质谱检测叶酸缺乏人胚肾细胞中低组蛋白H3赖氨酸79甲基化修饰

目的:探讨叶酸(Folic acid,FA)缺乏在培养的人胚肾细胞(HEK-293)中对细胞组蛋白修饰水平的影响。方法:人胚肾细胞分两组培养,一组正常培养,一组无叶酸培养。细胞提取组蛋白后通过高效液相色谱一线性离子阱/静电场轨道阱高分辨质谱(HPLC-LTQ/Orbitrap Ms)检测组蛋白的修饰以比较叶酸缺乏对人胚肾细胞组蛋白修饰的影响。结果:用高分辨质谱方法成功检测到人胚肾细胞的五个组蛋白变体H1,H3,H4,H2a和H2b上的33个组蛋白修饰位点,其中23个修饰位点为uniprot数据库上已经报道的组蛋白修饰位点,而其余10个为未报道修饰位点。通过质谱比较正常和叶酸缺乏组人胚肾细胞修饰谱发现H3K79me1和H3K79me2在叶酸缺乏培养组中检出率较低。进一步用蛋白免疫印迹的方法也证明了在叶酸缺乏的人胚肾细胞中H3K79me1水平低于正常培养组。结论:细胞中叶酸缺乏影响组蛋白甲基化包括H3K79me2和H3K79me1修饰水平,提示细胞外营养因素叶酸水平可影响组蛋白修饰水平从而参与疾病如神经管畸形(Neural tube defect,NTD)的发生。     

组蛋白 H3K79同型半胱氨酸修饰位点在神经管畸形中的作用

目的:探讨人类胚胎脑组织中是否存在H3K79同型半胱氨酸修饰(H3K79Hcy)及其在神经管畸形(NTDs)中的作用。方法:通过质谱检测组蛋白H3K79是否存在同型半胱氨酸修饰位点。进一步合成包含组蛋白H3K79位点的同型半胱氨酸(Hcy)修饰的肽段,并与牛血清白蛋白(BSA)偶联后免疫兔子得到抗组蛋白H3K79Hcy多克隆抗体,并对抗体进行特异性检测;采用此抗H3K79Hcy抗体比较人类高Hcy NTDs样本和正常对照样本的H3K79Hcy水平。结果:(1)人胚胎组织组蛋白H3K79位点存在同型半胱氨酸修饰;(2)高Hcy水平NTDs脑组织中H3K79Hcy修饰水平高于正常对照(P0.05)。结论:人胚胎组织存在H3K79Hcy修饰,此修饰异常可能促进神经管畸形的发生。     

曲古抑菌素A对体外培养牛成纤维细胞组蛋白乙酰化和甲基化的影响

Trichostatin A(TSA)是一种特异的组蛋白去乙酰化酶抑制剂。研究显示,TSA可以特异地抑制组蛋白去乙酰化酶活性,提高细胞的组蛋白乙酰化水平,激活基因的表达。但是,目前还不是很清楚TSA处理是否对组蛋白甲基化产生影响。本研究以成纤维细胞为研究对象,利用免疫细胞化学技术及激光共聚焦显微镜,探讨了TSA处理体细胞对其组蛋白乙酰化及甲基化修饰的影响。结果显示,随TSA浓度增加,体细胞形态发生明显的改变,细胞变得扁平且核区较大,处理后组蛋白H4K8位点的乙酰化水平随着TSA浓度的增加明显提高。检测组蛋白H3上两个甲基化位点发现,随组蛋白乙酰化水平的增加,H3K4位点的三甲基化（H3K4me3）水平也显著提高。但是,对于H3K9的二甲基化水平（H3K9me2）则没有明显变化。以上结果显示,TSA的处理不仅可以提高体细胞的组蛋白乙酰化水平,同时也增加了与基因表达激活相关组蛋白修饰位点的甲基化水平,但是对于与沉默基因相关的组蛋白修饰位点则没有明显的影响。     

