Restriction landmark genome scanning identifies culture-induced DNA methylation instability in the human embryonic stem cell epigenome

Widespread provision of human embryonic stem cells (hESCs) for therapeutic use, drug screening and disease modelling will require cell lines sustainable over long periods in culture. Since the short-term, in vitro culture of mammalian embryos can result in DNA methylation changes, the epigenetic stability of hESCs warrants investigation. Existing hESC lines have been derived and cultured under diverse conditions, providing the potential for programming differential changes into the epigenome that may result in inter-line variability over and above that inherited from the embryo. By examining the DNA methylation profiles of > 2000 genomic loci by Restriction Landmark Genome Scanning, we identified substantial inter-line epigenetic distance between six independently derived hESC lines. Lines were found to inherit further epigenetic changes over time in culture, with most changes arising in the earliest stages post-derivation. The loci affected varied between lines. The majority of culture-induced changes (82.3-87.5%) were stably inherited both within the undifferentiated cells and post-differentiation. Adapting a line to a serum-free culture system resulted in additional epigenetic instability. Overall 80.5% of the unstable loci uncovered in hESCs have been associated previously with an adult tumour phenotype. Our study shows that current methods of hESC propagation can rapidly programme stable and unpredictable epigenetic changes in the stem cell genome. This highlights the need for (i) novel screening strategies to determine the experimental utility and biosafety of hESCs and (ii) optimization and standardization of procedures for the derivation and culture of hESC lines that minimize culture-induced instability.     

RNA expression microarray analysis in mouse prospermatogonia: identification of candidate epigenetic modifiers.

The mammalian totipotent and pluripotent lineage exhibits genome-wide dynamics with respect to DNA methylation content. The first phase of global DNA demethylation and de novo remethylation occurs during preimplantation development and gastrulation, respectively, while the second phase occurs in primordial germ cells and primary oocytes/prospermatogonia, respectively. These dynamics are indicative of a comprehensive epigenetic resetting or reprogramming of the genome in preparation for major differentiation events. To gain further insight into the mechanisms driving DNA methylation dynamics and other types of epigenetic modification, we performed an RNA expression microarray analysis of fetal prospermatogonia at the stage when they are undergoing rapid de novo DNA remethylation. We have identified a number of highly or specifically expressed genes that could be important for determining epigenetic change in prospermatogonia. These data provide a useful resource in the discovery of molecular pathways involved in epigenetic reprogramming in the mammalian germ line.     

The early-life social environment and DNA methylation

DNA methylation is a chemical modification of DNA that confers, upon identical sequences, different identities that are reflected in different gene expression programming. DNA methylation has a well-established role in cellular differentiation by providing a mechanism for one genome to express multiple phenotypes in a multicellular organism. Recent data point however to the possibility that in addition to the innate process of cellular differentiation, DNA methylation can serve as a genome adaptation mechanism, adapting genome function to changing environmental contexts including social environments. A critical time point for this process is early life when cues from the social and physical environments define lifelong trajectories of physical and mental health. DNA methylation and additional epigenetic modifications could therefore serve as molecular links between 'nurture' and 'nature'. Data that are consistent with this new role for DNA methylation as a mechanism for conferring an 'environment' specific identity to DNA will be discussed.     

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

Cross-talk between DNA methylation and histone modifications drives the establishment of composite epigenetic signatures and is traditionally studied using correlative rather than direct approaches. Here, we present sequential ChIP-bisulfite-sequencing (ChIP-BS-seq) as an approach to quantitatively assess DNA methylation patterns associated with chromatin modifications or chromatin-associated factors directly. A chromatin-immunoprecipitation (ChIP)-capturing step is used to obtain a restricted representation of the genome occupied by the epigenetic feature of interest, for which a single-base resolution DNA methylation map is then generated. When applied to H3 lysine 27 trimethylation (H3K27me3), we found that H3K27me3 and DNA methylation are compatible throughout most of the genome, except for CpG islands, where these two marks are mutually exclusive. Further ChIP-BS-seq-based analysis in Dnmt triple-knockout (TKO) embryonic stem cells revealed that total loss of CpG methylation is associated with alteration of H3K27me3 levels throughout the genome: H3K27me3 in localized peaks is decreased while broad local enrichments (BLOCs) of H3K27me3 are formed. At an even broader scale, these BLOCs correspond to regions of high DNA methylation in wild-type ES cells, suggesting that DNA methylation prevents H3K27me3 deposition locally and at a megabase scale. Our strategy provides a unique way of investigating global interdependencies between DNA methylation and other chromatin features.     

