DNA甲基化——肿瘤产生的一种表观遗传学机制

在人类基因组中,DNA甲基化是一种表观遗传修饰,它与肿瘤的发生关系密切。抑癌基因和DNA修复基因的高甲基化、重复序列DNA的低甲基化、某些印记基因的印记丢失与多种肿瘤的发生有关。目前研究发现,基因组中甲基化的水平不仅受DNA 甲基化转移酶（DNMT）的影响,还与组蛋白甲基化、叶酸摄入、RNA干扰等多种因素有关。DNA甲基化在基因转录过程中扮有重要角色,并与组蛋白修饰、染色质构型重塑共同参与转录调控。     

DNA甲基化与基因表达调控研究进展

表观遗传修饰是指不改变DNA序列的、可遗传的对碱基和组蛋白的化学修饰,主要包括DNA甲基化、组蛋白修饰、染色质重塑以及非编码RNA等.表观遗传修饰是更高层次的基因表达调控手段.DNA甲基化是一种重要的表观遗传修饰,参与基因表达调控、基因印记、转座子沉默、X染色体失活以及癌症发生等重要生物学过程.近年来随着研究方法和技术的进步,全基因组DNA甲基化的研究广泛兴起,多个物种全基因组甲基化图谱被破译,全局水平对DNA甲基化的研究不仅利于在宏观层面上了解DNA甲基化的特性与规律,同时也为深入分析DNA甲基化的生物学功能与调控奠定了基础.结合最新研究进展综述DNA甲基化在基因组中的分布模式、规律以及和基因转录的关系等.     

非编码RNA与哺乳动物基因组印记的起源

基因组印记是由亲本来源不同而导致等位基因表达差异的一种遗传现象,主要发生在胎盘哺乳动物（真哺乳类）和显花植物中.大部分印记基因都分布在印记基因簇内,其中包含大量的非编码RNA基因.印记基因的表达受印记控制区（ICRs）的顺式调控.基因组印记产生的原因及过程是现代遗传学研究的一个热点问题,分析印记同源区从非印记物种到印记物种的过渡,为解决这一问题提供了重要启示.最近,原始哺乳动物（有袋类和单孔类）模式物种全基因组测序的完成,极大地促进了印记同源区的比较分析研究.本文对这些研究进行了回顾和分析,发现非编码RNA与哺乳动物基因组印记获得关系密切.主要依据为：（1）伴随着基因组印记的获得,印记区有大量的非编码RNA新基因出现;（2）与基因组印记相关的一些保守非编码RNA的表达发生了显著变化.此外,对15种脊椎动物中印记snoRNA基因系统分析的结果表明：印记snoRNA起源于真哺乳类与有袋类动物分化之后,并且在真哺乳类辐射进化之前发生了迅速的扩张,主要的基因家族在这一时期已经形成.这些结果进一步证明了非编码RNA与基因组印记获得的密切联系.非编码RNA可能主要通过调控印记表达和诱导染色体表观遗传修饰两种机制,参与哺乳动物基因组印记的获得.     

哺乳动物基因组印记的擦除、建立和维持机理

基因组印记主要依靠印记基因DNA甲基化方式调控,这种表观遗传修饰让多种哺乳动物出现基因单等位表达现象。印记的擦除发生在原始生殖细胞(primordial germ cells,PGCs)时期,其主要途径为活化诱导的胞苷脱氨酶(activation-induced cytidine deaminase,AID)、TET(ten-eleven translocation)蛋白介导的去甲基化。印记的建立发生在配子发生期,雌雄有明显的不同。印记的维持在多种因子的共同作用下完成,主要参与的蛋白有Dnmt1、Dppa3、KAP1和ZFP57等。印记的维持贯穿整个发育阶段,并通过细胞分裂遗传给子代。机体正常生长发育有赖于印记基因的正常表达。随着第一个印记基因IGF2R的发现,对于印记机制的研究不断推进。该文将概述基因组印记的建立、维持、擦除机理以及克隆动物中存在的印记基因异常重编程。     

DNA甲基化在动植物遗传育种中的研究进展

DNA甲基化是真核生物表观遗传学重要的机制之一,对基因转录水平的表达具有重要的调控作用。近年来,DNA甲基化在动植物遗传育种领域的研究引起了人们广泛的关注。我们从DNA甲基化与基因的表达调控、动植物基因组的甲基化状态、甲基敏感扩增片段多态性方法、DNA甲基化与杂种优势,以及DNA甲基化与分子标记等方面,简要综述了国内外有关DNA甲基化在动植物遗传育种研究中的进展,着重于全基因组DNA甲基化模式在动植物遗传育种中的相关研究和应用。     

