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。     

组蛋白H3K36甲基化修饰在DNA损伤修复中的作用

维持基因组的稳定性是保证生命活动正常进行的必要条件。内部或外界的刺激会造成DNA的损伤,引起基因组的不稳定,导致细胞死亡甚至肿瘤发生。DNA为基础的核小体上的组蛋白可以发生多种翻译后修饰,其中组蛋白H3第36位上的赖氨酸(H3K36)的甲基化修饰在抑制非正常转录起始、抑制组蛋白交换、调控RNA可变剪切中发挥重要作用。近几年来,多项研究结果也表明,H3K36修饰在双链断裂和错配修复等DNA损伤修复活动中也发挥了调控作用。因此,了解H3K36甲基化在DNA损伤修复中的作用,可为相关疾病的研究与治疗提供理论基础。     

组蛋白翻译后修饰与DNA损伤响应蛋白招募的调控

组蛋白翻译后修饰是细胞DNA损伤早期应答反应的重要内涵,一方面是松弛、开放染色质结构的必要分子调节事件,以便DNA损伤响应蛋白能接近DNA损伤位点;另一方面直接参与DNA损伤修复蛋白招募过程的调控。综述了在DNA损伤信号激发下,发生的组蛋白主要修饰类型,异组蛋白H2AX、H2A.Z在DNA损伤部位与组蛋白置换,及其对DNA损伤响应蛋白招募的调节作用和机制。     

组蛋白赖氨酸甲基化在表观遗传调控中的作用

组蛋白赖氨酸的甲基化在表观遗传调控中起着关键作用。组蛋白H3的K4、K9、K27、K36、K79和H4的K20均可被甲基化。组蛋白H3第9位赖氨酸的甲基化与基因的失活相关连; 组蛋白H3第4位赖氨酸和第36位赖氨酸的甲基化与基因的激活相关连; 组蛋白H3第27位赖氨酸的甲基化与同源盒基因沉默、X染色体失活、基因印记等基因沉默现象有关; 组蛋白H3第79位赖氨酸的甲基化与防止基因失活和DNA修复有关。与此同时, 组蛋白的去甲基化也受到更为广泛的关注。 关键词: 组蛋白赖氨酸甲基转移酶; 组蛋白赖氨酸甲基化; 组蛋白去甲基化     

组蛋白泛素化修饰及其在DNA损伤应答中的作用

泛素化修饰是真核生物细胞内重要的翻译后修饰类型,通过调节蛋白质活性、稳定性和亚细胞定位广泛参与细胞内各项信号传导与代谢过程,对维持正常生命活动具有重要意义。组蛋白作为染色质中主要的蛋白成分,与DNA复制转录、修复等行为密切相关,是研究翻译后修饰的热点。DNA损伤后,组蛋白泛素化修饰通过调节核小体结构、激活细胞周期检查点、影响修复因子的招募与装配等诸多途径参与损伤应答。同时,组蛋白泛素化修饰还能调节其他位点翻译后修饰,并通过这种串扰(crosstalk)作用调节DNA损伤应答。本文介绍了组蛋白泛素化修饰的主要位点和相关组分(包括E3连接酶、去泛素化酶与效应分子),以及这些修饰作用共同编译形成的信号网络在DNA损伤应答中的作用,最后总结了目前该领域研究所面临的一些问题,以期为科研人员进一步探索组蛋白密码在DNA损伤应答中的作用提供参考。     

组蛋白H3第10位丝氨酸的磷酸化：金属纳米材料早期毒性的潜在生物标志物

目的 阐明金属纳米材料（MNPs）对组蛋白H3第10位丝氨酸磷酸化（p-H3S10）修饰变化的影响，探讨典型MNPs暴露后细胞全基因表达的变化，为MNPs早期毒性筛选提供理论基础。方法 通过蛋白质免疫印迹及流式细胞术等方法评价了10种MNPs对p-H3S10修饰变化的影响。此外，利用转录组测序技术在转录水平上探讨了1种典型MNPs——纳米氧化铜对细胞全基因表达的影响。结果 除纳米氧化镍外，其余用于测试的9种MNPs均在不同程度上诱导了p-H3S10。进一步分析发现，MNPs诱导的p-H3S10与MNPs的细胞内蓄积高度相关，且细胞内金属离子的持续释放可能是MNPs诱导 p-H3S10的关键因素之一。另外，转录组测序的结果表明，纳米氧化铜的暴露导致了275个基因的显著差异表达（P<0.05），其中185个基因上调，90个基因下调。基因本体分析表明，在分子功能类别中，排名靠前的术语包括与多种转录因子活性、序列特异性DNA结合及丝裂原活化蛋白激酶活性相关的术语。京都基因和基因组百科全书分析表明，纳米氧化铜暴露后丝裂原活化蛋白激酶的信号级联显著上调。结论 MNPs的细胞内蓄积与其早期诱导的p-H3S10表达高度相关，并且细胞内MNPs持续释放的金属离子可能会在MNPs进入细胞后的很长一段时间内持续诱导p-H3S10的高表达。综上，p-H3S10具有作为评估MNPs毒性的生物标志物的潜力。     

