Correlation of gene modification between histone H3 lysine 4 trimethylation and DNA methylation in IgA nephropathy patients

AIM: To investigate the correlation of gene modification between histone H3 lysine 4 (H3K4) trimethylation and DNA methylation in IgA nephropathy patients. METHODS: H3K4 trimethylation variations were analyzed in peripheral blood mononuclear cells (PBMCs) from 40 IgAN patients and 40 healthy controls by the method of chromatin immunoprecipitation linked to microarrays (ChIP-chip). ChIP real-time PCR was used to validate the microarray results. Quantitative real-time PCR (qRT-PCR) was employed to analyze mRNA expression. DNA methylation in 4 selected positive genes was analyzed by the method of methylated DNA immunoprecipitation-quantitative PCR (MeDIP-qPCR). RESULTS: IgAN patients displayed higher H3K4 trimethylation level and lower DNA methylation level than those of the healthy controls. There were significant differences in DNA methylation and H3K4 trimethylation of 4 selected genes between IgAN patients and the healthy controls (P<0.05). CONCLUSION: Our studies indicate that significant alterations of H3K4 trimethylation and DNA methylation exist in IgAN patients. There is a correlation of gene modification between DNA mathylation and histone H3 lysine 4 trimethylation in IgAN patients.     

Advances in modulation of microRNA and DNA methylation in congenital heart diseases

Aberrations in microRNA (miRNA) expression and DNA methylation are causal factors for congenital heart diseases (CHD), which belongs to epigenetic mechanisms. Complex modulation of miRNA on DNA methylation is a critical regulator of gene expression, leading to disease development. The aim of this review is to provide recent progress in the regulation of miRNA and DNA methylation in CHD.     

Progress of embryonic stem cells during directional differentiation regulated by epigenetic modification

Embryonic stem cells undergo extensive self-renewal and have the capacity to differentiate along multiple cell lineages. Research on totipotency and directional differentiation of embryonic stem cells in order to treat intractable disease, such as cancer, heart failure, atherosclerosis by tissue regeneration and cell transplantation are investigated. Epigenetic modification, including DNA methylation, chromatin restructure, and non-coding RNA-mediated regulatory events, regulate the differentiation of embryonic stem cells without detectable genetic changes. These mechanisms are often associated with starting-up and maintenance of epigenetic silence. The achievement and focuses on the molecular mechanism of embryonic stem cells during directional differentiation regulated by epigenetic modification are reviewed.     

被子植物开花时间和花器官发育的表观遗传调控研究进展

成花转换是被子植物生活周期中的关键发育过程,植物通过调控基因表达模式而整合多条内外开花信号实现成花诱导。近几十年来,学者们为阐释植物成花转换的分子机制做了大量的分子遗传学研究。其中,影响植物生长发育的表观遗传修饰是调控成花转换过程的重要分子机制之一。表观遗传调控是植物在适宜环境条件下实现开花诱导和花器官发育的决定性因素。综述了有关开花时间和花器官发育的表观遗传学研究进展,包括染色质重塑、组蛋白甲基化和miRNAs。     

表观遗传与花期调控研究进展

 目前,关于高等植物成花机理的研究已经取得突破性进展,对表观遗传的研究也越来越深入,而将两者联系起来调控花期的研究虽然还处于初步探索阶段,但已取得了一定的理论成果。本文总结了常见的表观遗传（DNA 甲基化、组蛋白修饰、非编码RNA、染色质重塑）在不同开花诱导途径中调控花期的研究进展,为通过表观遗传途径调控花期技术研究提供参考。     

Histone acetylation and methylation modification of topoisomerase Ⅱα promoter regulatory factor Sp1 in patients with chronic benzene poisoning

AIM: To investigate the histone modification changes of topoisomerase Ⅱα(TOPOⅡα) promoter regulatory factor Sp1 in the patients with chronic benzene poisoning.METHODS: The bone marrow samples were collected from 25 chronic benzene poisoning cases and 25 controls. The chromatin immunoprecipitation assay was carried out to study the possible mechanism of TOPOⅡα promoter regulatory factor Sp1 expression changes. The mRNA expression of Sp1 was detected by RT-PCR.RESULTS: Compared with the controls, the histone H4 acetylation and histone H3 acetylation of Sp1 in the chronic benzene poisoning patients significantly decreased(P<0.01), and histone H3K9 methylation level of Sp1 increased(P<0.01), but the histone H3K4 methylation level of SP1 was not obviously changed(P>0.05). The mRNA expression of Sp1 in the chronic benzene poisoning patients was significantly lower than that in the controls(P<0.05).CONCLUSION: In chronic benzene poisoning patients, the histone acetylation and methylation modification changes of TOPO Ⅱα promoter regulatory factor Sp1 accompanied with the changes of mRNA level are observed. Histone H4 and H3 acetylation and H3K9 methylation modification of Sp1 may play an important role in the benzene,s hematopoietic toxicities.     

