DNA methylation, a key regulator of plant development and other processes

Recent research has demonstrated that DNA methylation plays an integral role in regulating the timing of flowering and in endosperm development. The identification of key genes controlling these processes, the expression of which is altered in plants with low methylation, opens the way to understanding how DNA methylation regulates plant development.     

The first high-resolution DNA "methylome"

Cytosine methylation plays a crucial role in the regulation of gene expression and the control of genome stability in higher eukaryotes. Despite its importance for normal development, the degree and genome-wide distribution of DNA methylation has remained largely unknown. In this issue of Cell, fill this gap by presenting a high-resolution map of DNA methylation in the genome of the flowering plant Arabidopsis.     

DNA甲基化及其对植物发育的调控

DNA甲基化属于一种表观遗传修饰,主要发生在CpG双核苷酸序列中的胞嘧啶上,是在DNA甲基转移酶催化下,以S-腺苷甲硫氨酸为甲基供体,将甲基转移到胞嘧啶上,生成5-甲基胞嘧啶的一种反应。DNA甲基化在植物生长过程中具有极其重要的作用。综述了植物DNA甲基化的特征、调控机制,及其对植物基因表达影响的研究进展。     

Plant chromatin: development and gene control

It is increasingly clear that chromatin is not just a device for packing DNA within the nucleus but also a dynamic material that changes as cellular environments alter. The precise control of chromatin modification in response to developmental and environmental cues determines the correct spatial and temporal expression of genes. Here, we review exciting discoveries that reveal chromatin participation in many facets of plant development. These include: chromatin modification from embryonic and meristematic development to flowering and seed formation, the involvement of DNA methylation and chromatin in controlling invasive DNA and in maintenance of epigenetic states, and the function of chromatin modifying and remodeling complexes such as SWI/SNF and histone acetylases and deacetylases in gene control. Given the role chromatin structure plays in every facet of plant development, chromatin research will undoubtedly be integral in both basic and applied plant biology.     

Epigenetic reprogramming during plant reproduction and seed development

Epigenetic processes such as DNA methylation are crucial for the development of flowering plants, and for protection of genome integrity via silencing of transposable elements (TEs). Recent advances in genome-wide profiling suggest that during reproduction DNA methylation patterns are at least partially transmitted or even enhanced in the next generation to ensure stable silencing of TEs. At the same time, parent-of-origin specific removal of DNA methylation in the accompanying tissue allows imprinted expression of genes. Here we summarize the dynamics of DNA methylation as a major epigenetic regulatory pathway during reproduction and seed development.     

钙在植物花发育过程中的作用

对于园林观赏植物,开花是一个非常重要的发育阶段,它直接影响花卉的品质。近年 来,植物花发育的分子生物学研究进展迅速,并取得了一些突破性成果。钙作为第二信使在植物信号转导中起着非常重要的作用,大量研究显示,钙有可能参与开花控制。本文总结了钙信号与植物花发育这一领域的最新研究进展,包括以下几个方面的内容：钙在植物成花诱 导（包括光周期诱导和低温诱导）中的作用;花芽分化时期钙在植物叶芽和花芽中的动态分布及组织培养条件下不同钙浓度对花芽分化的影响;钙与花衰老的关系。      

钙在植物花发育过程中的作用

对于园林观赏植物,开花是一个非常重要的发育阶段,它直接影响花卉的品质。近年来,植物花发育的分子生物学研究进展迅速,并取得了一些突破性成果。钙作为第二信使在植物信号转导中起着非常重要的作用,大量研究显示,钙有可能参与开花控制。本文总结了钙信号与植物花发育这一领域的最新研究进展,包括以下几个方面的内容：钙在植物成花诱导(包括光周期诱导和低温诱导)中的作用;花芽分化时期钙在植物叶芽和花芽中的动态分布及组织培养条件下不同钙浓度对花芽分化的影响;钙与花衰老的关系。     

Expression of exogenous DNA methyltransferases: Application in molecular and cell biology

DNA methyltransferases might be used as powerful tools for studies in molecular and cell biology due to their ability to recognize and modify nitrogen bases in specific sequences of the genome. Methylation of the eukaryotic genome using exogenous DNA methyltransferases appears to be a promising approach for studies on chromatin structure. Currently, the development of new methods for targeted methylation of specific genetic loci using DNA methyltransferases fused with DNA-binding proteins is especially interesting. In the present review, expression of exogenous DNA methyltransferase for purposes of in vivo analysis of the functional chromatin structure along with investigation of the functional role of DNA methylation in cell processes are discussed, as well as future prospects for application of DNA methyltransferases in epigenetic therapy and in plant selection.     