酿酒酵母组蛋白H3 K4L和K36L突变对细胞生长和GAL1、SSA3、PHO5表达的影响

组蛋白甲基化和乙酰化修饰对基因表达和细胞生长至关重要,为揭示组蛋白H3第4、36位赖氨酸(K)修饰对酵母生长和诱导基因表达的重要性及两位点功能差异,文章构建了两位点单独或共同突变为亮氨酸(L)的组蛋白突变株S4、S36和D436,对其在正常、半乳糖为单一碳源、高温、高盐等条件下的生长及GAL1、SSA3和PHO5表达进行比较。结果显示:D436对高温最敏感,各突变株对咖啡因显著敏感;3个突变株在高温、高盐、6-AU、咖啡因存在时的生长及GAL1、SSA3和PHO5的激活均明显慢于野生型;S4在高温、高盐条件下生长及GAL1激活慢于S36。H3-K4和H3-K36的翻译后修饰对细胞生长和适应不利环境非常重要,在对高温等逆境快速适应上,K4比K36更重要,组蛋白突变株的表型缺陷是因该条件下细胞生存所必需的诱导基因表达延迟所致,同一位点突变对不同基因表达有不同影响。3个突变株的缺陷表型严格上应是相应位点突变导致组蛋白修饰模式改变所造成的综合影响。     

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.     

乳腺癌细胞中EYA2调控H2A.X~(Y39)磷酸化修饰及其功能

我们的前期研究在乳腺癌细胞SKBR3中首次检测到了组蛋白H2A.X第39位酪氨酸残基(Y39)可以发生磷酸化修饰(H2A.X~(Y39ph))。该位点的磷酸化修饰是γ-H2A.X正确形成的必要条件,并促进损伤修复因子募集到DNA损伤区域,有助于损伤修复反应。经过深入研究,我们又发现磷酸酶分子EYA2(eyes absent 2)能够去除乳腺癌细胞SKBR3中H2A.X~(Y39)位点的磷酸化修饰。在DNA损伤后,与H2A.X结合的EYA2蛋白减少,这可能是DNA损伤修复阶段H2A.X~(Y39ph)水平上调的原因。乳腺癌细胞中低水平的EYA2通过上调H2A.X~(Y39ph)水平及下游增殖相关基因转录促进细胞增殖。我们的报道为H2A.X~(Y39ph)功能的深入研究提供了数据基础。     

乳腺癌细胞中H2A.X~(Y39)磷酸化调节γ-H2A.X形成及细胞增殖

组蛋白H2A.X第139位丝氨酸磷酸化,形成γ-H2A.X。γ-H2A.X的正确形成对于DNA损伤修复、基因组稳定性和肿瘤发生至关重要,但其形成的机制仍不明确。我们在乳腺癌细胞SKBR3中检测到H2A.X的一种新的修饰方式——第39位酪氨酸残基(Y39)磷酸化,这是国内外首次报道这一修饰。经过一系列内源性和外源性实验证实,H2A.X Y39位点的磷酸化修饰(H2A.X~(Y39ph))是γ-H2A.X形成的必要前提条件。高水平的H2A.X~(Y39ph)能够促进乳腺癌细胞增殖,这一功能依赖于Nanog和Oct4及下游靶基因的转录水平上调。这一新修饰位点的阐明为肿瘤发生和DNA损伤反应中染色质重塑研究提供了新机制。     

Cytotoxicity of sodium selenite in HaCaT cells induces cell death and alters the mRNA expression of PUMA,ATR, and mTOR genes