DNA甲基化与基因表达调节

DNA异常甲基化是一种表观遗传改变,常发生在启动子区的CpG岛。某些基因甲基化与基因表达密切相关,在生命过程中扮演着重要功能。一方面,DNA甲基化与高等动物的生长发育密切相关,另一方面,DNA甲基化和其他生命过程也有重要的联系。如X染色体失活、基因组印记、发育调控及细胞分化和肿瘤发生发展中起重要作用。     

基因印记与lncRNA

基因印记是一种表观遗传调控机制,在二倍体哺乳动物的发育过程中,基因印记可以调控来自亲代的等位基因差异表达。非编码RNA是不编码蛋白质的RNA,它在RNA水平调控基因表达。研究表明大多数印记基因中存在长非编码RNA（长度>200nt的非编码RNA）的转录,长非编码RNA主要通过顺式的转录干扰作用来实现基因印记。同时基因印记及其相关的长非编码RNA异常表达与许多先天疾病相关,迄今已发现数十种人类遗传疾病与基因印记有关,而lncRNA引起的基因印记在疾病的发生和治疗中起着重要作用。     

植物DNA甲基化及其表观遗传作用

表观遗传学(epigenetics)是研究没有DNA序列变化的、可遗传的基因表达的改变。目前研究表明,表观遗传学在植物生长发育过程中起着极其重要的作用,主要通过包括DNA甲基化、RNA干涉、基因组印记、转基因沉默等多个方面来调控植物的生长发育。其中,DNA甲基化是表观遗传学的最重要研究内容之一,是调节基因组功能的重要手段。现对植物DNA甲基化的特征、维持机制、调控机制、表观遗传作用及其研究方法进行简要论述。     

印记基因:发育中的重要调节因子

印记基因是一类单等位表达的基因,数量少但功能强大,构成了基因组印记这一表观遗传领域中的独特现象,来源于不同亲本的印记基因在个体发育过程中承担着不同的重要功能。除了印记基因状态的建立、保持,人们围绕印记基因在发育进程中的功能做了大量研究。印记基因最初在核移植研究中被发现,早期研究聚焦在个别基因簇上。随着组学技术的引入,更多的印记基因被筛选和鉴定出来,这也引起了该领域内的热烈讨论和关注。随着全基因组DNA甲基化及组蛋白修饰等研究方法的发展,人们对印记基因的两个经典调控模型又提出新的看法和思考,尤其是最近的一些研究成果对于解释印记基因在哺乳动物中的高度保守性及其存在的意义具有重要启示。本文立足于最新研究进展,从印记基因的特征和基本规律、发育中的调控作用、机制、研究方法、进化以及环境对其影响等几个方面进行了综述,旨在为人们全面了解印记基因概况及研究趋势提供参考和指导。     

胎盘发育过程中的表观遗传学改变及其相关疾病

胎盘介于胎儿与母体之间,是维持胎儿宫内生长发育的重要器官。在胎盘的正常发育过程中,子宫正常蜕膜化、滋养层细胞粘附与侵袭、胎盘血管生成与形成、胎盘印记基因表达都受到表观遗传修饰(如DNA甲基化、组蛋白修饰、非编码RNA等)的调控。研究已经证实环境因素如重金属、化合物、现代辅助生殖技术、营养物质均可导致胎盘上多种基因的表观遗传修饰异常。此外,胎盘基因表达存在性别差异也可能与表观遗传修饰有关。目前,在临床上可运用产前DNA甲基化水平分析技术检测异常的表观遗传修饰,并在疾病早期发现并做出诊断,从而为疾病预防及治疗提供依据。本文对胎盘正常发育过程中表观遗传修饰的调控及环境因素所致的胎盘基因表观遗传改变进行了综述,以期对胎盘相关疾病的诊断与治疗提供借鉴和参考。     

哺乳动物印记基因的研究进展

哺乳动物印记基因是指只表达亲本一方的遗传信息,而另一方处于关闭状态的一类基因。约80%的印记基因呈串出现在染色体上;在哺乳动物品种之间,印记基因具有较高的保守性;印记基因的复制通常表现为不同时性;一些印记基因具有印记遗传的时空性;少数印记基因只转录为mRNA而不翻译成蛋白质;印记基因的反意链通常表达,表达产生具有调节印记基因的作用。哺乳动物印记基因的调控序列的DNA甲基化、组蛋白乙酰酸化和组蛋白甲基化等引起其印记表达,其中DNA分子的甲基化是关键,它在生命周期中可被清除,也可被标记。印记基因之间的调控表达通常是相互作用的。克隆动物作为印记基因研究的实验动物模型,已获得许多有意义的研究结果。     