抽薹开花抑制因子FLC 表观遗传调控研究进展

FLOWERING LOCUS C（FLC）是植物抽薹开花调控网络中关键的开花决定因子。随着表观遗传学的发展，人们发现组蛋白修饰等表观调控FLC 的表达在植物抽薹开花时间调控中起着非常重要的作用。FLC 的抑制因子或促进因子通过改变组蛋白氨基酸的共价修饰（如乙酰化、甲基化等），影响FLC基因所在区域的染色质重塑，调控FLC 转录表达水平，从而调节植物抽薹开花。本文就近年来国内外对植物抽薹开花关键调控基因FLC 及表观遗传调控其表达研究现状进行了综述，并针对目前研究中存在的问题提出了今后的研究方向和重点。     

Proteomics analysis of acetylated protein in clear cell renal cell carcinoma

AIM To comprehensively analyze clear cell renal cell carcinoma （ccRCC）-associated acetylated proteins, acetylation sites and differentially expressed proteins （DEPs）, and to identify potential molecular markers and therapeutic targets for clinical application. METHODS The open search strategy was applied to re-analyze the mass spectrometric data of ccRCC clinical tissue samples including 8 pairs of cancer and paracancerous tissues. Mass spectrometric data of ccRCC containing 8 pairs of cancer and paracancerous tissues were downloaded from ProteomeXchange proteomics database, and subjected to database searching for the identification of acetylated proteins and acetylation sites. The DEPs were analyzed by power law global error model （PLGEM） algorithm and uploaded to cluster analysis, GO enrichment and KEGG pathway analysis. The expression of acetylated proteins was verified by Western blot using specific lysine acetylation antibody. RESULTS A total of 464 DEPs were identified by non-labeled quantitative proteomics, including 104 up-regulated and 360 down-regulated proteins. The GO enrichment and KEGG pathway analysis showed that the up-regulated proteins were mainly involved in the processes of vasoconstriction, complement and coagulation cascade system, and platelet activation. More importantly, a total of 503 acetylated proteins including 1 397 acetylation sites were identified. We found that the protein acetylation level in ccRCC was significantly down-regulated as compared with paracancerous tissues, which was verified by Western blot analysis. We also found that the acetylation levels of glutathione S-transferase kappa 1 （GSTK1） at sites K158, K163 and K165 were decreased in ccRCC as compared with paracancerous tissues. CONCLUSION The proteins involved in complement and coagulation cascade, vasoconstriction and platelet activation may play an important role in ccRCC malignant progression. The total acetylation level was significantly decreased in ccRCC tissues, suggesting an overall suppression of acetylation in renal cancer. Deacetylation of GSTK1 is likely a key molecular event in the renal malignant progression and a potential clinical biomarker.     

RNA methylation modifications in hepatocellular carcinoma

Epigenetics studies how cells affect the genome and produce related phenotypes without involving changes in nuclear DNA sequences. The main manifestation is that different types of genetic material are modified. These dynamic modifications affect gene expression and play an important regulatory role in the development of a variety of disea-ses, particularly tumors. In recent years, epigenetic modification has more and more new insights in the field of hepatocel-lular carcinoma. RNA methylation and DNA methylation are closely related to the pathogenesis of hepatocellular carcinoma and malignant transformation. This review aims to introduce the latest research advances in various RNA methylation modi-fications in the field of hepatocellular carcinoma. The different types of RNA methylation as the main line to introduce their research details in hepatocellular carcinoma provide new insights and ideas for the research and treatment of hepatocellular carcinoma.     