BackgroundBy identifying the molecular mechanisms underlying sodium selenite (Na₂SeO₃) cytotoxicity during exposure in non-tumor cells (HaCaT cells), we will improve the current understanding of its antiproliferative effects and modulation of gene expression in the main pathways related to the cell cycle, cell death, oxidative stress, and DNA damage and repair.MethodsNon-tumor HaCaT cells were treated with Na₂SeO₃ to induce cytotoxicity, and the effects were investigated using an MTT assay (cell viability), real-time cell analysis (profiling the cell index), flow cytometry (membrane integrity, cell cycle disruption, and apoptosis), a comet assay (genotoxicity, i.e., DNA damage), and RT-qPCR (mRNA expression of genes).ResultsTreatment with Na₂SeO₃ was cytotoxic at 10 μM, producing morphological changes in cells (cytoplasmic granulations); however, it did not have a genotoxic effect. Na₂SeO₃ induced cell membrane damage, cell death, and cell cycle arrest in HaCaT cells. It also altered the mRNA expression levels of PUMA, ATR, and mTOR genes. However, it had no effect on the mRNA expression of caspases or PARP1, BIRC5, BECN1, and c-MYC genes, suggesting that Na₂SeO₃ causes PUMA-dependent apoptosis in HaCaT cells. The mRNA expression of specific genes related to oxidative stress, DNA damage and repair, and cell cycle control were unchanged by Na₂SeO₃.ConclusionsWe demonstrated the cytotoxic effect of Na₂SeO₃ in HaCaT cells by analyzing mRNA expression patterns, changes in cell morphology, and proliferation kinetics.     

Overexpression of Slc30a7/ZnT7 increases the mitochondrial matrix levels of labile Zn2+ and modifies histone modification in hyperinsulinemic cardiomyoblasts

BackgroundCellular free Zn²⁺ concentrations ([Zn²⁺]) are primarily coordinated by Zn²⁺-transporters, although their roles are not well established in cardiomyocytes. Since we previously showed the important contribution of a Zn²⁺-transporter ZnT7 to [Zn²⁺]_i regulation in hyperglycemic cardiomyocytes, here, we aimed to examine a possible regulatory role of ZnT7 not only on [Zn²⁺]_i but also both the mitochondrial-free Zn²⁺ and/or Ca²⁺ in cardiomyocytes, focusing on the contribution of its overexpression to the mitochondrial function.MethodsWe mimicked either hyperinsulinemia (by 50-μM palmitic acid, PA-cells, for 24-h) or overexpressed ZnT7 (ZnT7OE-cells) in H9c2 cardiomyoblasts.ResultsOpposite to PA-cells, the [Zn²⁺]_i in ZnT7OE-cells was not different from untreated H9c2-cells. An investigation of immunofluorescence imaging by confocal microscopy demonstrated a ZnT7 localization on the mitochondrial matrix. We demonstrated the ZnT7 localization on the mitochondrial matrix by using immunofluorescence imaging. Later, we determined the mitochondrial levels of [Zn²⁺]_Mit and [Ca²⁺]_Mit by using the Zn²⁺ and Ca²⁺ sensitive FRET probe and a Ca²⁺-sensitive dye Fluo4, respectively. The [Zn²⁺]_Mit was found to increase significantly in ZnT7OE-cells, similar to the PA-cells while no significant changes in the [Ca²⁺]_Mit in these cells. To examine the contribution of ZnT7 overexpression on the mitochondria function, we determined the level of reactive oxygen species (ROS) and the mitochondrial membrane potential (MMP) in these cells in comparison to the PA-cells. There were significantly increased production of ROS and depolarization in MMP and increases in marker proteins of mitochondria-associated apoptosis and autophagy in ZnT7-OE cells, similar to the PA-cells, parallel to increases in K-acetylation. Moreover, we determined significant increases in trimethylation of histone H3 lysine27, H3K27me3, and the mono-methylation of histone H3 lysine36, H3K36 in the ZnT7OE-cells, demonstrating the role of [Zn²⁺]_Mit in epigenetic regulation of cardiomyocytes under hyperinsulinemia through histone modification.ConclusionsOverall, our data have shown an important contribution of high expression of ZnT7-OE, through its buffering and muffling capacity in cardiomyocytes, on the regulation of not only [Zn²⁺_]i but also both [Zn²⁺]_Mit and [Ca²⁺]_Mit affecting mitochondria function, in part, via histone modification.     

Methylations of histone H3 lysine 9 and lysine 36 are functionally linked to DNA replication checkpoint control in fission yeast

Recently, histone H4 lysine 20 and H3 lysine 79 methylations were functionally linked to DNA damage checkpoint. The crosstalk between histone methylation and the S-M checkpoint, however, has remained unclear. Here, we show that H3 lysine 9 (K9) and lysine 36 (K36) methylations catalyzed by two histone methyltransferases Clr4 and Set2 are involved in hydroxyurea (HU)-induced replication checkpoint. The clr4-set2 double mutants besides histone H3-K9 and K36 double mutants exhibited HU-sensitivity, a defective HU-induced S-M checkpoint, and a significant reduction of HU-induced phosphorylation of Cdc2. Intriguingly, the clr4-set2 double mutations impaired the HU-induced accumulation of a mitotic inhibitor Mik1. Double mutants in Alp13 and Swi6, which can specifically bind to H3-K36 and K9 methylations, exhibited phenotypes similar to those of the clr4-set2 mutants. Together, these findings suggest that methylations of histone H3-K9 and K36 by Clr4 and Set2 are functionally linked to DNA replication checkpoint via accumulation of Mik1.     