The role of DMDs in the maintenance of epigenetic states

An important aspect of genome reprogramming is the establishment and maintenance of gamete-specific DNA methylation patterns that distinguish the parental alleles of imprinted genes. Disrupting the accurate transmission of genomic imprints by interfering with these methylation patterns causes severe defects in fetal growth and development. The inheritance of sex-specific DNA methylation patterns from both parents is thus a fundamental molecular definition of genomic imprinting. The other cardinal aspect is the regulation of imprinted gene expression over a long genomic distance, spanning a few clustered imprinted genes. There is converging experimental evidence that differentially methylated domains (DMDs), located in non-coding regions of imprinted genes, are involved in both processes. As such, DMDs are the imprinting backbone upon which the fundamental processes of sex-specific methylation and imprinted gene expression are built.     

Multilocus epimutations of imprintome in the pathology of human embryo development

Genomic imprinting is one of the key epigenetic phenomena involved in embryonic development of eutherians and humans. Molecular mechanisms of imprinting disturbances in the pathology of prenatal and postnatal onthogenesis are to a great extent related to methylation abnormalities of the imprinted genes. Over recent years, data are accumulating on multiple abnormalities of methylation simultaneously in several imprinted loci in the development of various pathologies that raises the issue of deciphering the structural and functional organization of imprintome and the interaction of imprinted genes. The present work analyzes DNA methylation of 51 imprinted genes in the placental tissues of human spontaneous abortions. We revealed multiple epimutations in from four to 12 imprinted genes in every embryo. Most of the epimutations (78%) were of a postzygotic origin. It has been established for the first time that the total incidence of methylation disturbance in maternal and paternal alleles of the imprinted genes leading to embryo development suppression is significantly higher than the incidence of epimutations, which stimulate embryogenesis. This fact supports at the epigenetic level the hypothesis of parent-offspring conflict that describes the occurrence of a monoallelic expression of imprinted genes in mammalian evolution.     

Differential methylation persists at the mouse Rasgrf1 DMR in tissues displaying monoallelic and biallelic expression

A subset of mammalian genes exhibits genomic imprinting, whereby one parental allele is preferentially expressed. Differential DNA methylation at imprinted loci serves both to mark the parental origin of the alleles and to regulate their expression. In mouse, the imprinted gene Rasgrf1 is associated with a paternally methylated imprinting control region which functions as an enhancer blocker in its unmethylated state. Because Rasgrf1 is imprinted in a tissue-specific manner, we investigated the methylation pattern in monoallelic and biallelic tissues to determine if methylation of this region is required for both imprinted and non-imprinted expression. Our analysis indicates that DNA methylation is restricted to the paternal allele in both monoallelic and biallelic tissues of somatic and extraembryonic lineages. Therefore, methylation serves to mark the paternal Rasgrf1 allele throughout development, but additional factors are required for appropriate tissue-specific regulation of expression at this locus.     

Erasing genomic imprinting memory in mouse clone embryos produced from day 11.5 primordial germ cells

Genomic imprinting is an epigenetic mechanism that causes functional differences between paternal and maternal genomes, and plays an essential role in mammalian development. Stage-specific changes in the DNA methylation patterns of imprinted genes suggest that their imprints are erased some time during the primordial germ cell (PGC) stage, before their gametic patterns are re-established during gametogenesis according to the sex of individuals. To define the exact timing and pattern of the erasure process, we have analyzed parental-origin-specific expression of imprinted genes and DNA methylation patterns of differentially methylated regions (DMRs) in embryos, each derived from a single day 11.5 to day 13.5 PGC by nuclear transfer. Cloned embryos produced from day 12.5 to day 13.5 PGCs showed growth retardation and early embryonic lethality around day 9.5. Imprinted genes lost their parental-origin-specific expression patterns completely and became biallelic or silenced. We confirmed that clones derived from both male and female PGCs gave the same result, demonstrating the existence of a common default state of genomic imprinting to male and female germlines. When we produced clone embryos from day 11.5 PGCs, their development was significantly improved, allowing them to survive until at least the day 11.5 embryonic stage. Interestingly, several intermediate states of genomic imprinting between somatic cell states and the default states were seen in these embryos. Loss of the monoallelic expression of imprinted genes proceeded in a step-wise manner coordinated specifically for each imprinted gene. DNA demethylation of the DMRs of the imprinted genes in exact accordance with the loss of their imprinted monoallelic expression was also observed. Analysis of DNA methylation in day 10.5 to day 12.5 PGCs demonstrated that PGC clones represented the DNA methylation status of donor PGCs well. These findings provide strong evidence that the erasure process of genomic imprinting memory proceeds in the day 10.5 to day 11.5 PGCs, with the timing precisely controlled for each imprinted gene. The nuclear transfer technique enabled us to analyze the imprinting status of each PGC and clearly demonstrated a close relationship between expression and DNA methylation patterns and the ability of imprinted genes to support development.     

