• Molecules and Cells
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• v.42 no.11
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• pp.773-782
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• 2019

Cellular senescence is an irreversible form of cell cycle arrest. Senescent cells have a unique gene expression profile that is frequently accompanied by senescence-associated heterochromatic foci (SAHFs). Protein kinase CK2 (CK2) downregulation can induce trimethylation of histone H3 Lys 9 (H3K9me3) and SAHFs formation by activating SUV39h1. Here, we present evidence that the PI3K-AKT-mTOR-reactive oxygen species-p53 pathway is necessary for CK2 downregulation-mediated H3K9me3 and SAHFs formation. CK2 downregulation promotes SUV39h1 stability by inhibiting its proteasomal degradation in a p53-dependent manner. Moreover, the dephosphorylation status of Ser 392 on p53, a possible CK2 target site, enhances the nuclear import and subsequent stabilization of SUV39h1 by inhibiting the interactions between p53, MDM2, and SUV39h1. Furthermore, $p21^{Cip1/WAF1}$ is required for CK2 downregulation-mediated H3K9me3, and dephosphorylation of Ser 392 on p53 is important for efficient transcription of $p21^{Cip1/WAF}$. Taken together, these results suggest that CK2 downregulation induces dephosphorylation of Ser 392 on p53, which subsequently increases the stability of SUV39h1 and the expression of $p21^{Cip1/WAF1}$, leading to H3K9me3 and SAHFs formation.

• 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.

• Genomics & Informatics
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• v.18 no.4
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• pp.42.1-42.9
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• 2020

Chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-Seq) is a powerful technology to profile the location of proteins of interest on a whole-genome scale. To identify the enrichment location of proteins, many programs and algorithms have been proposed. However, none of the commonly used peak calling programs could accurately explain the binding features of target proteins detected by ChIP-Seq. Here, publicly available data on 12 histone modifications, including H3K4ac/me1/me2/me3, H3K9ac/me3, H3K27ac/me3, H3K36me3, H3K56ac, and H3K79me1/me2, generated from a human embryonic stem cell line (H1), were profiled with five peak callers (CisGenome, MACS1, MACS2, PeakSeq, and SISSRs). The performance of the peak calling programs was compared in terms of reproducibility between replicates, examination of enriched regions to variable sequencing depths, the specificity-to-noise signal, and sensitivity of peak prediction. There were no major differences among peak callers when analyzing point source histone modifications. The peak calling results from histone modifications with low fidelity, such as H3K4ac, H3K56ac, and H3K79me1/me2, showed low performance in all parameters, which indicates that their peak positions might not be located accurately. Our comparative results could provide a helpful guide to choose a suitable peak calling program for specific histone modifications.

• Bulletin of the Korean Chemical Society
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• v.26 no.2
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• pp.233-237
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• 2005

Cyclopentadiene compounds, 2-[CR'R(OMe)]-1,3-Me$_2C_5H_3$ (R, R' = 2,2'-biphenyl, 2) and 2-[CR'R(OSiMe$_3$)]-1,3-Me$_2C_5H_3$ (R, R' = 2,2'-biphenyl, 3; R = ph, R' = ph, 4; R = 2-naphthyl, R' = H, 5) are readily synthesized from 2-bromo-3-methoxy-1,3-dimethylcyclopentene (1). Reaction of the cyclopentadienes with Ti(NMe$_2$)$_4$ in toluene results in clean formation of the cyclopentadienyl tris(dimethylamido)titanium complexes, which are transformed to the trichloride complexes, 2-[CR'R(OMe)]-1,3-Me$_2C_5H_2$}TiCl$_3$ (R, R' = 2,2'-biphenyl, 6) and {2-[CR'R(OSiMe$_3$)]-1,3-Me$_2C_5H_2$}TiCl$_3$ (R, R' = 2,2'-biphenyl, 7; R = ph, R' = ph, 8; R = 2-naphthyl, R' = H, 9). Attempts to form C1-bridged Cp/oxido complexes by elimination of MeCl or Me$_3$SiCl were not successful. X-ray structures of 6, 7 and an intermediate complex {2-[Ph$_2$C(OSiMe$_3$)]-1,3-Me$_2C_5H_2$}TiCl$_2$(NMe$_2$) (10) were determined.

