• Genomics & Informatics
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• v.10 no.3
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• pp.145-152
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• 2012

Chromatin structure and dynamics that are influenced by epigenetic marks, such as histone modification and DNA methylation, play a crucial role in modulating gene transcription. To understand the relationship between histone modifications and regulatory elements in breast cancer cells, we compared our chromatin immunoprecipitation sequencing (ChIP-Seq) histone modification patterns for histone H3K4me1, H3K4me3, H3K9/16ac, and H3K27me3 in MCF-7 cells with publicly available formaldehyde-assisted isolation of regulatory elements (FAIRE)-chip signals in human chromosomes 8, 11, and 12, identified by a method called FAIRE. Active regulatory elements defined by FAIRE were highly associated with active histone modifications, like H3K4me3 and H3K9/16ac, especially near transcription start sites. The H3K9/16ac-enriched genes that overlapped with FAIRE signals (FAIRE-H3K9/14ac) were moderately correlated with gene expression levels. We also identified functional sequence motifs at H3K4me1-enriched FAIRE sites upstream of putative promoters, suggesting that regulatory elements could be associated with H3K4me1 to be regarded as distal regulatory elements. Our results might provide an insight into epigenetic regulatory mechanisms explaining the association of histone modifications with open chromatin structure in breast cancer cells.

• Journal of Embryo Transfer
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• v.27 no.2
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• pp.107-111
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• 2012

Miniature pig sperm cryopreservation is continually researched in biotechnology for breed conservation and reproduction. It is important to control the temperature at each stage of cryopreservation and cryoprotectant. It is also necessary to find the optimal cryoprotectant concentration and chemical elements of the extender. Recently, many studies have used various cryoprotectant materials, such as dimethyl sulphoxide (DMSO), ethylene glycol (EG), antifreeze protein (AFP), amides, and glycerol. Glycerol is a commonly used cryoprotectant. However, glycerol has critical cytotoxic properties, including osmotic pressure and it can cause irreversible damage to live cells. Therefore, We focused on membrane fluidity modifications can reduce cell damage from freezing and thawing procedures and evaluated on the positive effects of trehalose to the viability, chromatin integrity, and motility of boar sperm. Miniature pig sperm was separated from semen by washing with modified- Modena B (mMB) extender. After centrifugation, the pellet was diluted with the prepared first extender. This experiment was designed to compare the effects that sperm cryopreservation using two different extenders has on sperm chromatin. The control group used the glycerol only and it was compared with the glycerol and glycerol plus trehalose extender. Sperm viability and motility were evaluated using WST1 assays and computer-assisted semen assays (CASA). Chromatin structure was examined using acridine orange staining. For the motility descriptors, trehalose caused a significant (p<0.01) increase in total motility ($57.80{\pm}4.60%$ in glycerol vs. $75.50{\pm}6.14%$ in glycerol + trehalose) and progressive ($51.20{\pm}5.45%$ in glycerol vs. $70.74{\pm}8.06%$ in glycerol + trehalose). A significant (p<0.05) increase in VAP ($42.70{\pm}5.73{\mu}m/s$ vs. $59.65{\pm}9.47{\mu}m/s$), VSL ($23.06{\pm}3.27{\mu}m/s$ vs. $34.60{\pm}6.58{\mu}m/s$), VCL ($75.36{\pm}11.36{\mu}m/s$ vs. $99.55{\pm}12.91{\mu}m/s$), STR ($54.4{\pm}2.19%$ vs. $58.0{\pm}1.63%$), and LIN ($32.2{\pm}2.05%$ vs. $36.0{\pm}2.45%$) were also detected, respectively. The sperm DNA fragmentation index was 48.8% to glycerol only and 30.6% to glycerol plus trehalose. Trehalose added group showed higher percentages of sperm motility, stability of chromatin structure than glycerol only. In this study, we suggest that trehalose is effective in reducing freezing damage to miniature pig sperm and can reduce chromatin damage during cryopreservation.

