Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation

Epigenetic silenced alleles of the Arabidopsis SUPERMAN locus (the clark kent alleles) are associated with dense hypermethylation at noncanonical cytosines (CpXpG and asymmetric sites, where X = A, T, C, or G). A genetic screen for suppressors of a hypermethylated clark kent mutant identified nine loss-of-function alleles of CHROMOMETHYLASE3 (CMT3), a novel cytosine methyltransferase homolog. These cmt3 mutants display a wild-type morphology but exhibit decreased CpXpG methylation of the SUP gene and of other sequences throughout the genome. They also show reactivated expression of endogenous retrotransposon sequences. These results show that a non-CpG DNA methyltransferase is responsible for maintaining epigenetic gene silencing.     

植物转基因沉默的机制及克服方法

植物转基因沉默可以发生在染色体DNA、转录和转录后3种不同的层次上,转录水平基因沉默机制涉及DNA甲基化、位置效应、重复序列和同源序列等的作用,转录后水平基因沉默机制常用RNA阈值模型、异常RNA模型、双链RNA模型和未成熟翻译终止模型等解释。使用去甲基化、控制外源基因的拷贝数及结合位点、利用MAR序列、优化使用增强子、启动子等手段可以解除部分转基因沉默。     

Advances of Researches on the Mechanism of Transgene Silencing in Transgenic Plants

转基因沉默是导致外源基因不能在转化植株中正常表达的重要原因。在此,从转录水平和转录后水平两个方面,综述了转基因植物中外源基因沉默的机制。DNA甲基化是引起外源基因沉默的主要原因。人们目前用以下几种模型来解释转录后水平基因沉默的机制,如RNA阈值模型、异常RNA和异位配对模型及双链RNA模型。对外源基因沉默机制的探讨是顺利开展植物基因工程的迫切要求,也将促进植物功能基因组学研究的进一步深入。     

植物DNA甲基化研究进展

[目的]概述植物DNA甲基化的研究进展。[方法]综述了植物DNA甲基转移酶s、iRNA指导的DNA甲基化过程,阐明了DNA甲基化与其他表观遗传修饰的关系。[结果]DNA甲基化在表观遗传控制体系中起着重要作用,维持着生物进化过程中基因组和表观遗传的稳定性。RNA介导的DNA甲基化作用中s,iRNA起着不可替代的作用,但RdDM和甲基化在基因调控中的作用需要更进一步研究。[结论]全面了解DNA甲基化及其在植物发育和逆境胁迫应答中的作用,可以在转录水平上增强或抑制外源基因和内源基因沉默,便于制定更合理的改良重要转基因作物的策略。     

DNA methylation and epigenetic inheritance in plants and filamentous fungi

Plants and filamentous fungi share with mammals enzymes responsible for DNA methylation. In these organisms, DNA methylation is associated with gene silencing and transposon control. However, plants and fungi differ from mammals in the genomic distribution, sequence specificity, and heritability of methylation. We consider the role that transposons play in establishing methylation patterns and the epigenetic consequences of their perturbation.     

Gene body-specific methylation on the active X chromosome

Differential DNA methylation is important for the epigenetic regulation of gene expression. Allele-specific methylation of the inactive X chromosome has been demonstrated at promoter CpG islands, but the overall pattern of methylation on the active X(Xa) and inactive X (Xi) chromosomes is unknown. We performed allele-specific analysis of more than 1000 informative loci along the human X chromosome. The Xa displays more than two times as much allele-specific methylation as Xi. This methylation is concentrated at gene bodies, affecting multiple neighboring CpGs. Before X inactivation, all of these Xa gene body-methylated sites are biallelically methylated. Thus, a bipartite methylation-demethylation program results in Xa-specific hypomethylation at gene promoters and hypermethylation at gene bodies. These results suggest a relationship between global methylation and expression potentiality.     

外遗传分子生物学研究进展

该文综述了外遗传 (Epigenetics)这一新的分子生物学研究领域的提出、发展和最新研究进展 .指出外遗传是DNA碱基序列之外的遗传系统 .阐述了DNA甲基化、RNA介导的基因沉默、基因组印记和组蛋白密码等外遗传相关因素在生物体生长发育过程中对基因表达的重要调控作用 ,以及这些因素与生物体的防御机制和生物遗传信息的传递间存在的密切联系 ,并提出了从外遗传角度探索物种进化和生物适应逆境的新途径 .     