Promoter methylation status and demethylation-induced expression of SFRP genes in human acute leukemia cell lines

AIM: To investigate the relationship between promoter hypermethylation of secreted frizzled-related protein (SFRP) genes and acute leukemia (AL)，and to study the mechanism how 5-aza-2-deoxycytidine (5-Aza-CdR) reverses the hypermethylation of SFRP genes in human AL cell lines. METHODS：Methylation-specific PCR (MSP) was used to detect the methylation levels of SFRP1, SFRP2, SFRP4 and SFRP5 genes in different human AL cell lines (Molt-4, Jurkat, HL-60 and NB4). The methylation levels of these genes in Jurkat cell line before and after 5-Aza-CdR treatment were also analyzed by MSP. The expression of SFRP1, SFRP2, SFRP4 and SFRP5 mRNA was detected by real-time fluorescence quantitative RT-PCR. The mRNA levels of DNA methyltransferase (DNMT) 1, DNMT3A and DNMT3B were analyzed by semiquantitative RT-PCR. RESULTS：None of normal human blood or bone marrow mononuclear cells showed methylation of SFRP genes. Hypermethylation in the promoter regions of SFRP1, SFRP2 and SFRP5 genes was observed in all of the four AL cell lines. SFRP4 gene was totally methylated in NB4, Molt-4 and Jurkat cell lines but partially methylated in HL60 cell line. Treatment with 5-Aza-CdR for 72 h successfully reversed the hypermethylation of SFRP genes, and significantly increased the mRNA expression of SFRP. Moreover, the mRNA expression of DNMT1, DNMT3A and DNMT3B was down-regulated by 5-Aza-CdR in a concentration-dependent manner. CONCLUSION：Methylated SFRP genes may serve as potential independent biomarkers for early detection of AL. 5-Aza-CdR activates SFRP gene expression by demethylation of SFRP genes and down-regulation of DNMT1, DNMT3A and DNMT3B mRNA expression.     

虎奶菇菌丝体和菌核基因组甲基化分析

以虎奶菇[Pleurotus tuber-regium (Fr.) Singer]菌丝体和菌核为材料,利用MSAP技术分析其甲基化水平,并对甲基化差异片段进行回收测序,探究虎奶菇生长与DNA全基因组甲基化的关系.结果 表明,菌丝体和菌核的DNA甲基化率分别为7.94％和9.54％,其中半甲基化率分别为4.50％和4.0...     

利用酶联免疫反应鉴定芜菁SP11基因甲基化率的新方法

DNA甲基化是调控基因表达的一个重要方式,是表观遗传学研究的重点内容。目前测定某一基因DNA甲基化程度主要是先通过重亚硫酸盐转化,PCR扩增,再通过克隆、测序,检测PCR产物中胞嘧啶(C)转化为胸腺嘧啶(T)的比例。基于这种原理,建立了酶联免疫反应检测PCR产物中胞嘧啶转化为胸腺嘧啶的比例,计算出DNA甲基化率的新方法,并成功利用该方法测定了芜青(Brassica rapa L.ssp.rapiferu Metzg)纯合子和杂合子植株中隐性SP11基因启动子区域DNA甲基化程度。与原有克隆测序方法相比,该方法更加经济、省时。     

森林草莓6mA甲基转移酶基因鉴定及功能分析

通过生物信息学手段，鉴定出森林草莓（Fragaria vesca）基因组中两类可能的6mA甲基转移酶基因5个（3个MT-A70、2个DAMT基因）。对细菌、真菌、动物和植物中的6mA甲基转移酶基因的系统进化分析及染色体定位表明，森林草莓MT-A70基因可分为3个亚家族，且在动、植物分化前就已经存在：两个DAMT基因由物种特异的串联重复产生，且结构变化快，推测其在进化历程中功能发生了分化。转录组数据及实时定量荧光PCR分析显示，各个基因均具有时空表达特异性和非生物胁迫响应。其中1个DAMT基因表达量在果实中较高且随果实成熟上调，推测可能参与调控果实成熟。此外，这5个基因在冷胁迫下表达水平有不同程度下调：而在热胁迫下各基因表达量变化显著不同。由此推测6mA甲基转移酶基因可能参与了森林草莓的生长发育和对冷、热胁迫的响应。     

龙眼染色质重塑因子Snf2基因家族的进化动力学研究及在体胚发生早期的表达

以龙眼(Dimocarpus longan Lour.)'红核子'品种早期体细胞胚胎发生的胚性愈伤组织(embryogenic callus,EC)、不完全胚性紧实结构(incomplete embryogenic compact structures,ICpEC)和球形胚(globular embryos,GE)为材...     