• Journal of Life Science
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• v.25 no.6
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• pp.703-708
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• 2015

Hox genes encode a highly conserved family of homeodomain-containing transcription factors controlling vertebrate pattern formation along the anteroposterior body axis during embryogenesis. Retinoic acid (RA) is a key morphogen in embryogenesis and a critical regulator of both adult and embryonic cellular activity. Specifically, RA regulates Hox gene expression in mouse- or human-derived embryonic carcinoma (EC) cells. Histone modification has been reported to play a pivotal role in the process of RA-induced gene expression and cell differentiation. As histone modification is thought to play an essential role in RA-induced Hox gene expression, we examined RA-induced initiation of collinear expression of Hox genes and the corresponding histone modifications in F9 murine embryonic teratocarcinoma (EC) cells. Hox expression patterns and histone modifications were analyzed by semiquantitative RT-PCR, RNA-sequencing, and chromatin immuno-precipitation (ChIP)-PCR analyses. The Hoxc4 gene (D0) was initiated earlier than the Hoxc5 to –c10 genes (D3) upon RA treatment (day 0 [D0], day 1 [D1], and day 3 [D3]). The Hox nonexpressing D0 sample had a strong repressive marker, H3K27me3, than the D1 and D3 samples. In the D1 and D3 samples, reduced enrichment of the H3K27me3 marker was observed in the whole cluster. The active H3K4me3 marker was closely associated with the collinear expression of Hoxc genes. Thus, the Hoxc4 gene (D1) and all Hoxc genes (D3) expressed H3K4me3 upon transcription activation. In conclusion, these data indicated that removing H3K27me3 and acquiring H3K4me3 regulated RA-induced Hoxc gene collinearity in F9 cells.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.7
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• pp.3173-3178
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• 2012

The enhancer of zeste homolog 2 (EZH2) methyl transferase and histone 3 lysine 27 (H3K27me3) protein can repress gene transcription, and their aberrant expression has been observed in various human cancers. This study determined their expression levels in gastric cancer tissues with reference to clinicopathological features and patient survival. We collected 117 gastric cancer and corresponding normal tissues for immunohistochemistry analysis. In gastric cancers, 82/117 (70.1%) were positive for EZH2 and 66/117 (56.4%) for H3K27me3 proteins in contrast to only 5.41% and 7.25% of normal gastric mucosa specimens, respectively. Kaplan-Meier survival data showed the average overall and disease-free survival of EZH2 high expression patients was 25.2 and 20.2 months, respectively, shorter than that with EZH2 low expression (40.5 and 35.9 months). The average overall survival and disease-free survival of high H3K27me3 expression patients was 23.4 and 17.4 months, shorter than without H3K27me3 expression (37.6 and 34.5 months). The average overall survival and disease-free survival of patients with both EZH2 and H3K27me3 expression was 18.8 and 12.9 months, respectively, shorter than that with either alone (34.7 and 31.2 months) or with low levels of both (43.9 and 39.9 months). Multivariate Cox regression analysis showed that H3K27me3 and EZH2 expression, tumor size differentiation and clinical stage were all independent prognostic factors for predicting patient survival. This study demonstrated that detection of both EZH2 and H3K27me3 proteins can predict poor survival of gastric cancer patients, superior to single protein detection. In addition, H3K27me3 and EZH2 protein expression could predict lymph node metastasis.

• Korean Journal of Soil Science and Fertilizer
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• v.22 no.4
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• pp.271-279
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• 1989