Genomic imprinting in plants: observations and evolutionary implications

The epigenetic phenomenon of genomic imprinting occurs among both plants and animals. In species where imprinting is observed, there are parent-of-origin effects on the expression of imprinted genes in offspring. This review focuses on imprinting in plants with examples from maize, where gene imprinting was first described, and Arabidopsis. Our current understanding of imprinting in plants is presented in the context of cytosine methylation and imprinting in mammals, where developmentally essential genes are imprinted. Important considerations include the structure and organization of imprinted genes and the role of regional, differential methylation. Imprinting in plants may be related to other epigenetic phenomena including paramutation and transgene silencing. Finally, we discuss the role of gene structure and evolutionary implications of imprinting in plants.     

Convergent evolution of genomic imprinting in plants and mammals

Parental genomic imprinting is characterized by the expression of a selected panel of genes from one of the two parental alleles. Recent evidence shows that DNA methylation and histone modifications are responsible for this parent-of-origin-dependent expression of imprinted genes. Because similar epigenetic marks have been recruited independently in plants and mammals, the only organisms in which imprinted gene loci have been identified so far, this phenomenon represents a case for convergent evolution. Here we discuss the emerging parallels in imprinting in both taxa. We also describe the significance of imprinting for reproduction and discuss potential models for its evolution.     

Multilocus epimutations of imprintome in the pathology of embryo development

Genomic imprinting is one of the most significant epigenetic phenomena, which is involved in the support of eutherians and human embryo development. Molecular mechanisms of imprinting disturbance in the pathology of pre- and postnatal ontogeny are related to a considerable degree to aberrant DNA methylation of imprinted genes. At present time data about multiple abnormalities of DNA methylation arising simultaneously in several imprinted loci are accumulated. This fact brings up the problem of interpretation of imprintome structural and functional organization, as well as interaction of imprinted genes. At present study DNA methylation analysis of 51 imprinted genes in placental tissues of human spontaneous abortions was performed. The presence of several epimutations affected from four to 12 imprinted genes was observed in each embryo. Majority of epimutations (78%) had a postzygotic origin. It was shown for the first time that the total incidence of abnormal DNA methylation of maternal and paternal alleles of imprinted genes, which lead to suppression of embryo development, is significantly higher than the incidence of epimutations, which can lead to stimulation of ontogenesis processes. This fact supports at the epigenetic level the "sex conflict" hypothesis, which explains the appearance of monoallelic imprinted genes expression in the evolution of mammals.     

Establishment of paternal allele-specific DNA methylation at the imprinted mouse Gtl2 locus

The monoallelic expression of imprinted genes is controlled by epigenetic factors including DNA methylation and histone modifications. In mouse, the imprinted gene Gtl2 is associated with two differentially methylated regions: the IG-DMR, which serves as a gametic imprinting mark at which paternal allele-specific DNA methylation is inherited from sperm, and the Gtl2-DMR, which acquires DNA methylation on the paternal allele after fertilization. The timeframe during which DNA methylation is acquired at secondary DMRs during post-fertilization development and the relationship between secondary DMRs and imprinted expression have not been well established. In order to better understand the role of secondary DMRs in imprinting, we examined the methylation status of the Gtl2-DMR in pre- and post-implantation embryos. Paternal allele-specific DNA methylation of this region correlates with imprinted expression of Gtl2 during post-implantation development but is not required to implement imprinted expression during pre-implantation development, suggesting that this secondary DMR may play a role in maintaining imprinted expression. Furthermore, our developmental profile of DNA methylation patterns at the Cdkn1c- and Gtl2-DMRs illustrates that the temporal acquisition of DNA methylation at imprinted genes during post-fertilization development is not universally controlled.Key words: genomic imprinting, DNA methylation, Gtl2, secondary DMR, epigenetics