DNA甲基化与肿瘤

表观遗传指不涉及DNA序列改变的,可随细胞分裂而遗传的基因组修饰作用;DNA甲基化是其中研究最多的基因表达调节机制。异常DNA甲基化可致肿瘤发生,它亦是肿瘤基因诊断和治疗的靶点。文章介绍DNA甲基化基本概念、作用效果及其可能机制;并讨论异常DNA甲基化与肿瘤的关联,包括肿瘤中DNA异常甲基化原因、异常甲基化致瘤机制及基因甲基化研究在肿瘤诊治中的应用等。     

Different measures of “genome-wide” DNA methylation exhibit unique properties in placental and somatic tissues

DNA methylation of CpGs located in two types of repetitive elements—LINE1 (L1) and Alu—is used to assess “global” changes in DNA methylation in studies of human disease and environmental exposure. L1 and Alu contribute close to 30% of all base pairs in the human genome and transposition of repetitive elements is repressed through DNA methylation. Few studies have investigated whether repetitive element DNA methylation is associated with DNA methylation at other genomic regions, or the biological and technical factors that influence potential associations. Here, we assess L1 and Alu DNA methylation by Pyrosequencing of consensus sequences and using subsets of probes included in the Illumina Infinium HumanMethylation27 BeadChip array. We show that evolutionary age and assay method affect the assessment of repetitive element DNA methylation. Additionally, we compare Pyrosequencing results for repetitive elements to average DNA methylation of CpG islands, as assessed by array probes classified into strong, weak and non-islands. We demonstrate that each of these dispersed sequences exhibits different patterns of tissue-specific DNA methylation. Correlation of DNA methylation suggests an association between L1 and weak CpG island DNA methylation in some of the tissues examined. We caution, however, that L1, Alu and CpG island DNA methylation are distinct measures of dispersed DNA methylation and one should not be used in lieu of another. Analysis of DNA methylation data is complex and assays may be influenced by environment and pathology in different or complementary ways.     

DNA methylation in plants: relationship to small RNAs and histone modifications, and functions in transposon inactivation

DNA methylation is a type of epigenetic marking that strongly influences chromatin structure and gene expression in plants and mammals. Over the past decade, DNA methylation has been intensively investigated in order to elucidate its control mechanisms. These studies have shown that small RNAs are involved in the induction of DNA methylation, that there is a relationship between DNA methylation and histone methylation, and that the base excision repair pathway has an important role in DNA demethylation. Some aspects of DNA methylation have also been shown to be shared with mammals, suggesting that the regulatory pathways are, in part at least, evolutionarily conserved. Considerable progress has been made in elucidating the mechanisms that control DNA methylation; however, many aspects of the mechanisms that read the information encoded by DNA methylation and mediate this into downstream regulation remain uncertain, although some candidate proteins have been identified. DNA methylation has a vital role in the inactivation of transposons, suggesting that DNA methylation is a key factor in the evolution and adaptation of plants.     

Different measures of “genome-wide” DNA methylation exhibit unique properties in placental and somatic tissues

DNA methylation of CpGs located in two types of repetitive elements—LINE1 (L1) and Alu—is used to assess “global” changes in DNA methylation in studies of human disease and environmental exposure. L1 and Alu contribute close to 30% of all base pairs in the human genome and transposition of repetitive elements is repressed through DNA methylation. Few studies have investigated whether repetitive element DNA methylation is associated with DNA methylation at other genomic regions, or the biological and technical factors that influence potential associations. Here, we assess L1 and Alu DNA methylation by Pyrosequencing of consensus sequences and using subsets of probes included in the Illumina Infinium HumanMethylation27 BeadChip array. We show that evolutionary age and assay method affect the assessment of repetitive element DNA methylation. Additionally, we compare Pyrosequencing results for repetitive elements to average DNA methylation of CpG islands, as assessed by array probes classified into strong, weak and non-islands. We demonstrate that each of these dispersed sequences exhibits different patterns of tissue-specific DNA methylation. Correlation of DNA methylation suggests an association between L1 and weak CpG island DNA methylation in some of the tissues examined. We caution, however, that L1, Alu and CpG island DNA methylation are distinct measures of dispersed DNA methylation and one should not be used in lieu of another. Analysis of DNA methylation data is complex and assays may be influenced by environment and pathology in different or complementary ways.     