Age-related decline in histone H1 fraction in human diploid fibroblast cultures

The age-related increase in cell volume and nuclear size of cultured human diploid fibroblasts reflected the accumulation of proteins in cytoplasm and nuclei of growth-retarded fibroblasts.Determination of the amount of nuclear proteins, which were fractionated into 0.15 M NaCl-soluble proteins, 0.4 N H₂SO₄-extractable proteins and residual acidic proteins, indicated that age-related increase in nuclear proteins was due mainly to the accumulation of residual acidic proteins.However, electrophoretic fractionation of histones from various passages of fibroblast cultures on acid urea polyacrylamide gel revealed that the relative amount of H1 fraction decreased with in vitro aging. This was further confirmed by mixing experiments examining the distribution of radioactivity of the histones from cell mixtures of young and senescent cultures labeled with [³H]lysine or [¹⁴C]lysine.A pulse label and chase experiment indicated that the observed decrease in the amount of histone H1 was mainly due to decrease in synthesis of histone H1 in senescent human fibroblast cultures.     

Oxidative stress alters global histone modification and DNA methylation

The JmjC domain-containing histone demethylases can remove histone lysine methylation and thereby regulate gene expression. The JmjC domain uses iron Fe(II) and α-ketoglutarate (αKG) as cofactors in an oxidative demethylation reaction via hydroxymethyl lysine. We hypothesize that reactive oxygen species will oxidize Fe(II) to Fe(III), thereby attenuating the activity of JmjC domain-containing histone demethylases. To minimize secondary responses from cells, extremely short periods of oxidative stress (3 h) were used to investigate this question. Cells that were exposed to hydrogen peroxide (H₂O₂) for 3 h exhibited increases in several histone methylation marks including H3K4me3 and decreases of histone acetylation marks including H3K9ac and H4K8ac; preincubation with ascorbate attenuated these changes. The oxidative stress level was measured by generation of 2′,7′-dichlorofluorescein, GSH/GSSG ratio, and protein carbonyl content. A cell-free system indicated that H₂O₂ inhibited histone demethylase activity where increased Fe(II) rescued this inhibition. TET protein showed a decreased activity under oxidative stress. Cells exposed to a low-dose and long-term (3 weeks) oxidative stress also showed increased global levels of H3K4me3 and H3K27me3. However, these global methylation changes did not persist after washout. The cells exposed to short-term oxidative stress also appeared to have higher activity of class I/II histone deacetylase (HDAC) but not class III HDAC. In conclusion, we have found that oxidative stress transiently alters the epigenetic program process through modulating the activity of enzymes responsible for demethylation and deacetylation of histones.     

The TrxG Complex Mediates Cytokine Induced De Novo Enhancer Formation in Islets

To better understand how β-cells respond to proinflammatory cytokines we mapped the locations of histone 3 lysine 4 monomethylation (H3K4me1), a post-translational histone modification enriched at active and poised cis-regulatory regions, in IFNγ, Il-1β, and TNFα treated pancreatic islets. We identified 96,721 putative cis-regulatory loci, of which 3,590 were generated de novo, 3,204 had increased H3K4me1, and 5,354 had decreased H3K4me1 in IFNγ, Il-1β, and TNFα exposed islets. Roughly 10% of the de novo and increased regions were enriched for the repressive histone modification histone 3 lysine 27 trimethylation (H3K27me3) in untreated cells, and these were frequently associated with chemokine genes. We show that IFNγ, Il-1β, and TNFα exposure overcomes this repression and induces chemokine gene activation in as little as three hours, and that this expression persists for days in absence of continued IFNγ, Il-1β, and TNFα exposure. We implicate trithorax group (TrxG) complexes as likely players in the conversion of these repressed loci to an active state. To block the activity of these complexes, we suppressed Wdr5, a core component of the TrxG complexes, and used the H3K27me3 demethylase inhibitor GSK-J4. We show that GSK-J4 is particularly effective in blunting IFNγ, Il-1β, and TNFα-induced chemokine gene expression in β-cells; however, it induced significant islet-cell apoptosis and β-cell dysfunction. Wdr5 suppression also reduced IFNγ, Il-1β, and TNFα induced chemokine gene expression in β-cells without affecting islet-cell survival or β-cell function after 48hrs, but did begin to increase islet-cell apoptosis and β-cell dysfunction after four days of treatment. Taken together these data suggest that the TrxG complex is potentially a viable target for preventing cytokine induced chemokine gene expression in β-cells.