Comprehensive understanding of mechanisms of epigenetic regulation requires identification of molecules bound to genomic regions of interest in vivo. We have developed a novel method, insertional chromatin immunopreci...Comprehensive understanding of mechanisms of epigenetic regulation requires identification of molecules bound to genomic regions of interest in vivo. We have developed a novel method, insertional chromatin immunoprecipitatin (iChIP), to isolate specific genomic regions retaining molecular interaction in order to perform non-biased identification of interacting molecules in vivo. Here, we developed a second-generation tagged LexA DNA-binding domain, 3xFNLDD, for the iChIP analysis. 3xFNLDD consists of 3 x FLAG tags, a nuclear localization signal (NLS), the DNA-binding domain (DB) and the dimerization domain of the LexA protein. Expression of 3xFNLDD can be detected by immunoblot analysis as well as flowcytometry. We showed that iChIP using 3xFNLDD is able to consistently isolate more than 10% of input genomic DNA, several-fold more efficient compared to the first-generation tagged LexA DB. 3xFNLDD would be a useful tool to perform the iChIP analysis for locus-specific biochemical epigenetics.展开更多
Plants use a sophisticated immune system to perceive pathogen infection and activate immune responses in a tightly controlled manner.In barley,Hv WRKY2 acts as a repressor in barley disease resistance to the powdery m...Plants use a sophisticated immune system to perceive pathogen infection and activate immune responses in a tightly controlled manner.In barley,Hv WRKY2 acts as a repressor in barley disease resistance to the powdery mildew fungus,Blumeria graminis f.sp.hordei(Bgh).However,the molecular features of Hv WRKY2 in its DNA-binding and repressor functions,as well as its target genes,are uncharacterized.We show that the W-box binding of Hv WRKY2 requires an intact WRKY domain and an upstream sequence of~75 amino acids,and the Hv WRKY2 W-box binding activity is linked to its repressor function in disease resistance.Chromatin immunoprecipitation(ChIP)-seq analysis identified HvCEBiP,a putative chitin receptor gene,as a target gene of Hv WRKY2 in overexpressing transgenic barley plants.ChIP-qPCR and Electrophoretic Mobility Shift Assay(EMSA)verified the direct binding of Hv WRKY2 to a W-boxcontaining sequence in the HvCEBiP promoter.Hv CEBiP positively regulates resistance against Bgh in barley.Our findings suggest that Hv WRKY2 represses barley basal immunity by directly targeting pathogen-associated molecular pattern(PAMP)recognition receptor genes,suggesting that Hv CEBiP and likely chitin signaling function in barley PAMP-triggered immune responses to Bgh infection.展开更多
The multifunctional protein p100 is a vital transcriptional regulator that increases gene transcription by forming a physical bridge between promoter-specific transcription factors and the basal transcription machiner...The multifunctional protein p100 is a vital transcriptional regulator that increases gene transcription by forming a physical bridge between promoter-specific transcription factors and the basal transcription machinery.To identify potential signal transduction pathways in which human p100 acts as a coregulator and to find target promoter regions that may interact with p100,we performed a promoter microarray assay called chromatin immunoprecipitation-guided ligation and selection(ChIP-GLAS).From this assay,we determined that a set of promoter fragments,including several factors in the transforming growth factor beta(TGF-β)signaling pathway,exhibited interaction with p100.The ChIP-GLAS data were validated by RT-PCR assessing the mRNA expression of various factors in the TGF-b signaling pathway in cell lines.展开更多
人Elp3(human elongator protein 3,hElp3)具有组蛋白乙酰转移酶活性,是与延伸中的RNA聚合酶Ⅱ结合的elongator复合物的催化亚基,可参与组蛋白的乙酰化修饰与基因的转录延伸.Elp3及其复合物功能异常与人类多种疾病相关.为运用染色质免...人Elp3(human elongator protein 3,hElp3)具有组蛋白乙酰转移酶活性,是与延伸中的RNA聚合酶Ⅱ结合的elongator复合物的催化亚基,可参与组蛋白的乙酰化修饰与基因的转录延伸.Elp3及其复合物功能异常与人类多种疾病相关.为运用染色质免疫沉淀等手段深入研究Elp3功能,PCR法克隆pYES2-hElp3质粒中编码hElp3的N端亲水区段(1～69氨基酸残基),构建原核表达载体pMXB10-hElp3-210,经IPTG诱导和几丁质柱纯化后,免疫兔制备多克隆抗体.ELISA检测显示,该抗体有较高的效价(不低于1∶2 500).免疫印迹实验结果表明,该抗体可与纯化的及HeLa细胞中的hElp3蛋白特异性结合.运用该抗体对转入elp3Δ菌株的人Elp3的染色质免疫沉淀实验结果表明,人Elp3可参与酵母SSA3基因的转录调控,这可能是人Elp3能够部分补偿酵母SSA3基因延迟表达缺陷的原因.展开更多