Mean values representing the particle size distribution and some chemical properties for the cultivated soils were obtained from the analysis results of the typical profiles, which were described by the detailed soil maps throughout Korea. Analysis results of 5,215 soil samples (3,075 for paddy and 2,140 for upland) were available for the determination of mean values. The results are under. 1. Paddy topsoil contained 20.4% for clay, 5.8 for pH, 2.6% for organic matter, 10.4me/100g for exchangeable K, and 89ppm for available $P_2O_5$. Upland topsoil did 17.3% for clay, 5.5 for pH, 1.8% for organic matter, 9.lme/100g for CEC, 0.29me/100g for exchangeable K, and 103ppm for availabal $P_2O_5$. 2. Soil properies for paddy were markedly influenced by the reliefs. Topsoil contained 21.4% for clay, 6.0 for pH, 2.2% for organic matter, 10.8me/100g for CEC, 0.39me/100g for exchang-cable K and 57ppm for available $P_2O_5$ on the fluvio-marine plain, 15.3%, 5.7, 2.0%, 8.6me/100g, 0.17me/100g and 76ppm on the alluvial plain, 18.8%, 5.9, 2.7%, 10.4me/100g, 0.19me/100g and 80ppm on the valleys and fans, 25.0%, 5.7, 2.5%, 11.5me/100g, 0.26me/100g, 0.27me/100g and 141ppm on the moutain foot slopes, respectively. 3. Soil Properties for upland, also, were markedly influenced by the reliefs. Topsoil contained 5.5% for clay, 5.7 for pH, 1.1% for organic matter, 4.7me/100g for CEC, 0.17me/100g for exchangeable K and 50ppm for available $P_2O_5$ on the fluvio-marine plain, 10.3%, 5.5, 1.4%, 7.6me/100g, 0.26me/100g and 160ppm on the alluvial plain, 13.9%, 5.4, 1.8%, 9.3me/100g, 0.24me/100g and and 184ppm on the valleys and fans, 29.8%, 5.3, 2.1%, 11.2me/100g 0.40me/100g and 58ppm on the alluvial plain, 20.0%, 5.7, 2.7%, 11.4me/100g, 0.32me/100g and 116ppm on the mountain foot slopes, and 24.6%, 5.3, 1.8%, 10.2me/100g, 0.28me/100g and 51ppm on the rolling and Hill. 4. All chemical properties did not reach the ideal value for maximizing land capability. 5. Organic matter, exchangeable cations and available $P_2O_5$ were not normally distributed. Intervals of one and two standard deviations about mean of an approximately normal distribution were calculated.

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

• BMB Reports
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• v.55 no.3
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• pp.111-112
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• 2022

We visualized the distribution of heterochromatin in a single nucleus using plasmonic nanoparticle-conjugated H3K9me3 and H3K27me3 antibodies. Due to distance-dependent plasmonic coupling effects between nanoprobes, their scattering spectra shift to longer wavelengths as the distance between heterochromatin histone markers reduced during oncogene-induced senescence (OIS). These observations were supported by simulating scattering profiles based on considerations of particle numbers, interparticle distances, and the spatial arrangements of plasmonic nanoprobes. Using this plasmon-based colourimetric imaging, we estimated changes in distances between H3K9me3 and H3K27me3 during the formation of senescence-associated heterochromatin foci in OIS cells. We anticipate that the devised analytical technique combined with high-spatial imaging and spectral simulation will eventually lead to a new means of diagnosing and monitoring disease progression and cellular senescence.

• Bulletin of the Korean Chemical Society
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• v.26 no.9
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• pp.1359-1365
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• 2005

A series of new chiral [iminophosphoranyl]ferrocenes, {${\eta}^5-C_5H_4-(PPh_2=N-2,6-R_2-C_6H_3)$}Fe{${\eta}^5-C_5H_3-1-PPh^2-2-CH(Me)NMe_2$} (1: R = Me, $^iPr$), {${\eta}^5{-C_5H_4-(PPh_2=N-2,6-R_2}^1-C_6H_3)$}Fe{${\eta}^5-C_5H_3-1-(PPh_2=N-2,6-R_2-C_6H_3)-2-CH(Me)R_2$} (2: $R^1\;=\;Me,\;^iPr;\;R^2\;=\;NMe_2$, OMe), and $({\eta}^5-C_5H_5)Fe${${\eta}^5-C_5H_4-1-PR_2-2-CH(Me)N=PPh_3$} (3:R = Ph, $C_6H_{11}$) have been prepared from the reaction of [1,1'-diphenylphosphino-2-(N,N-dimethylamino) ethyl]ferrocene with arylazides (1 & 2) and the reaction of phosphine dichlorides ($R_3PCl_{2}$) with [1,1'-diphenylphosphino-2-aminoethyl]ferrocene (3), respectively. They form palladium complexes of the type $[Pd(C_3H_5)(L)]BF_4$ (4-6: L = 1-3), where the ligand (L) adopts an ${\eta}^2-N,N\;(2)\;or\;{\eta}^2$-P,N (3) as expected. In the case of 1, a potential terdentate, an ${\eta}^2$-P,N mode is realized with the exclusion of the –=NAr group from the coordination sphere. Complexes 4-6 were employed as catalysts for allylic alkylation of 1,3-diphenylallyl acetate leading to an almost stoichiometric product yield with modest enantiomeric excess (up to 74% ee). Rh(I)-complexes incorporating 1-3 were also prepared in situ for allylic alkylation of cinnamyl acetate as a probe for both regio- and enantioselectivities of the reaction. The reaction exhibited high regiocontrol in favor of a linear achiral isomer regardless of the ligand employed.