8-氯腺苷诱导的组蛋白H3K79双甲基化促进NBS1和p21的基因转录激活

组蛋白H3第79位赖氨酸甲基化（H3K79me）修饰有单甲基、双甲基及三甲基3种形式,是常染色质的标志.然而,对于组蛋白H3K79三种甲基化各自在基因转录、DNA损伤修复中所起的作用尚不十分清楚.本研究以8-氯腺苷（8-Cl-Ado）为DNA双链断裂（DNA double-stranded breaks,DSB）诱导剂,采用Western 印迹,在人肺癌细胞H1299检测出了DNA修复分子NBS1、细胞周期检验点相关分子p21,并发现H3K79me1、H3K79me2和H3K79me3三种甲基化修饰的组蛋白明显增加;染色质免疫共沉淀结合实时定量PCR实验显示,只H3K79me2与DNA损伤检验点分子p21、DNA修复分子NBS1的启动子区域相结合,说明H3K79双甲基化修饰与这些基因的转录激活有关.结果提示,在8-氯腺苷引起 DSB时,是H3K79me2、而不是H3K79me1和H3K79me3参与NBS1和p21基因转录激活时的染色质重塑.8-氯腺苷诱导H3K79双甲基化增强、促进H3K79me2所在染色质区域的NBS1和p21基因转录激活可能是8-Cl-Ado抑制肿瘤细胞生长作用机制之一.     

组蛋白修饰对胚胎干细胞分化过程[]的调控机制

选用人类胚胎干细胞系和由人类胚胎干细胞系分化来的神经干细胞系为研究对象,分析组蛋白修饰对胚胎干细胞分化过程的调控作用。得到了两种细胞系差异表达基因转录起始位点侧翼区域内八种组蛋白修饰的分布模式,以及组蛋白修饰功能簇。研究表明在两类细胞系中,八种组蛋白修饰谱分布模式一致,且呈现两种分布类型; H3K27ac,H3K4me3和H3K9ac组成的功能簇是保守的;H3K27me3,H3K36me3和H3K79me1组成的功能簇以及H3K9me3和H3K27me3组成的功能簇在胚胎干细胞向神经干细胞分化的过程中消失。结果揭示了组蛋白修饰对胚胎干细胞系向神经干细胞系分化过程的部分调控机制,为该分化过程分子调控机制的研究提供部分重要的理论基础。     

组蛋白去甲基化酶KDM5A调控H3K4me3参与神经管畸形发生的分子机制

神经管畸形(NTDs)的病因与防治是出生缺陷领域研究的重点,叶酸可以预防神经管畸形但其机制不明。本文借助低叶酸细胞模型和低叶酸NTDs小鼠模型通过染色质免疫共沉淀、Cut&Tag等技术,探讨了组蛋白去甲基化酶lysine demethylase 5A(KDM5A)及其调控的下游组蛋白H3K4me3修饰在叶酸缺乏导致的NTDs发生中的潜在分子机制。结果显示,低叶酸的细胞模型中,qRT-PCR、Western印迹结果显示,KDM5A分子表达明显下降(P<0.05)。作为组蛋白H3K4me3调控的上游关键酶,进一步通过染色质免疫共沉淀ChIP、ChIP-qPCR实验证实,叶酸缺乏下组蛋白H3K4me3在神经发育基因Axin2和Atoh1基因启动子区富集增加(P<0.05)。通过构建KDM5A基因敲除细胞模型,借助Cut&Tag试验证实,KDM5A基因敲除后H3K4me3主要富集在神经发育基因上。最后在低叶酸导致的NTDs小鼠模型的脑组织中,RT-qPCR、Western印迹以及ChIP-qPCR实验显示,E9.5 d的NTDs胎鼠脑组织中KDM5A表达下降(P&l...     