植物DNA甲基化研究进展

DNA基化是一种重要的表观遗传修饰方式,强烈地影响植物染色质结构和基因的表达,因此植物DNA基化的研究对植物生长发育及进化过程的研究发展起着重要作用。本文概述了植物DNA基化的特征,并对植物DNA基化的发生机制、生物学功能、检测分析方法等方面进行了综述,旨在深入了解DNA基化对植物的影响。     

植物DNA甲基化及其研究策略

DNA甲基化是表观遗传学研究的热点问题之一, 植物DNA甲基化的研究对植物研究领域的发展有着举足轻重的作用。本文阐述了植物DNA甲基化的相关机制, 其中包括RdDM(RNA-dependent DNA methylation)、DNA 甲基化与组蛋白修饰 以及DNA 去甲基化等近几年研究的热点问题; 讨论了DNA甲基化在植物发育中的功能(包括基因组防御和调控基因表达)、DNA甲基化与转基因沉默的关系以及其在表观遗传学中的地位。最后就目前国内外研究植物DNA甲基化所采取的常用策略,即高效液相色谱法、亚硫酸盐测序法、甲基化敏感的限制性内切酶结合Southern杂交分析法和MSAP(methylation-sensitive amplified Polymorphism)法进行了详尽的介绍和讨论。     

植物DNA甲基化及其研究策略

DNA甲基化是表观遗传学研究的热点问题之一,植物DNA甲基化的研究对植物研究领域的发展有着举足轻重的作用。本文阐述了植物DNA甲基化的相关机制,其中包括RdDM（RNA—dependent DNA methylation）、DNA甲基化与组蛋白修饰以及DNA去甲基化等近几年研究的热点问题：讨论了DNA甲基化在植物发育中的功能（包括基因组防御和调控基因表达）、DNA甲基化与转基因沉默的关系以及其在表观遗传学中的地位。最后就目前国内外研究植物DNA甲基化所采取的常用策略,即高效液相色谱法、亚硫酸盐测序法、甲基化敏感的限制性内切酶结合Southern杂交分析法和MSAP（methylation—sensitive amplified polymorphism）法进行了详尽的介绍和讨论。     

Role of CpG context and content in evolutionary signatures of brain DNA methylation

DNA methylation is essential in brain function and behavior; therefore, understanding the role of DNA methylation in brain-based disorders begins with the study of DNA methylation profiles in normal brain. Determining the patterns and scale of methylation conservation and alteration in an evolutionary context enables the design of focused but effective methylation studies of disease states. We applied an enzymatic-based approach, Methylation Mapping Analysis by Paired-end Sequencing (Methyl-MAPS), which utilizes second-generation sequencing technology to provide an unbiased representation of genome-wide DNA methylation profiles of human and mouse brains. In this large-scale study, we assayed CpG methylation in cerebral cortex of neurologically and psychiatrically normal human postmortem specimens, as well as mouse forebrain specimens. Cross-species human-mouse DNA methylation conservation analysis shows that DNA methylation is not correlated with sequence conservation. Instead, greater DNA methylation conservation is correlated with increasing CpG density. In addition to CpG density, these data show that genomic context is a critical factor in DNA methylation conservation and alteration signatures throughout mammalian brain evolution. We identify key genomic features that can be targeted for identification of epigenetic loci that may be developmentally and evolutionarily conserved and wherein aberrations in DNA methylation patterns can confer risk for disease.     

Role of CpG context and content in evolutionary signatures of brain DNA methylation

DNA methylation is essential in brain function and behavior; therefore, understanding the role of DNA methylation in brain-based disorders begins with the study of DNA methylation profiles in normal brain. Determining the patterns and scale of methylation conservation and alteration in an evolutionary context enables the design of focused but effective methylation studies of disease states. We applied an enzymatic-based approach, Methylation Mapping Analysis by Paired-end Sequencing (Methyl-MAPS), which utilizes second-generation sequencing technology to provide an unbiased representation of genome-wide DNA methylation profiles of human and mouse brains. In this large-scale study, we assayed CpG methylation in cerebral cortex of neurologically and psychiatrically normal human postmortem specimens, as well as mouse forebrain specimens. Cross-species human-mouse DNA methylation conservation analysis shows that DNA methylation is not correlated with sequence conservation. Instead, greater DNA methylation conservation is correlated with increasing CpG density. In addition to CpG density, these data show that genomic context is a critical factor in DNA methylation conservation and alteration signatures throughout mammalian brain evolution. We identify key genomic features that can be targeted for identification of epigenetic loci that may be developmentally and evolutionarily conserved and wherein aberrations in DNA methylation patterns can confer risk for disease.     

