• Molecules and Cells
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• 제42권11호
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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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• 제10권3호
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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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• 제18권4호
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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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• 제26권2호
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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.

• 생명과학회지
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• 제25권6호
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• pp.703-708
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• 2015

Hox 유전자는 호메오도메인을 포함한 전사인자로써, 발생 과정 중 전후축을 따라 몸의 형태 형성을 조절하는 역할을 한다. 레티노산(RA)은 발생 과정에서 필수적인 형태형성인자이며 세포의 특성을 결정하는데 중요한 조절자이다. 특히, RA는 생쥐나 인간으로부터 만들어진 배아암종(EC)세포에서 Hox 유전자의 발현을 조절한다고 밝혀져 있다. 또한 RA에 의한 세포 분화와 유전자 조절 과정에 히스톤 변이가 중요한 역할을 하는 것으로 보고되어 있다. 히스톤 변이가 RA에 의해 유도되는 Hox 유전자의 발현에 특이적인 역할을 할 것으로 유추되기 때문에, 이 연구의 목적은 F9 생쥐배아 기형암종세포에서 RA에 의해 유도되는 Hoxc 유전자의 순차적인 발현이 히스톤 변이에 의해 일어나는 것인지를 조사하는 것이다. Hox 유전자의 발현 양상과 히스톤 변이는 semi-quantitative RT-PCR, RNA-sequencing과 chromatin immuno-precipitation (ChIP)-PCR 기법을 이용하여 관찰하였다. RA 처리 후(0일(D0), 1일(D1), 3일(D3)), Hoxc4 유전자의 발현(D1)은 Hoxc5부터 –c10 유전자(D3)보다 먼저 시작되었다. Hox가 발현하지 않는 D0 샘플은 전사 억제 마커인 H3K27me3이 모든 Hoxc 좌위에 강하게 표지 되어 있었으나 D1과 D3 샘플에서는 모든 좌위의 H3K27me3 표지가 확연히 줄어들어 있었다. 전사 발현 마커인 H3K4me3가 Hoxc 유전자의 순차적인 발현과 더 연관성이 있는 것으로 보이는데 D1에서 Hoxc4 발현과 함께 H3K4me3이 표지 되어 있었고, D3에서는 Hoxc 유전자 발현과 함께 모든 좌위에서 H3K4me3 마커가 존재했기 때문이다. 모든 결과를 종합해 보았을 때 F9 세포에서 RA에 의해 유도된 Hoxc 유전자의 순차적인 발현은 Hoxc 좌위에서 H3K27me3가 사라지고, H3K4me3가 표지 되는 히스톤 메틸화의 변이에 의해 결정되는 것으로 사료된다.

• Asian Pacific Journal of Cancer Prevention
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• 제13권7호
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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.

• 한국토양비료학회지
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• 제22권4호
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• pp.271-279
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• 1989

토양환경(土壤環境) 개량(改良)의 기초자료(基礎資料)인 토양(土壤)의 입경분포(粒徑分布) 및 몇가지 화학성(化學性)에 대(對)한 대표(代表)값을 지형별(地形別)(용암류태지(熔岩流台地) 제외(除外))로 파악(把握)하기 위하여 5,216개(個)(답(畓)3.075 그리고 전(田)2,140)의 시(市) 군(郡) 대표토양(代表土壤) 분석치(分析値)를 이용(利用) 전산(電算)처리하였다. 1. 논토양(土壤) 표토(表土)에서 대표(代表)값은 점토(粘土) 20.4%, pH 5.8, 유기물(有機物) 2.6%, CEC 10.4me/100g, 치환성(置換性) K 0.26me/100g 그리고 유효린산(有效燐酸) 89ppm이었다. 밭토양(土壤)에선 각각(各各) 17.3%, 5.5, 1.8% 9.1, 0.29me/100g 그리고 103ppm이었다. 2. 토양특성(土壤特性)은 지형(地形)에 따라 큰 차리(差異)를 나타내었다. 논토양(土壤) 표토(表土)에서 하해혼성평탄지(河海混成平坦地)는 점토(粘土) 21.4%, pH 6.0, 유기물(有機物) 2.2%, CEC 10.8me/100g, 치환성(置換性) K 0.39me/100g 그리고 유효인산(有效燐酸) 57ppm, 하성평탄지(河成平坦地)는 각각(各各) 15.3%, 5.7, 2.0%, 8.6me/100g, 0.17me/100g 그리고 76ppm, 곡간(谷間).선상지(扇狀地)는 각각(各各) 18.8%, 5.9, 2.7%, 10.4me/100g, 0.19me/100g 그리고 80ppm, 홍적태지(洪積台地)는 각각(各各) 20.0%, 5.7, 2.5%, 11.5me/100g, 10.26me/100g 그리고 91ppm, 산록경사지(山麓傾斜地)는 각각(各各) 21.5%, 5.7, 3.4%, 10.6me/100g, 10.27me/100g 그리고 141ppm이었다. 3. 밭토양(土壤) 표토(表土)의 경우(境遇) 하해혼성평탄지(河海混成坪坦地)는 점토(粘土) 5.5%, pH 5.7, 유기물(有機物) 1.1%, CEC 4.7me/100g, 치환성(置換性) K 0.17me/100g 그리고 유효린담(有效燐談) 50ppm, 하성평탄지(河成平坦地)는 각각(各各) 10.3%, 5.5, 1.4%, 7.6me/100g, 0.26me/100g, 그리고 160ppm, 곡간선상지(谷間扇狀地)는 각각(各各) 13.9%, 5.4, 1.8%, 9.3me/100g, 0.34me/100g 그리고 184ppm, 홍적태지(洪積台地)는 각각(各各) 29.87%, 5.3, 2.1%, 11.2me/100g, 0.40me/100g 그리고 58ppm, 산록경사지(山麓傾斜地)는 각각(各各) 20.0%, 5.7, 2.7%, 11.4me/100g, 0.32me/100g, 그리고 116ppm, 구릉지(丘陵地)는 각각(各各) 24.6%, 5.3, 1.8%, 10.2me/100g, 0.28me/100g, 그리고 51ppm 이었다. 4. 토양중(土壤中) 점토(粘土)을 제외(除外)하고는 pH, 유기물(有機物), CEC, 치환성(置換性) K 및 유효린산(有效燐酸)의 함양(含量)은 개량목표치(改良目標値)에 미달(未達)하였고 지형(地形)에 따라 큰 차리(差異)를 보였다. 5. 토양중(土壤中) 유기물(有機物), 치환성염기(置換性鹽基) 및 유효린산(有效燐酸)의 함양(含量)은 정규분포(正規分布)하지 않았으며, 토양특성(土壤特性)이 정규분포(正規分布)한다는 가정하(假定下)에 평균(平均)값의 68 및 95% 구간(區間)이 계산(計算)되었다.

• Genes and Genomics
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• 제40권12호
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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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• 제55권3호
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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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• 제26권9호
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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.