植物组蛋白赖氨酸甲基化建立过程及其遗传性研究进展

表观遗传学主要包括DNA甲基化、组蛋白修饰和非编码RNA,组蛋白甲基化作为组蛋白修饰中的一种重要修饰,在植物体的发育和环境适应中发挥着重要作用。组蛋白甲基化主要发生在赖氨酸残基上,同时根据不同的赖氨酸位点和每个赖氨酸位点甲基化程度的不同,形成了不同的赖氨酸甲基化修饰。根据对基因的不同功能,通常将组蛋白赖氨酸甲基化修饰分为2大类:(1)能够促进基因表达的,如H3K4me3和H3K36me3;(2)能够抑制基因表达的,如H3K9me2和H3K27me3。不同的组蛋白赖氨酸甲基化去甲基化过程需要相应的阅读(reader)、书写(writer)和擦除(eraser)3种蛋白。同时,组蛋白赖氨酸甲基化的遗传性质目前还不是很清楚。综述了植物中组蛋白赖氨酸甲基化建立与去除过程,以及对组蛋白赖氨酸甲基化可遗传性的探讨。     

雷公藤内酯醇对多发性骨髓瘤细胞凋亡及组蛋白H3K4甲基化的影响

目的：探讨雷公藤内酯醇（TPL）对多发性骨髓瘤RPMI8226细胞增殖、凋亡和组蛋白H3K4甲基化的影响。方法：以人多发性骨髓瘤细胞株RPMI8226为研究对象,在不同浓度（10、20、40、80、160 nmol/L） TPL中共培养不同时间（24 h、48 h、72 h）后,采用噻唑蓝（MTT）法检测细胞增殖活性;流式细胞术检测细胞凋亡和细胞周期;Western blot法检测组蛋白H3K4me2、H3K4me3的甲基化状态,实时荧光定量RT-PCR分析组蛋白甲基化酶SMYD3和组蛋白去甲基化酶LSD1的表达水平。结果：TPL对RPMI8226细胞有明显的增殖抑制作用,呈剂量和时间依赖性（P<0.05）;TPL对RPMI8226细胞有明显诱导凋亡的作用,并且随着TPL作用浓度的增加,细胞凋亡比例逐渐增加（P<0.05）;同时TPL还可以诱导RPMI8226细胞周期阻滞于G₂/M期;TPL以浓度依赖性降低组蛋白H3K4me2、H3K4me3的甲基化水平（P<0.05,P<0.01）,并抑制SMYD3和上调LSD1的表达（P<0.05）。结论：TPL可抑制RPMI8226细胞增殖、引起细胞周期阻滞于G₂/M期,并诱导其凋亡;通过抑制组蛋白甲基化酶SMYD3和增强组蛋白去甲基化酶LSD1的表达,降低组蛋白H3K4me3和H3K4me2的甲基化水平,这可能是TPL诱导多发性骨髓瘤细胞凋亡和抗肿瘤作用的机制之一。     

小鼠不同细胞间组蛋白修饰变化对MafA基因转录表达的影响

目的通过比较不同细胞类型之间MafA基因转录起始区的组蛋白修饰差异,探讨组蛋白修饰对MafA基因转录表达的作用。方法采用染色质免疫共沉淀-实时定量PCR法检测小鼠胰岛素瘤β细胞（NIT-1）、NIH小鼠成纤维细胞（NIH3T3）及小鼠胚胎干细胞（mES）三者中的MafA和MLH1基因转录起始区组蛋白修饰（H3K4m3、H3K9m3和H3乙酰化）的状况。同时采用实时定量RT-PCR检测上述三种细胞各基因mRNA表达水平。分析基因的H3K4m3、H3K9m3和H3乙酰化修饰与基因表达之间的相互关系。结果 （1）以mES细胞为参照,NIT-1细胞MafA基因的转录起始区的H3K4m3修饰水平明显增高（P〈0.05）,H3K9m3修饰水平明显降低（P〈0.05）;NIH 3T3细胞MafA基因的转录起始区的H3K9m3修饰水平明显增高（P〈0.05）,H3K4m3修饰水平明显降低（P〈0.05）;（2）MafA基因的仅在NIT-1细胞表达,其表达与H3K4m3修饰存在直线相关（相关系数0.995）;与H3K9m3修饰存在直线负相关（相关系数-0.751）;（3）管家基因MLH1的表达与所检测组蛋白修饰无相关性。结论 H3K9m3与H3K4m3修饰能相互协调,共同调控MafA基因的表达,对胚胎干细胞向β细胞分化具有重要的意义。     