转座子沉默与DNA甲基化

转座子(transposable elements,TEs)在生物体基因组可以通过转座或逆转座移动,它拷贝数的大规模增加是基因组不稳定的重要因素,因此,维持TEs沉默是宿主进化的方向。DNA甲基化被认为是沉默TEs的可遗传表观遗传修饰方式,同时也在维持基因组稳定、基因印迹、调节基因表达中发挥作用。本研究综述了TEs对生物基因组进化和基因表达的影响,重点总结了以DNA甲基化为主的转座子沉默机制的最新研究进展,归纳了环境因素通过DNA去甲基化调控转座子跳跃的机理。图4参82     

Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1

The Arabidopsis gene DDM1 is required to maintain DNA methylation levels and is responsible for transposon and transgene silencing. However, rather than encoding a DNA methyltransferase, DDM1 has similarity to the SWI/SNF family of adenosine triphosphate-dependent chromatin remodeling genes, suggesting an indirect role in DNA methylation. Here we show that DDM1 is also required to maintain histone H3 methylation patterns. In wild-type heterochromatin, transposons and silent genes are associated with histone H3 methylated at lysine 9, whereas known genes are preferentially associated with methylated lysine 4. In ddm1 heterochromatin, DNA methylation is lost, and methylation of lysine 9 is largely replaced by methylation of lysine 4. Because DNA methylation has recently been shown to depend on histone H3 lysine 9 methylation, our results suggest that transposon methylation may be guided by histone H3 methylation in plant genomes. This would account for the epigenetic inheritance of hypomethylated DNA once histone H3 methylation patterns are altered.     

DNA甲基化在植物生长发育中的作用

DNA甲基化是植物体细胞基因组中一种常见的DNA共价修饰方式。在植物的正常生长发育中,DNA甲基化与外来基因的防御、内源基因表达的调节及转基因沉默等之间有着极大的关系。     

DNA干扰现象及其作用机理研究进展

与体内某一基因相同的DNA序列可特异性抑制细胞内靶标基因的表达,这种现象称之为DNA干扰(DNAi)。DNAi是随着转录后基因沉默现象而在烟草属植物上被发现,之后在一些动植物及其细胞上也被发现。在原核生物中也存在DNAi现象,且原核生物的Ago在体外也能实现DNAi。原核生物DNAi的机理主要是Ago以DNA为向导切割DNA或RNA,而真核生物可能是基因转录后抑制、基因组甲基化和启动子结合的转录抑制等。本文还对DNAi的进一步研究和应用进行了讨论和展望。     

含B染色体的黑麦基因组DNA甲基化变异研究

运用RAPD法检测黑麦JNK居群中含有和不含B染色体的基因组DNA的序列差异,并从100个10碱基随机引物中筛选出5个,采用CRED-RA法,检测含有和不含B染色体基因组DNA的甲基化变异。结果表明,含有和不含B染色体的黑麦基因组中均可以发生CmCGG甲基化修饰,但与不含B染色体的基因组相比,含有B染色体的黑麦基因组中发生了更广泛的CmCGG甲基化变异,这可能是B染色体产生表型抑制或基因沉默的一个重要原因。     

Study on DNA Cytosine Methylation of Cotton （Gossypium hirsutum L.） Genome and Its Implication for Salt Tolerance

To study the relations between DNA methylation and abiotic stress responses in cotton （Gossypium hirsutum L.）,the methylation-sensitive amplified polymorphism （MSAP） method was used to investigate the differences in methylation level and the change of cytosine methylation patterns under salt （NaCl） stress in two different salt-tolerant cotton lines.The results showed that the number of the cytosine methylation of CCGG sites in high salt-tolerant cotton line was less than that in low salt-tolerant line.Under salt stress,extensive cytosine methylation alterations including hypermethylation and demethylation as well as the potential conversion of methylation types occurred in the salt-treated cotton line compared with the corresponding control.Interestingly,salt stress-induced demethylation loci that occurred in high salt- tolerant cotton line were greater than those in low salt-tolerant cotton line,however,salt stress-induced hypermethylation loci in the high salt-tolerant cotton line were less than those in low salttolerant cotton line.It suggested that the demethylation positively contributed to salt tolerance and the hypermethylation had negative effect on salt tolerance in cotton.     

Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana

Differential cytosine methylation of repeats and genes is important for coordination of genome stability and proper gene expression. Through genetic screen of mutants showing ectopic cytosine methylation in a genic region, we identified a jmjC-domain gene, IBM1 (increase in bonsai methylation 1), in Arabidopsis thaliana. In addition to the ectopic cytosine methylation, the ibm1 mutations induced a variety of developmental phenotypes, which depend on methylation of histone H3 at lysine 9. Paradoxically, the developmental phenotypes of the ibm1 were enhanced by the mutation in the chromatin-remodeling gene DDM1 (decrease in DNA methylation 1), which is necessary for keeping methylation and silencing of repeated heterochromatin loci. Our results demonstrate the importance of chromatin remodeling and histone modifications in the differential epigenetic control of repeats and genes.     

Widespread role for the flowering-time regulators FCA and FPA in RNA-mediated chromatin silencing

The RRM-domain proteins FCA and FPA have previously been characterized as flowering-time regulators in Arabidopsis. We show that they are required for RNA-mediated chromatin silencing of a range of loci in the genome. At some target loci, FCA and FPA promote asymmetric DNA methylation, whereas at others they function in parallel to DNA methylation. Female gametophytic development and early embryonic development are particularly susceptible to malfunctions in FCA and FPA. We propose that FCA and FPA regulate chromatin silencing of single and low-copy genes and interact in a locus-dependent manner with the canonical small interfering RNA-directed DNA methylation pathway to regulate common targets.