piRNAs, transposon silencing, and germline genome integrity

Integrity of the germline genome is essential for the production of viable gametes and successful reproduction. In mammals, the generation of gametes involves extensive epigenetic changes (DNA methylation and histone modification) in conjunction with changes in chromosome structure to ensure flawless progression through meiotic recombination and packaging of the genome into mature gametes. Although epigenetic reprogramming is essential for mammalian reproduction, reprogramming also provides a permissive window for exploitation by transposable elements (TEs), autonomously replicating endogenous elements. Expression and propagation of TEs during the reprogramming period can result in insertional mutagenesis that compromises genome integrity leading to reproductive problems and sporadic inherited diseases in offspring. Recent work has identified the germ cell associated PIWI Interacting RNA (piRNA) pathway in conjunction with the DNA methylation and histone modification machinery in silencing TEs. In this review we will highlight these recent advances in piRNA mediated regulation of TEs in the mouse germline, as well as mention the repercussions of failure to properly regulate TEs.     

植物开花的组蛋白甲基化调控分子机理

开花是指植物从营养生长转变到生殖生长的生理过程, 是植物个体发育和后代繁衍的中心环节, 既受遗传基础决定,同时又受到温度和光周期等多种环境因素的调控。在拟南芥中, 已经分离了大量的与开花相关的基因, 从遗传学上已初步形成了一个开花调控的网络。组蛋白甲基化是植物发育过程的重要调节方式, 近年来关于其参与开花调控的研究有了重要进展。本文综述了具有代表性的组蛋白H3赖氨酸甲基化修饰参与调控植物开花发育的机制, 提出该研究领域的发展方向和前景。     

Linkage disequilibrium analysis of allelic heterogeneity in DNA methylation

Heterogeneity of DNA methylation status among alleles is observed in various cell types and is involved in epigenetic gene regulation and cancer biology. However, the individual methylation profile within each allele has not yet been examined at the whole-genome level. In the present study, we applied linkage disequilibrium analysis to the DNA methylation data obtained from whole-genome bisulfite sequencing studies in mouse germline and other types of cells. We found that the methylation status of 2 consecutive CpG sites showed deviation from equilibrium frequency toward concordant linkage (both methylated or both unmethylated) in germline cells. In the imprinting loci where methylation of constituent alleles is known, our analysis detected the deviation toward the concordant linkage as expected. In addition, we applied this analysis to the transitional zone between methylated and unmethylated regions and to the cells undergoing epigenetic reprogramming. In both cases, deviation to the concordant-linked alleles was conspicuous, indicating that the methylation pattern is not random but rather concordant within each allele. These results will provide the key to understanding the mechanism underlying allelic heterogeneity.     

孝顺竹开花过程中DNA甲基化水平动态研究

以孝顺竹为材料,利用HPLC和MSAP技术在其未开花至开花的生长过程中进行甲基化水平的检测,分析竹子开花过程中基因组DNA甲基化的动态,以揭示DNA甲基化水平与竹子开花现象的相关性。结果显示:(1)孝顺竹基因组DNA甲基化率在不同的时间处于动态变化中,进入开花状态的孝顺竹植株其甲基化水平极显著低于开花竹丛中未开花植株和未开花竹丛;开花和未开花植株的总甲基化率分别为9.00%和12.42%,全甲基化率分别为5.06%和7.53%。(2)MSAP位点中有66.83%的位点在开花和未开花材料中甲基化状态保持一致,33.17%的位点在开花和未开花植株中发生甲基化变化:其中22.28%的位点在开花植株中发生完全的去甲基化,1.98%的谱带在开花植株中发生甲基化,8.91%的位点在开花和未开花材料中甲基化水平呈现上升或降低的趋势。研究表明,开花的孝顺竹同时发生甲基化和去甲基化,但发生去甲基化的概率明显大于发生甲基化的概率,最终导致其甲基化水平极显著降低。     

DNA methylation in health and disease

DNA methylation has recently moved to centre stage in the aetiology of human neurodevelopmental syndromes such as the fragile X, ICF and Rett syndromes. These diseases result from the misregulation of genes that occurs with the loss of appropriate epigenetic controls during neuronal development. Recent advances have connected DNA methylation to chromatin-remodelling enzymes, and understanding this link will be central to the design of new therapeutic tools.     

