by irradiation. 5. Priming activity of chromatins showed a higher value in testis and the activity was greater in organs with higher metabolic activity. 6. Inhibition of Actinomycin D observable in chromatin for testis, liver, spleen and brain declined without relationship between irradiated and non-irradiated conditions. Ammonium sulfate in DNA of chromatin from histone showed increased priming activity with dissociation by Electrostatics. It may give different effect of ammonium sulfate on stimulation by property of chromatins. 7. It is suggested that the results support a proposal that the higher sensitivity of radioactive in testis, spleen by irradiated showed a increase and decrease lower-sensitivity of radioactive from brain, liver than did priming activity under the radioactive conditions.