植物表观遗传修饰与病原菌胁迫应答研究进展

真核生物基因表达受到染色质结构的调控,组蛋白与DNA的共价修饰构成表观遗传标签,并在植物胁迫应答如防御病原菌侵染过程中起重要作用.病原菌侵染可引起基因组整体DNA甲基化模式变化及胁迫应答基因的位点特异性去甲基化,导致植物抗性基因表达上调或下调,并进一步调控植物对病原菌的胁迫应答;组蛋白去乙酰化酶HDAC通过茉莉酸途径增强植物对病原菌的胁迫应答;此外,染色质重塑复合物Swr1复合体通过识别DNA基元和组蛋白乙酰化修饰状态靶向基因启动子,负调控SA敏感基因.该文从DNA甲基化、组蛋白乙酰化、甲基化修饰,染色质重塑等方面着重阐述植物与病原菌互作过程中发生的主要事件的分子基础及其研究进展.     

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.     

Histone acetylation and chromatin pattern in cancer. A review

Chromatin phenotype is known to be significantly disrupted in cancer. This has been demonstrated in many morphologic studies on cancer and in recent years by the application of digital texture analysis for quantitative evaluation of chromatin phenotype in neoplasia. Studies have consistently demonstrated the role of chromatin phenotype as a biomarker of diagnosis and prognosis. The underlying molecular mechanisms for chromatin reorganization and its role as a biomarker are largely unknown, but epigenetic processes are likely to be a main factor that not only modify chromatin arrangement but in doing so alter gene expression profiles in a reversible fashion. Of the range of epigenetic modifications that might control chromatin phenotype, histone acetylation is a strong candidate because of its role in the direct modification of chromatin, both through local relaxation of nucleosomal structure and recruitment of chromatin remodeling complexes. The reversible nature of histone acetylation is therapeutically attractive for treatment of aberrant histone acetylation; however, it still remains to be seen whether histone deacetylase inhibitors are clinically applicable or for use primarily as valuable research tools. This review explores the role of histone acetylation in cancer development, as a potential therapeutic candidate and a potential biomarker in tissue pathology.     

The CaMV 35S enhancer has a function to change the histone modification state at insertion loci in Arabidopsis thaliana

Chromatin regions with different states usually harbor distinct epigenetic information, through which gene expression is regulated. Recent studies using mammalian cells showed that a chromatin state signature is associated with active developmental enhancers, defined by high levels of histone H3 lysine 27 acetylation (H3K27ac) and strong depletion of H3K27 trimethylation (H3K27me3). These findings also imply that active enhancers may play a role in creating a chromatin state by changing histone modification markers, which in turn affects gene expression. To explore whether an active enhancer in plants affect histone modifications, we investigated the cauliflower mosaic virus 35S enhancer (35S_enh) for understanding its action model in Arabidopsis. We report that the 35S_enh has a function to change the histone modification pattern at its presenting loci, by characterization of the 35S_enh activated BREVIPEDICELLUS (BP) silencing lines and the randomly selected 35S_enh activation tagging lines. By analyzing histone modification markers reflecting the plant chromatin state, we show that the 35S_enh is generally correlated with the reduced level of H3K27me3 and the increased level of H3K4me3 at the insertion loci. Our data are consistent with those in mammals and suggest that the enhancer sequence correlating with the active chromatin state signature may be generally present in the eukaryotic kingdom.     

植物中表观遗传修饰研究进展

表观遗传是指DNA序列不发生变化, 但基因表达发生了可遗传的改变, 主要涉及DNA与染色体上的一些可逆修饰以及一些转录调控机制。DNA甲基化、组蛋白修饰和非编码RNA调控是表观遗传学研究的三大支柱。三者在植物生长发育、应对生物和非生物胁迫以及适应环境变化中发挥着极其重要的作用。该文综述了植物中DNA甲基化、组蛋白修饰、非编码RNA调控的研究进展及其对植物株高、生育期、花型、果实着色以及应对环境胁迫等方面的影响。     

Relationship between DNA methylation, histone H4 acetylation and gene expression in the mouse imprinted Igf2-H19 domain

DNA methylation and histone H4 acetylation play a role in gene regulation by modulating the structure of the chromatin. Recently, these two epigenetic modifications have dynamically and physically been linked. Evidence suggests that both modifications are involved in regulating imprinted genes - a subset of genes whose expression depends on their parental origin. Using immunoprecipitation assays, we investigate the relationship between DNA methylation, histone H4 acetylation and gene expression in the well-characterised imprinted Igf2-H19 domain on mouse chromosome 7. A systematic regional analysis of the acetylation status of the domain shows that parental-specific differences in acetylation of the core histone H4 are present in the promoter regions of both Igf2 and H19 genes, with the expressed alleles being more acetylated than the silent alleles. A correlation between DNA methylation, histone hypoacetylation and gene repression is evident only at the promoter region of the H19 gene. Treatment with trichostatin A, a specific inhibitor of histone deacetylase, reduces the expression of the active maternal H19 allele and this can be correlated with regional changes in acetylation within the upstream regulatory domain. The data suggest that histone H4 acetylation and DNA methylation have distinct functions on the maternal and paternal Igf2-H19 domains.     

The re-expression of the epigenetically silenced e-cadherin gene by a polyamine analogue lysine-specific demethylase-1 (LSD1) inhibitor in human acute myeloid leukemia cell lines

Aberrant epigenetic silencing of tumor suppressor genes is a common feature observed during the transformation process of many cancers, including those of hematologic origin. Histone modifications, including acetylation, phosphorylation, and methylation, collaborate with DNA CpG island methylation to regulate gene expression. The dynamic process of histone methylation is the latest of these epigenetic modifications to be described, and the identification and characterization of LSD1 as a demethylase of lysine 4 of histone H3 (H3K4) has confirmed that both the enzyme and the modified histone play important roles as regulators of gene expression. LSD1 activity contributes to the suppression of gene expression by demethylating promoter-region mono- and dimethyl-H3K4 histone marks that are associated with active gene expression. As most post-translational modifications are reversible, the enzymes involved in the modification of histones have become targets for chemotherapeutic intervention. In this study, we examined the effects of the polyamine analogue LSD1 inhibitor 2d (1,15-bis{N ⁵-[3,3-(diphenyl)propyl]-N ¹-biguanido}-4,12-diazapentadecane) in human acute myeloid leukemia (AML) cell lines. In each line studied, 2d evoked cytotoxicity and inhibited LSD1 activity, as evidenced by increases in the global levels of mono- and di-methylated H3K4 proteins. Global increases in other chromatin modifications were also observed following exposure to 2d, suggesting a broad response to this compound with respect to chromatin regulation. On a gene-specific level, treatment with 2d resulted in the re-expression of e-cadherin, a tumor suppressor gene frequently silenced by epigenetic modification in AML. Quantitative chromatin immunoprecipitation analysis of the e-cadherin promoter further confirmed that this re-expression was concurrent with changes in both active and repressive histone marks that were consistent with LSD1 inhibition. As hematologic malignancies have demonstrated promising clinical responses to agents targeting epigenetic silencing, this polyamine analogue LSD1 inhibitor presents an exciting new avenue for the development of novel therapeutic agents for the treatment of AML.