Epigenetics for anthropologists: An introduction to methods

The study of epigenetics, or chemical modifications to the genome that may alter gene expression, is a growing area of interest for social scientists. Anthropologists and human biologists are interested in epigenetics specifically, as it provides a potential link between the environment and the genome, as well as a new layer of complexity for the study of human biological variation. In pace with the rapid increase in interest in epigenetic research, the range of methods has greatly expanded over the past decade. The primary objective of this article is to provide an overview of the current methods for assaying DNA methylation, the most commonly studied epigenetic modification. We will address considerations for all steps required to plan and conduct an analysis of DNA methylation, from appropriate sample collection, to the most commonly used methods for laboratory analyses of locus‐specific and genome‐wide approaches, and recommendations for statistical analyses. Key challenges in the study of DNA methylation are also discussed, including tissue specificity, the stability of measures, timing of sample collection, statistical considerations, batch effects, and challenges related to analysis and interpretation of data. Our hope is that this review serves as a primer for anthropologists and human biologists interested in incorporating epigenetic data into their research programs. Am. J. Hum. Biol. 27:295–303, 2015. © 2015 Wiley Periodicals, Inc.     

Mammalian DNA (cytosine-5) methyltransferases and their expression

Two classes of functional DNA (cytosine-5) methyltransferases have been discovered in mammals to date. One class methylates the unmodified DNA and is designated as the de novo enzyme, whereas the other maintains the methylation status of the daughter strand during DNA replication and thus is referred to as a maintenance DNA methyltransferase. Each enzyme catalyzes methyl group transfer from S-adenosyl-L-methionine to cytosine bases in DNA. During methylation the enzyme flips its target base out of the DNA duplex into a typically concave catalytic pocket. This flipped cytosine base is then a substrate for the enzyme-catalyzed reaction. The newly formed 5-methylcytosine confers epigenetic information on the parental genome without altering nucleotide sequences. This epigenetic information is inherited during DNA replication and cell division. In mammals, DNA methylation participates in gene expression, protection of the genome against selfish DNA, parental imprinting, mammalian X chromosome inactivation, developmental regulation, T cell development, and various diseases.     

Epigenetic risks related to assisted reproductive technologies: risk analysis and epigenetic inheritance

A broad spectrum of assisted reproductive technologies has become available for couples with fertility problems. Follow-up studies of children born as a result of assisted reproduction have shown that neonatal outcome and malformation rates are not different from those of the general population, except for a low birthweight and a slight increase in chromosomal abnormalities. The safety aspect of assisted reproduction at the epigenetic level has not been well studied. Epigenetics refers to phenomena where modifications of DNA methylation and/or chromatin structure underlie changes in gene expression and phenotype characteristics. This article intends to analyse epigenetic risks related to assisted reproduction on the basis of an overview of epigenetic reprogramming events in the gamete and early embryo. Two epigenetic modifications, methylation and imprinting, are considered in more detail. The interference of in-vitro embryo culture, immature sperm cells and nuclear transfer with epigenetic reprogramming is discussed, as well as the possibility of epigenetic inheritance.     

哺乳动物卵母细胞的DNA甲基化和组蛋白修饰

哺乳动物卵母细胞发育过程中呈现出独特的表观遗传修饰模式。包括DNA甲基化和组蛋白修饰等在内的表观遗传修饰的建立,是一个复杂但高度有序的过程,对哺乳动物卵母细胞成熟和早期胚胎发育至关重要。因此,探究并揭示卵母细胞表观遗传特征建立的机制,对深入理解哺乳动物生殖发育机理和相关疾病的发生发展具有重要意义。本文以小鼠和人类为典型代表,阐述了哺乳动物卵母细胞发育过程中DNA甲基化以及组蛋白甲基化、乙酰化、泛素化、磷酸化和乳酸化的分布模式和动态变化特征,总结并探讨了这些表观遗传修饰之间潜在的关联及影响其发挥生物学功能的多种调控因素。     

Reproductive epigenetics

Epigenetics refers to covalent modifications of DNA and core histones that regulate gene activity without altering DNA sequence. To date, the best-characterized DNA modification associated with the modulation of gene activity is methylation of cytosine residues within CpG dinucleotides. Human disorders associated with epigenetic abnormalities include rare imprinting diseases, molar pregnancies, and childhood cancers. Germ cell development and early embryo development are critical times when epigenetic patterns are initiated or maintained. This review focuses on the epigenetic modification DNA methylation and discusses recent progress that has been made in understanding when and how epigenetic patterns are differentially established in the male and female germlines, the mouse, and human disorders associated with abnormalities in epigenetic programming in germ cells and early embryos, as well as genetic and other modulators (e.g. nutrition and drugs) of reproductive epigenetic events.     