组蛋白甲基化修饰与早期胚胎发育及相关疾病的研究进展

早期胚胎发育受到表观遗传的多重级联调控.组蛋白修饰是表观遗传调控的重要组成部分,组蛋白翻译后修饰通过影响组蛋白与DNA结合的紧密程度,调控染色质状态与基因表达,参与了胚胎发育及相关疾病发生的过程.在早期胚胎发育过程中,组蛋白甲基化修饰H3K4me3, H3K27me3与H3K9me3通过协调染色质的开放与关闭参与调控发育相关基因的表达,沉默逆转录转座子以及参与经典与非经典的印记调控.早期胚胎阶段作为表观遗传重编程的关键时间窗口,在此阶段组蛋白修饰酶的表达与组蛋白修饰容易受到不良环境的影响,导致胚胎期及子代多种疾病的发生.本文详细地对组蛋白H3K4me3, H3K27me3, H3K9me3修饰在早期胚胎发育与疾病发生中的作用与功能进行了综述,为今后表观遗传学在早期胚胎发育相关疾病的干预治疗提供理论基础.     

Discovering common combinatorial histone modification patterns in the human genome

Histone modifications play a crucial role in regulating gene expression and cell lineage determination and maintenance at the epigenetic level. To systematically investigate this phenomenon, this paper presented a statistical hybrid clustering algorithm to identify common combinatorial histone modification patterns. We applied the algorithm to 39 histone modification marks in human CD4 + T cells and detected 854 common combinatorial histone modification patterns. Our results could cover 211 (76.17%) patterns among 277 patterns identified by the tandem mass spectrometry experiments. Based on the frequency statistical analysis, it was found that the co-occurrence frequencies of 20 backbone modifications are greater than or close to 0.2 in the 854 patterns. we also found that 15 modifications (H2BK120ac, H4K91ac, H2BK20ac, etc.), three histone acetylations (H2AK9ac, H4K16ac, and H4K12ac) and five histone methylations (H3K79me1, H3K79me2, 3K79me3, H4K20me1, and H2BK5me1) were most likely prone to coexist respectively in these patterns. In addition, we found that DNA methylation tends to combine with histone acetylation rather than histone methylation.     

Visualization of multivalent histone modification in a single cell reveals highly concerted epigenetic changes on differentiation of embryonic stem cells

Combinations of histone modifications have significant biological roles, such as maintenance of pluripotency and cancer development, but cannot be analyzed at the single cell level. Here, we visualized a combination of histone modifications by applying the in situ proximity ligation assay, which detects two proteins in close vicinity (∼30 nm). The specificity of the method [designated as imaging of a combination of histone modifications (iChmo)] was confirmed by positive signals from H3K4me3/acetylated H3K9, H3K4me3/RNA polymerase II and H3K9me3/H4K20me3, and negative signals from H3K4me3/H3K9me3. Bivalent modification was clearly visualized by iChmo in wild-type embryonic stem cells (ESCs) known to have it, whereas rarely in Suz12 knockout ESCs and mouse embryonic fibroblasts known to have little of it. iChmo was applied to analysis of epigenetic and phenotypic changes of heterogeneous cell population, namely, ESCs at an early stage of differentiation, and this revealed that the bivalent modification disappeared in a highly concerted manner, whereas phenotypic differentiation proceeded with large variations among cells. Also, using this method, we were able to visualize a combination of repressive histone marks in tissue samples. The application of iChmo to samples with heterogeneous cell population and tissue samples is expected to clarify unknown biological and pathological significance of various combinations of epigenetic modifications.     