目的探讨骨髓间充质干细胞(BMSCs)在平滑肌微环境中发生分化后平滑肌标志性基因乙酰化水平的变化,以及组蛋白乙酰化修饰在干细胞分化中的作用及机制。方法体外培养BMSCs和膀胱平滑肌细胞(BSMCs),选择同批次的第3代BMSCs,将与BSMCs共培...目的探讨骨髓间充质干细胞(BMSCs)在平滑肌微环境中发生分化后平滑肌标志性基因乙酰化水平的变化,以及组蛋白乙酰化修饰在干细胞分化中的作用及机制。方法体外培养BMSCs和膀胱平滑肌细胞(BSMCs),选择同批次的第3代BMSCs,将与BSMCs共培养3d的BMSCs作为实验组,未经共培养的BMSCs作为对照组,采用RT-PCR检测两组BMSCs中平滑肌α肌动蛋白(α-SMA)、钙调节蛋白(calponin)、平滑肌肌球蛋白重链(SM-MHC)的表达丰度。采用条件为80%、20次、0.5 s、8个循环的超声破碎实验组及对照组BMSCs的DNA,以H3K9抗体结合特定乙酰化位点,采用免疫共沉淀技术(ChIP)沉淀BMSCs组蛋白乙酰化位点基因,接头PCR扩增所获基因,Real-time PCR检测所获基因中3种目的基因(α-SMA、Calponin、SM-MHC)的表达水平。结果 RT-PCR检测结果显示,实验组BMSCs中的平滑肌标志性基因(α-SMA、Calponin、SM-MHC)的mRNA表达水平较对照组明显增高[分别为0.176±0.003 vs. 0.070±0.002,0.079±0.002vs.0.051±0.003,0.091±0.004vs.0.034±0.001],差异均有统计学意义(P<0.01)。分光光度计检测ChIP后获得的DNA,结果表明H3K9乙酰化抗体沉淀所获DNA浓度高于Ig G抗体,且实验组高于对照组(P<0.05)。RealtimePCR分析BMSCs分化前后目的基因组蛋白H3K9乙酰化水平,结果显示,BMSCs分化后,实验组的平滑肌标志性基因α-SMA、calponin、SM-MHC的mRNA转录水平明显高于对照组[分别为9.26±5.03 vs. 1.01±0.05,2.33±0.65 vs.0.99±0.05,2.63±0.37vs.1.00±0.03],差异均有统计学意义(P>0.05)。结论在平滑肌微环境中,BSMCs特定位点H3K9乙酰化程度的增加可促进BMSCs向BSMCs的分化。展开更多
文摘Comprehensive understanding of mechanisms of epigenetic regulation requires identification of molecules bound to genomic regions of interest in vivo. We have developed a novel method, insertional chromatin immunoprecipitatin (iChIP), to isolate specific genomic regions retaining molecular interaction in order to perform non-biased identification of interacting molecules in vivo. Here, we developed a second-generation tagged LexA DNA-binding domain, 3xFNLDD, for the iChIP analysis. 3xFNLDD consists of 3 x FLAG tags, a nuclear localization signal (NLS), the DNA-binding domain (DB) and the dimerization domain of the LexA protein. Expression of 3xFNLDD can be detected by immunoblot analysis as well as flowcytometry. We showed that iChIP using 3xFNLDD is able to consistently isolate more than 10% of input genomic DNA, several-fold more efficient compared to the first-generation tagged LexA DB. 3xFNLDD would be a useful tool to perform the iChIP analysis for locus-specific biochemical epigenetics.
基金supported by National Key Research and Development Program of China(2018YFD1000703,2018YFD1000700)Strategic Priority Research Program of the Chinese Academy of Sciences(XDB11020400)+3 种基金National Program on Research and Development of Transgenic Plants(2016ZX08009-003-001)Startup Fund for Advanced Talents of Lushan Botanical GardenChinese Academy of Science(2020ZWZX03 and 2020ZWZX05)the“Double Hundred and Double Thousand”Talent Project of Jiujiang City(jjsbsq2020026)。
文摘Plants use a sophisticated immune system to perceive pathogen infection and activate immune responses in a tightly controlled manner.In barley,Hv WRKY2 acts as a repressor in barley disease resistance to the powdery mildew fungus,Blumeria graminis f.sp.hordei(Bgh).However,the molecular features of Hv WRKY2 in its DNA-binding and repressor functions,as well as its target genes,are uncharacterized.We show that the W-box binding of Hv WRKY2 requires an intact WRKY domain and an upstream sequence of~75 amino acids,and the Hv WRKY2 W-box binding activity is linked to its repressor function in disease resistance.Chromatin immunoprecipitation(ChIP)-seq analysis identified HvCEBiP,a putative chitin receptor gene,as a target gene of Hv WRKY2 in overexpressing transgenic barley plants.ChIP-qPCR and Electrophoretic Mobility Shift Assay(EMSA)verified the direct binding of Hv WRKY2 to a W-boxcontaining sequence in the HvCEBiP promoter.Hv CEBiP positively regulates resistance against Bgh in barley.Our findings suggest that Hv WRKY2 represses barley basal immunity by directly targeting pathogen-associated molecular pattern(PAMP)recognition receptor genes,suggesting that Hv CEBiP and likely chitin signaling function in barley PAMP-triggered immune responses to Bgh infection.