Critical period of nonpromoter DNA methylation acquisition during prenatal male germ cell development

The prenatal period of germ cell development is a key time of epigenetic programming in the male, a window of development that has been shown to be influenced by maternal factors such as dietary methyl donor supply. DNA methylation occurring outside of promoter regions differs significantly between sperm and somatic tissues and has recently been linked with the regulation of gene expression during development as well as successful germline development. We examined DNA methylation at nonpromoter, intergenic sequences in purified prenatal and postnatal germ cells isolated from wildtype mice and mice deficient in the DNA methyltransferase cofactor DNMT3L. Erasure of the parental DNA methylation pattern occurred by 13.5 days post coitum (dpc) with the exception of approximately 8% of loci demonstrating incomplete erasure. For most loci, DNA methylation acquisition occurred between embryonic day 13.5 to 16.5 indicating that the key phase of epigenetic pattern establishment for intergenic sequences in male germ cells occurs prior to birth. In DNMT3L-deficient germ cells at 16.5 dpc, average DNA methylation levels were low, about 30% of wildtype levels; however, by postnatal day 6, about half of the DNMT3L deficiency-specific hypomethylated loci had acquired normal methylation levels. Those loci normally methylated earliest in the prenatal period were the least affected in the DNMT3L-deficient mice, suggesting that some loci may be more susceptible than others to perturbations occurring prenatally. These results indicate that the critical period of DNA methylation programming of nonpromoter, intergenic sequences occurs in male germline progenitor cells in the prenatal period, a time when external perturbations of epigenetic patterns could result in diminished fertility.     

植物开花的组蛋白甲基化调控分子机理

开花是指植物从营养生长转变到生殖生长的生理过程,是植物个体发育和后代繁衍的中心环节,既受遗传基础决定,同时又受到温度和光周期等多种环境因素的调控。在拟南芥中,已经分离了大量的与开花相关的基因,从遗传学上已初步形成了一个开花调控的网络。组蛋白甲基化是植物发育过程的重要调节方式,近年来关于其参与开花调控的研究有了重要进展。本文综述了具有代表性的组蛋白H3赖氨酸甲基化修饰参与调控植物开花发育的机制,提出该研究领域的发展方向和前景。     

NATURAL VARIATION IN EPIGENETIC GENE REGULATION AND ITS EFFECTS ON PLANT DEVELOPMENTAL TRAITS

In plants, epigenetic variation contributes to phenotypic differences in developmental traits. At the mechanistic level, this variation is conferred by DNA methylation and histone modifications. We describe several examples in which changes in gene expression caused by variation in DNA methylation lead to alterations in plant development. In these examples, the presence of repeated sequences or transposons within the promoters of the affected genes are associated with DNA methylation and gene inactivation. Small interfering RNAs expressed from these sequences recruit DNA methylation to the gene. Some of these methylated alleles are unstable giving rise to revertant sectors during mitosis and to progeny in which the methylated state is lost. However, others are stable for many generations and persist through speciation. These examples indicate that although DNA methylation influences gene expression, this is frequently dependent on classical changes to DNA sequence such as transposon insertions. By contrast, forms of histone methylation cause repression of gene expression that is stably inherited through mitosis but that can also be erased over time or during meiosis. A striking example involves the induction of flowering by exposure to low winter temperatures in Arabidopsis thaliana and its relatives. Histone methylation participates in repression of expression of an inhibitor of flowering during cold. In annual, semelparous species such as A. thaliana, this histone methylation is stably inherited through mitosis after return from cold to warm temperatures allowing the plant to flower continuously during spring and summer until it senesces. However, in perennial, iteroparous relatives the histone modification rapidly disappears when temperatures rise, allowing expression of the floral inhibitor to increase and limiting flowering to a short interval. In this case, epigenetic histone modifications control a key adaptive trait, and their pattern changes rapidly during evolution associated with life‐history strategy. We discuss these examples of epigenetic developmental traits with emphasis on the underlying mechanisms, their stability, and adaptive value.     

Epigenetic and physiological effects of gibberellin inhibitors and chemical pruners on the floral transition of azalea

The ability to control the timing of flowering is a key strategy in planning the production of ornamental species such as azaleas; however, it requires a thorough understanding of floral transition. DNA methylation is involved in controlling the functional state of chromatin and gene expression during floral induction pathways in response to environmental and developmental signals. Plant hormone signalling is also known to regulate suites of morphogenic processes in plants and its role in flowering-time control is starting to emerge as a key controlling step. This work investigates if the gibberellin (GA) inhibitors and chemical pinching applied in improvement of azalea flowering alter the dynamics of DNA methylation or the levels of polyamines (PAs), GAs and cytokinins (CKs) during floral transition, and whether these changes could be related to the effects observed on flowering ability. DNA methylation during floral transition and endogenous content of PAs, GAs and CKs were analysed after the application of GA synthesis inhibitors (daminozide, paclobutrazol and chlormequat chloride) and a chemical pruner (fatty acids). The application of GA biosynthesis inhibitors caused alterations in levels of PAs, GAs and CKs and in global DNA methylation levels during floral transition; also, these changes in plant growth regulators and DNA methylation were correlated with flower development. DNA methylation, PA, GA and CK levels can be used as predictive markers of plant floral capacity in azalea.