DNA甲基化与脂肪组织生长发育

DNA甲基化作为一种重要的表观遗传学修饰方式,在维持正常细胞功能、遗传印记、胚胎发育以及人类肿瘤发生中起着重要作用。DNA甲基化最重要的作用是调控基因表达,它是细胞调控基因表达的重要表观遗传机制之一。近年来的研究发现,DNA甲基化在脂肪组织生长发育以及肥胖症发生过程中发挥着重要作用。DNA甲基化通过调控脂肪细胞分化转录因子、转录辅助因子以及其他脂肪代谢相关基因的表达,从而调控脂肪组织的生长发育。该文综述了脂肪组织生长发育过程中DNA甲基化的最新研究进展,探讨了脂肪组织DNA甲基化的研究趋势和未来发展方向。     

First evidence of DNA methylation in insect Tribolium castaneum

DNA methylation has been studied in many eukaryotic organisms, in particular vertebrates, and was implicated in developmental and phenotypic variations. Little is known about the role of DNA methylation in invertebrates, although insects are considered as excellent models for studying the evolution of DNA methylation. In the red flour beetle, Tribolium castaneum (Tenebrionidae, Coleoptera), no evidence of DNA methylation has been found till now. In this paper, a cytosine methylation in Tribolium castaneum embryos was detected by methylation sensitive restriction endonucleases and immuno-dot blot assay. DNA methylation in embryos is followed by a global demethylation in larvae, pupae and adults. DNA demethylation seems to proceed actively through 5-hydroxymethylcytosine, most probably by the action of TET enzyme. Bisulfite sequencing of a highly abundant satellite DNA located in pericentromeric heterochromatin revealed similar profile of cytosine methylation in adults and embryos. Cytosine methylation was not only restricted to CpG sites but was found at CpA, CpT and CpC sites. In addition, complete cytosine demethylation of heterochromatic satellite DNA was induced by heat stress. The results reveal existence of DNA methylation cycling in T. castaneum ranging from strong overall cytosine methylation in embryos to a weak DNA methylation in other developmental stages. Nevertheless, DNA methylation is preserved within heterochromatin during development, indicating its role in heterochromatin formation and maintenance. It is, however, strongly affected by heat stress, suggesting a role for DNA methylation in heterochromatin structure modulation during heat stress response.     

不同倍性西瓜基因组DNA甲基化水平与模式的MSAP分析

DNA甲基化是表观遗传修饰的主要方式之一,在基因表达调控中发挥重要作用。本研究以不同倍性（2x、3x、4x）西瓜为试材,采用基于DNA甲基化敏感酶的扩增多态性分析（Methylation-Sensitive Ampliftcation Polymorphism,MSAP）方法,在全基因组水平上探究西瓜同源多倍化过程中DNA序列中CCGG位点的甲基化水平及模式变化特征。研究中选用23对选扩引物,共检测到1883个基因位点。二倍体、三倍体、四倍体中检测到的位点数分别为647、655和581;其中发生甲基化的位点数分别为181、150和159。相应的扩增总甲基化率分别为28．0％、22．9％和27．4％：全甲基化位点数分别为121、80和82,相应的全甲基化率分别为18．7％、12．2％和14．1％。进一步对不同倍性西瓜DNA甲基化模式的变化特征进行分析,结果显示：四倍体西瓜与二倍体西瓜相比有超过半数的位点（54．4％）DNA甲基化模式发生了变化,其与三倍体西瓜相比也有近一半的位点（45．4％）DNA甲基化模式发生了变化,并且变化趋势都以四倍体西瓜甲基化程度升高为主：而三倍体西瓜与二倍体西瓜相比．虽然也有41．6％的位点DNA甲基化模式发生了改变,但变化趋势以三倍体西瓜甲基化程度降低略占优势：与之相似,三倍体西瓜与四倍体相比较。甲基化的变化趋势也是以三倍体西瓜甲基化程度降低为主。以上结果表明：不同倍性西瓜中DNA甲基化事件虽均有发生．但不论是从总甲基化率还是全甲基化率来看,DNA甲基化水平与倍性高低关系不大．三倍体西瓜表现出较为显著的低甲基化水平特征。DNA甲基化模式的分析也表明。与二倍体及四倍体西瓜相比．三倍体西瓜DNA甲基化模式的调整主要以去甲基化为主。显示出三倍体西瓜基因组独特的DNA甲基化特征。本研究为进一步从表观遗传学的角度探讨西瓜的三倍体优?     

Analysis of Age-Related Global DNA Methylation in Chicken

DNA methylation is an epigenetic modification that plays an important role in the normal development and function of organisms. The level of DNA methylation is species-, tissue-, and organelle-specific, and the methylation pattern is determined during embryogenesis. DNA methylation has also been correlated with age. The aim of this study was to determine the global DNA methylation levels and their correlation with age in the chicken, using a Polish autosexing chicken breed, Polbar. A quantitative technique based on an immunoenzymatic assay was used for global DNA methylation analysis. The results show increased global DNA methylation levels with older Polbar embryos. Global DNA methylation levels decrease with the age of hens in the postembryonic stage. This study expands the current knowledge of the Polbar epigenome and the general knowledge of the function of epigenetic mechanisms in birds.