大鼠C6胶质瘤细胞中gdnf基因启动子Ⅰ区组蛋白高乙酰化可能参与了其高转录调控过程

目的:探讨大鼠C6胶质瘤细胞中gdnf基因高转录与其启动子Ⅰ区组蛋白乙酰化的关系。方法:应用Real-time PCR和ChIP-PCR技术分别检测了大鼠正常星形胶质细胞和C6胶质瘤细胞中gdnf基因mRNA的表达水平以及其启动子Ⅰ区组蛋白H3K9的乙酰化程度;利用Real-time PCR技术,检测了不同浓度的组蛋白乙酰基转移酶抑制剂姜黄素(Curcumin)或去乙酰化酶抑制剂曲古抑菌素A(TSA)处理对C6胶质瘤细胞中gdnf基因mRNA表达的影响。结果:较之正常星形胶质细胞,C6胶质瘤细胞中gdnf基因mRNA的表达量极显著增高(P0.01),并且其启动子Ⅰ区H3K9的乙酰化水平也显著升高(P0.05)。C6胶质瘤细胞经Curcumin处理24 h后,gdnf基因mRNA的表达量随药物浓度的升高而降低,且100μmol/L作用浓度时其表达量下降了74.17%(P0.001);相反,TSA处理后gdnf基因mRNA的表达量呈上升趋势,且200nmol/L组其表达量约上升145.35%(P0.05)。结论:在大鼠C6胶质瘤细胞中gdnf基因启动子Ⅰ区H3K9发生了高乙酰化修饰,这种修饰可能是其高转录的原因。     

The autoimmune regulator PHD finger binds to non-methylated histone H3K4 to activate gene expression

Mutations in the gene autoimmune regulator (AIRE) cause autoimmune polyendocrinopathy candidiasis ectodermal dystrophy. AIRE is expressed in thymic medullary epithelial cells, where it promotes the expression of tissue-restricted antigens. By the combined use of biochemical and biophysical methods, we show that AIRE selectively interacts with histone H3 through its first plant homeodomain (PHD) finger (AIRE-PHD1) and preferentially binds to non-methylated H3K4 (H3K4me0). Accordingly, in vivo AIRE binds to and activates promoters containing low levels of H3K4me3 in human embryonic kidney 293 cells. We conclude that AIRE-PHD1 is an important member of a newly identified class of PHD fingers that specifically recognize H3K4me0, thus providing a new link between the status of histone modifications and the regulation of tissue-restricted antigen expression in thymus.     

A conserved, extended chromatin opening within alpha-globin locus during development

Histone modifications play an important role in eukaryotic gene regulation. However, the dynamic alteration of histone modification during development is poorly understood. In addition, the relationship between histone modification and globin gene switching remains unclear. Here, we assessed the dynamic pattern of histone modification (H3 acetylation, H4 acetylation, H3 K4 methylation, and H3 K79 methylation) along the murine alpha-globin locus, as well as along the human alpha-globin locus in transgenic mice, during globin gene switching in vivo. During the switching, histone modification at embryonic zeta-gene and fetal/adult alpha-genes displayed different developmental patterns. The level of histone modification at zeta-gene was developmentally regulated, in accordance with the level of zeta-gene expression, whereas the alpha-genes kept high level of histone modification at both developmental stages, regardless of their expression levels. Histone deacetylase inhibition selectively increased acetylation at the inactive zeta-gene in fetal livers, although it did not reactivate the gene expression. More importantly, an obvious increasing of histone modification level at major regulatory elements and fetal/adult alpha-genes was observed during the switching, suggesting that a conserved, extended chromatin opening within the locus occurs during globin gene switching.