• Applied Microscopy
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• v.22 no.2
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• pp.97-117
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• 1992

In order to study process of spermiogenesis of the Korean greater horseshoe bat, Rhinolophus ferrumequinum korai, the cycle of seminiferous epithelium was examined by the light and electron microscope and the following results were obtained based on the epithelial cell differentiation. 1. Spermiogenesis occurred from early July to mid-Octber, and spermatogenic activity was vigorous from mid-August to late September. Spermatocytes including spermatogonia were found to be degenerated in only July. It is deduced that the degeneration serves as the mechanism to regulate effective use of energy to prepare for mating and hibernating periods, and regulation of breeding cycle. 2. Spermiogenesis of the Korean greater horseshoe bat was divided according to differentiation of the cell structure, into Golgi, cap, acrosome, maturation and spermiation phases; Golgi, cap and spermiation phases were further divided into two steps of early and late phase respectively, and acrosome phase into three steps of early, mid and late phases, and maturation phase has only one step. Hence, the spermiogenesis consists of ten phases. The first research was done in this article on the changes of chromatin with nucleus, the time of appearance and disappearance of chromatin granules, in case of Korean greater horseshoe bat (Rhinolophus ferrumequinum korai). Chromatin granule began to be condensed in late Golgi and the condensation proceeded to form an irregular mass of a electron-dense chromatin in a form of circular cylinder in the center of nucleus at the phase of maturation. Finally, the chromatin condensation proceeded and perfect nucleus of sperm with homogeneous density was formed when the sperm was separated from Sertoli cell. Therefore, appearance and disappearance of chromatin granules occurred in the period of time between late Golgi and maturation phase, The tail of sperm began to develop in early cap phase, Numerous lipid droplets were obseved in the cytoplasm of spermatids during the maturation phase, which seemed to be used as energy source necessary to make mature sperm during spermiogenesis.

• Proceedings of the Korean Society of Sericultural Science Conference
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• 2003.10a
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• pp.19-22
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• 2003

Chromatin structure plays a critical role in the regulation of transcription. Drosophila GAGA factor directs chromatin remodeling to its binding sites. We found that Drosaphiia FACT, a heterodimer of dSPT16 and dSSRPl, is associated with GAGA factor through its dSSRPl subunit, binds to a nucleosome and facilitates GAGA factor-directed chromatin remodeling. Immunostaining of polytene chromosomes revealed colocalization of GAGA factor and FACT in many specific loci. (omitted)

• Korean Journal of Plant Tissue Culture
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• v.27 no.5
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• pp.359-366
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• 2000

Epigenetics represents a chromatin-mediated transcriptional repression which plays a control role in both animal and plant development. A number of different mechanisms have been described to be involved in the formation of chromatin structure: especially DNA methylation, nucleosomal histone modification, DNA replication timing, and binding of chromatin remodelling proteins. Epigenetic phenomena include genomic imprinting, dosage compensation of X-chromosome linked genes, mutual allelic interactions, paramutation, transvection, silencing of invasive DNA sequences, etc. They are often unstable and inherited in a non-Mendelian way. A number of epigenetic defects has been preferentially described in floral development. Here, epigenetic phenomena in model angiosperm plants and their corresponding mechanisms are reviewed.

• 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.

• Clinical and Experimental Reproductive Medicine
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• v.48 no.2
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• pp.142-149
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• 2021