基金This work was supported by grants from the National Basic Research Program(973 Program,2009CB918903)863 Project of the Ministry of Science and Technology of China(2007AA02Z115)+3 种基金NSFC(90919032,30970562,30670441,30811130394 and 30870562)Tianjin Municipal Science and Technology Commission(08ZCGHHZ01900 and 08JCYBJC07700)Specialized Fund for the Doctoral Program of Higher Education(20091202110001)Tianjin Educational Committee Foundation(2008ZD01).
文摘The multifunctional protein p100 is a vital transcriptional regulator that increases gene transcription by forming a physical bridge between promoter-specific transcription factors and the basal transcription machinery.To identify potential signal transduction pathways in which human p100 acts as a coregulator and to find target promoter regions that may interact with p100,we performed a promoter microarray assay called chromatin immunoprecipitation-guided ligation and selection(ChIP-GLAS).From this assay,we determined that a set of promoter fragments,including several factors in the transforming growth factor beta(TGF-β)signaling pathway,exhibited interaction with p100.The ChIP-GLAS data were validated by RT-PCR assessing the mRNA expression of various factors in the TGF-b signaling pathway in cell lines.
文摘人Elp3(human elongator protein 3,hElp3)具有组蛋白乙酰转移酶活性,是与延伸中的RNA聚合酶Ⅱ结合的elongator复合物的催化亚基,可参与组蛋白的乙酰化修饰与基因的转录延伸.Elp3及其复合物功能异常与人类多种疾病相关.为运用染色质免疫沉淀等手段深入研究Elp3功能,PCR法克隆pYES2-hElp3质粒中编码hElp3的N端亲水区段(1～69氨基酸残基),构建原核表达载体pMXB10-hElp3-210,经IPTG诱导和几丁质柱纯化后,免疫兔制备多克隆抗体.ELISA检测显示,该抗体有较高的效价(不低于1∶2 500).免疫印迹实验结果表明,该抗体可与纯化的及HeLa细胞中的hElp3蛋白特异性结合.运用该抗体对转入elp3Δ菌株的人Elp3的染色质免疫沉淀实验结果表明,人Elp3可参与酵母SSA3基因的转录调控,这可能是人Elp3能够部分补偿酵母SSA3基因延迟表达缺陷的原因.
文摘目的探讨骨髓间充质干细胞(BMSCs)在平滑肌微环境中发生分化后平滑肌标志性基因乙酰化水平的变化,以及组蛋白乙酰化修饰在干细胞分化中的作用及机制。方法体外培养BMSCs和膀胱平滑肌细胞(BSMCs),选择同批次的第3代BMSCs,将与BSMCs共培养3d的BMSCs作为实验组,未经共培养的BMSCs作为对照组,采用RT-PCR检测两组BMSCs中平滑肌α肌动蛋白(α-SMA)、钙调节蛋白(calponin)、平滑肌肌球蛋白重链(SM-MHC)的表达丰度。采用条件为80%、20次、0.5 s、8个循环的超声破碎实验组及对照组BMSCs的DNA,以H3K9抗体结合特定乙酰化位点,采用免疫共沉淀技术(ChIP)沉淀BMSCs组蛋白乙酰化位点基因,接头PCR扩增所获基因,Real-time PCR检测所获基因中3种目的基因(α-SMA、Calponin、SM-MHC)的表达水平。结果 RT-PCR检测结果显示,实验组BMSCs中的平滑肌标志性基因(α-SMA、Calponin、SM-MHC)的mRNA表达水平较对照组明显增高[分别为0.176±0.003 vs. 0.070±0.002,0.079±0.002vs.0.051±0.003,0.091±0.004vs.0.034±0.001],差异均有统计学意义(P<0.01)。分光光度计检测ChIP后获得的DNA,结果表明H3K9乙酰化抗体沉淀所获DNA浓度高于Ig G抗体,且实验组高于对照组(P<0.05)。RealtimePCR分析BMSCs分化前后目的基因组蛋白H3K9乙酰化水平,结果显示,BMSCs分化后,实验组的平滑肌标志性基因α-SMA、calponin、SM-MHC的mRNA转录水平明显高于对照组[分别为9.26±5.03 vs. 1.01±0.05,2.33±0.65 vs.0.99±0.05,2.63±0.37vs.1.00±0.03],差异均有统计学意义(P>0.05)。结论在平滑肌微环境中,BSMCs特定位点H3K9乙酰化程度的增加可促进BMSCs向BSMCs的分化。