Genome-wide DNA methylation of palate embryonic tissue in process of embryonic mouse cleft palate formation

AIM:To analyze genome-wide DNA differential methylation site-related genes and genomic diffe-rential methylation levels involved in embryonic mouse cleft palate formation. METHODS:MethylRAD-Seq was performed on the gestational day 13.5 (GD13.5), GD14.5 and GD16.5 in experimental group and control group, which is a method for genome-wide DNA methylation profiling using methylation-dependent restriction enzymes. A comparison was made to process the different location of the methylation site and the methylation level differential genes among genome-wide different functional components (3'-untranslated region, 5'-untranslated region, TSS2000, intron, exon, and intergenic region). The genome-wide DNA differential methylation site-related genes and methylation differential genes were analyzed using GO function enrichment and KEGG pathway enrichment. RESULTS:(1) The peak number and peak value of methylation sites in different components of DNA did not change significantly in the control group, and the methylation level of the experimental group decreased gradually over time. (2) GO function enrichment analysis and KEGG pathway enrichment ana-lysis were performed to process methylation level differential genes and genome-wide DNA differential methylation site-rela-ted genes, among which there were 6 genes (Fgf16, Jarid2, Kdm6a, Nr3c1, Tbx22 and Trp53) involved in embryonic mouse cleft palate formation. (3) MAPK, Wnt, TGF-β and other signaling pathways were found to participate in the formation of cleft palate. CONCLUSION:DNA methylation plays an important regulatory role in the process of cleft palate formation.     

Analysis of different methylation patterns of histone H3 between androgen-dependent and androgen-independent prostate cancer cells by heavy methyl SILAC

AIM：To study the epigenetic mechanisms involved in the evolution of prostate cancer from an androgen-dependent state to an androgen-independent state, and the global difference of histone H3 methylation between androgen-dependent and -independent prostate cancer cells. METHODS：The methylation sites and patterns of histone H3 in androgen-dependent prostate cancer cell line LNCaP and androgen-independent prostate cancer cell line DU145 were analyzed by heavy methyl stable isotope labeling with amino acids in cell culture (SILAC) coupled with 2D LC-MS/MS. Western blotting was used to verify the results from MS. The differential expression of related methylases and demethylases was tested by real-time PCR. RESULTS：Five methylation sites on histone H3 were found in both cell lines, the patterns of which were as follows: H3K14me2, H3R17me1, H3K36me1, H3K36me2, H3K36me3, H3R72me2, H3K79me1 and H3K79me2. There were 2 different peptides both containing methylated H3K36, “KSAPATGGVKKPHR” and “KSAPSTGGVKKPHR”, which were different from the 31th amino acid residue “A” and “S”. The former peptide belonging to histone H3 variants, H31T, H31 and H32, was mainly identified in DU145 cells, the total peptide counts of which were much more than that of the latter peptide belonging to histone H3 variant H31T, suggesting that these 2 cell lines expressed different histone H3 variants. Mono- and dimethylation of H3K36 were not different between these 2 cell lines, but the trimethylation was significantly higher in DU145 cells than that in LNCaP cells. Many H3K36 demethyltransferases were decreased in DU145 cells compared with LNCaP cells. CONCLUSION：The differential expression of histone H3 variants and H3K36 demethyltransferases may result in up-regulation of H3K36 tri-methylation during the evolution of prostate cancer from an androgen-dependent state to an androgen-independent state.     

Association between methylation status of apoptosis-related genes and chemosensitivity of lung adenocarcinoma cell line P15

AIM: To investigate the association between methylation status of apoptosis-related genes and chemosensitivity in the lung adenocarcinoma cell line P15.METHODS: Methylation-specific PCR was applied to detect the methylation status of p73, p14^ARF, p16^INK4a and bax genes of P15 cells in untreated control group and decitabine (DAC) treatment group. RT-PCR was used to detect the expression of p73, bcl-xL, bad, bax, p14^ARF and p16^INK4a at mRNA level. Colony formation assay and cell growth inhibition assay were used to detect the sensitivity of P15 cells to cis-diaminedichloroplatinum (C-DDP) before and after DAC treatment. DAPI staining was used to determine the apoptosis of P15 cells exposed to C-DDP before and after DAC treatment. RESULTS: p73, p16^INK4a and bax were expressed in the methylation status. After DAC treatment, p16^INK4a expression was decreased, and the expression of p73 and bax disappeared. The expression of p73, p16^INK4a and bax in the unmethylated status was weak, but the enhanced expression was observed following DAC treatment. After P15 cells were treated with DAC and C-DDP, the colony formation rate of the P15 cells was significantly decreased as compared with untreated control group. The apoptotic P15 cells in DAC+C-DDP treatment group were significantly higher than those in untreated control group (P<0.05). CONCLUSION: After treated with DAC, the sensitivity of P15 cells to C-DDP is increased due to the activation of silenced pro-apoptotic genes. DAC and C-DDP synergistically promote tumor cell apoptosis. They have significant anti-tumor effect.