Objective: Bacteriospermia and urogenital infections are common problems in male infertility. This study aimed to evaluate the effects of bacteriospermia on sperm parameters and clinical outcomes in semen samples infected with two common bacteria (Staphylococcus saprophyticus and Escherichia coli) in northern Iran. Methods: Microbiological tests were performed to isolate and identify organisms from 435 semen samples from infertile couples. Semen samples were assessed according to the World Health Organization criteria. The protamine status, chromatin structure, chromatin condensation, and acrosome reaction of sperm and assisted reproductive outcomes were determined in couples with different male infertility factors. Results: Among the total cases, the two most prevalent pathogens were considered: S. saprophyticus (38.2%) and E. coli (52.9%). In the semen samples infected with E. coli, the spontaneous acrosome reaction and abnormal chromatin condensation were more common (p<0.05). Significant increases in abnormal chromatin condensation and deprotamination were seen in the presence of S. saprophyticus. In washed semen, tight adhesion between the sperm midpiece and S. saprophyticus was observed. There was also a significant decrease in the fertilization rate using semen samples infected with S. saprophyticus and E. coli during in vitro fertilization cycles (p<0.001). In addition, the presence of S. saprophyticus and E. coli in semen samples was associated with a lower likelihood of clinical pregnancy in couples with various factors of male infertility. Conclusion: Poor results of assisted reproductive techniques may be correlated with semen samples infected with two common bacteria in northern Iran.

• Journal of Life Science
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• v.21 no.4
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• pp.616-620
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• 2011

Lysine residues of histone H3 and H4 are covalently modified in the chromatin of eukaryotic cells. Lysine 27 in histone H3 was acetylated (H3K27ac) or methylated at three levels; mono-, di-, and trimethylation (H3K27me1, H3K27me2, and H3K27me3). These modifications at H3K27 were related with gene transcription and/or chromatin structure in distinct patterns. Generally, H3K27ac and H3K27me1 were enriched in active chromatin, such as the locus control region or transcriptionally active genes, while transcriptionally inactive genes were highly marked by H3K27me2 and H3K27me3. These modifications appear to have been catalyzed by distinct histone-modifying enzymes. Recent studies suggest that the four kinds of modifications at H3K27 have inter-correlation in gene transcription or chromatin structure formation.

• Journal of Life Science
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• v.17 no.3 s.83
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• pp.381-385
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• 2007

Facilitates chromatin transcription (FACT) is a chromatin-specific elongation factor required for transcription of chromatin templates in vivo and in vitro. FACT consists of human homologue of the Saccharomyces cerevisiae Spt16/Cdc68 protein (hSpt16) and the high mobility group-1-like protein structure-specific recognition protein-1 (SSRP-1). Here we show that the protein level of hSpt16 is massively down-regulated in quiescent T98C cells using both immunofluorescence and western blot analysis. In contrast, we observe high level of the hspt16 expression in the proliferative T98G cells. Interestingly, the expression of SSRP-1 is not altered in both quiescent and proliferative states. Taken together, our findings implicate that the expression of hSpt16 is associated with the proliferative state and can be used as a proliferation marker.

• Clinical and Experimental Reproductive Medicine
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• v.47 no.4
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• pp.277-283
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• 2020

Objective: The sperm DNA fragmentation index (DFI) guides the clinician's choice of an appropriate assisted reproductive technology (ART) procedure. The DFI can be determined using commercially available methodologies, including sperm chromatin dispersion (SCD) kits and sperm chromatin structure assay (SCSA). Currently, when DFI is evaluated using SCD kits, the result is analyzed in reference to the SCSA-derived threshold for the choice of an ART procedure. In this study, we compared DFI values obtained using SCSA with those obtained using SCD and determined whether the difference affects the choice of ART procedure. Methods: We compared SCSA to two SCD kits, CANfrag (n=36) and Halosperm (n=31), to assess the DFI values obtained, the correlations between tests, the technical repeatability, and the impact of DFI on the choice of ART. Results: We obtained higher median DFI values using SCD kits than when using SCSA, and this difference was significant for the CANfrag kit (p<0.001). The SCD kits had significantly higher coefficients of variation than SCSA (p<0.001). In vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) would be chosen for a significantly higher proportion of patients if a decision were made based on DFI derived from SCD rather than DFI determined using SCSA (p=0.003). Conclusion: Our results indicate that SCD kit-specific thresholds should be established in order to avoid the unnecessary use of IVF/ICSI based on sperm DNA damage for the management of infertility. Appropriate measures should be taken to mitigate the increased variability inherent to the methods used in these tests.