DNA甲基化与印记基因

[摘要] 遗传外修饰指不影响DNA遗传编码而调控基因组活性的过程,甲基化转移酶在该过程中发挥着重要的作用。配子的遗传外编程是印记建立的必要条件,与印记的形成机制有关,对基因组功能有重要影响。DNA甲基化、组蛋白乙酰化在印记基因表达过程中相互作用。印记基因可以解释肿瘤的发生以及一些遗传性疾病。有逐渐增多的证据表明,辅助生殖技术 (assisted reproductive technologies,ART)与印记基因存在联系,探索ART影响印记基因的机制将有助于ART技术的完善,防止ART相关并发症的发生。本文就DNA甲基化与印记基因研究进展进行综述。     

透明细胞肾细胞癌的表观遗传学研究进展

正肾脏肿瘤的发病率在人类泌尿系统肿瘤中排名第3,约占恶性肿瘤的3%,发病年龄主要在50~70岁,每年导致90 000多例患者死亡,且呈递增趋势~([1])。肾癌的具体发病机制不详,除遗传因素外,吸烟、肥胖、污染和辐射等也是重要因素。大多数透明细胞肾细胞癌(clear cell renal cell carcinoma,ccRCC)患者在早期无任何症状,20%~30%患者在     

Developmental origins of male subfertility: role of infection,inflammation, and environmental factors

Male gamete development begins with the specification of primordial cells in the epiblast of the early embryo and is not complete until spermatozoa mature in the epididymis of adult males. This protracted developmental process involves extensive alteration of the paternal germline epigenome. Initially, epigenetic reprogramming in fetal germ cells results in removal of most DNA methylation, including parent-specific epigenetic information. The germ cells then establish sex-specific epigenetic information through de novo methylation and undergo spermatogenesis. Chromatin in haploid germ cells is repackaged into protamines during spermiogenesis, providing further widespread epigenetic reorganization. Finally, after fertilization, epigenetic reprogramming in the preimplantation embryo is necessary for regaining totipotency. These events provide substantial windows during which epigenetic errors either may be corrected or may occur in the germline. There is now increasing evidence that environmental factors such as exposure to toxicants, the parents’ and individual’s diet, and even infectious and inflammatory events in the male reproductive tract may influence epigenetic reprogramming. This, together with other damage inflicted on the germline chromatin, may result in negative consequences for fertility and health. Large epidemiological birth cohort studies have yielded insight into possible causative environmental factors. Together with experimental animal studies, a clearer view of environmental impacts on fetal development and their intergenerational and even transgenerational effects on reproductive health has emerged and is reviewed in this article.     

Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation

DNA methylation is an essential epigenetic modification that plays a key role associated with the regulation of gene expression during differentiation, but in disease states such as cancer, the DNA methylation landscape is often deregulated. There are now numerous technologies available to interrogate the DNA methylation status of CpG sites in a targeted or genome-wide fashion, but each method, due to intrinsic biases, potentially interrogates different fractions of the genome. In this study, we compare the affinity-purification of methylated DNA between two popular genome-wide techniques, methylated DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain-based capture (MBDCap), and show that each technique operates in a different domain of the CpG density landscape. We explored the effect of whole-genome amplification and illustrate that it can reduce sensitivity for detecting DNA methylation in GC-rich regions of the genome. By using MBDCap, we compare and contrast microarray- and sequencing-based readouts and highlight the impact that copy number variation (CNV) can make in differential comparisons of methylomes. These studies reveal that the analysis of DNA methylation data and genome coverage is highly dependent on the method employed, and consideration must be made in light of the GC content, the extent of DNA amplification, and the copy number.     

再生医学研究新进展：DNA甲基化与细胞重编程

背景：使用一些生长因子能使终分化的体细胞重编程而产生多能性干细胞。 目的：讨论表观遗传机制在细胞重编程和调节中的作用,揭示表观遗传基因调控的变化、表观遗传修饰标记的稳定性及其对基因组表达的影响。 方法：在PubMed数据库及CNKI数据库,以“DNA甲基化,细胞重编程,干细胞”为关键词检索1990/2008相关的文章。 结果与结论：尽管在体内细胞分化通常是单向和不可逆的,但这个过程可被重编程而改变。使用一些生长因子能使终分化的体细胞重编程而产生多能性干细胞。目前为止,导入转录因子、DNA去甲基化、表观基因改变已被用于诱导重编程。通过了解其分子机制,揭示表观遗传基因调控的变化、表观遗传修饰标记的稳定性及其对基因组表达的影响,对基因治疗的发展有重要意义。然而依然许多问题有待深入研究,如：是AID还是 DNA去甲基酶对DNA去甲基化起重要作用？DNA去甲基化需要什么条件？肿瘤细胞中CpG片段能否去甲基化,癌细胞是否更难重编程？     

Impaired epigenetic gene activity regulation and human diseases

The epigenetic (i.e. heritable states that are mediated by changes in DNA other than nucleotide sequence) mechanisms of regulation of gene expression have been recently the focus of intensive studies. Genomic imprinting refers to the epigenetic gene marking that results in monoallelic expression. The epigenetic mechanism of imprinting is based on the gamete-specific methylation of some mammalian genes, which restricts their expression on one of the parental chromosomes. The imprinted genes control fetal and placental development, cell proliferation and adult behavior. Changes in the normal imprinting patterns give rise to numerous genetic diseases, including cancer. Examining the molecular processes that mediate these methylation genome changes will give use a great insight into the mechanisms of regulation of gene activity and into the etiology of some human genetic diseases.