DNA羟甲基化与表观遗传学调控

表观遗传学中的DNA甲基化与疾病的发生发展密不可分. DNA甲基化中的5-甲基胞嘧啶易发生氧化形成5 羟甲基胞嘧啶.此过程又称为羟甲基化修饰,已成为表观遗传学研究的一种新热点.羟甲基化与10-11易位家族蛋白（ten-eleven translocation,TET）的作用密切相关,它参与了基因的表达调控以及DNA去甲基化过程. 最近的羟甲基化研究主要集中在癌症和精神性疾病.针对日趋增多的相关研究,本文对DNA羟甲基化进行了全景式综述.     

哺乳动物DNA甲基化修饰的动态调控机制

DNA甲基化是最主要的表观遗传修饰之一,主要发生在胞嘧啶第五位碳原子上,称为5-甲基胞嘧啶。哺乳动物DNA甲基化由从头DNA甲基转移酶DNMT3A/3B在胚胎发育早期建立。细胞分裂过程中甲基化模式的维持由DNA甲基转移酶DNMT1实现。TET家族蛋白氧化5-甲基胞嘧啶成为5-羟甲基胞嘧啶、5-醛基胞嘧啶和5-羧基胞嘧啶,从而起始DNA的去甲基化过程。这些DNA甲基化修饰酶精确调节DNA甲基化的动态过程,在整个生命发育过程中发挥重要作用,其失调也与多种疾病发生密切相关。本文对近年来DNA甲基化修饰酶的结构与功能研究进行讨论。     

哺乳动物DNA甲基化修饰的动态调控机制

DNA甲基化是生命体最主要的表观遗传修饰之一。哺乳动物DNA甲基化主要发生在胞嘧啶第五位碳原子上,称为5-甲基胞嘧啶(5-methylcytosine,5m C)。哺乳动物DNA甲基化由从头DNA甲基转移酶DNMT3A/3B在胚胎发育早期建立,甲基化模式的维持由DNA甲基转移酶DNMT1实现。TET家族蛋白氧化5-甲基胞嘧啶起始DNA的去甲基化过程。这些DNA甲基化修饰酶精确调节DNA甲基化的动态过程,在整个生命发育过程中发挥重要作用,其失调也与多种疾病发生密切相关。现结合国内外同行研究进展,介绍课题组近年来对DNA甲基化修饰酶的结构与功能研究。     

DNA羟甲基化修饰在消化系统肿瘤中的研究进展

DNA羟甲基化修饰是基因组表观遗传学的重要调控方式,指5-甲基胞嘧啶(5-m C)在TET蛋白家族的催化作用下氧化生成5-羟甲基胞嘧啶(5-hm C),完成DNA胞嘧啶的去甲基化过程。基因组甲基化异常导致了多种肿瘤的发生,羟甲基化修饰作为去甲基化的一种,同样与肿瘤发生密不可分。在消化系统肿瘤发生发展过程中存在5-hm C含量的变化,其原因可能与TET蛋白家族、IDH突变等密切相关,提示DNA羟甲基化修饰参与了消化系统肿瘤的发生发展过程。本文围绕DNA羟甲基化修饰与消化系统肿瘤之间的关系进行综述,旨在为消化系统肿瘤羟甲基化修饰研究提供新方向。     

DNA羟甲基化调控动脉粥样硬化的研究进展

DNA羟甲基化作为一种表观遗传学修饰,对基因的表达调控起到了重要作用。近年来,越来越多的研究发现在心血管疾病中可见5-羟甲基胞嘧啶(5-hydroxymethylcytosine, 5hmC)和染色体10/11易位(ten-eleven translocation,TET)家族蛋白的异常改变,提示这些心血管疾病与DNA羟甲基化的调控密切相关。DNA羟甲基化水平与动脉粥样硬化常见的危险因素如衰老、性别、高血压和吸烟存在一定关联,并且和动脉粥样硬化发生过程中所涉及的免疫炎症反应以及内皮细胞和血管平滑肌细胞的功能相关。本文综述了DNA羟甲基化和TET家族蛋白对于动脉粥样硬化的作用机制及研究现状,以期为动脉粥样硬化的发生发展及诊断治疗提供表观遗传学方面的研究思路。     

TET酶的生物学功能及相关机制的研究进展

DNA甲基化（DNA methylation）及去甲基化属于常见的表观遗传修饰,可介导多种生理和病理过程。DNA甲基化及去甲基化修饰参与基因的表达调控,且二者的动态平衡可以维持遗传表达稳定性。DNA甲基转移酶（DNA methyltransferase,DNMT）主要包括DNMT1、DNMT3A、DNMT3B、DNMT3L,DNA去甲基化酶（DNA demethylase）主要指10-11易位蛋白（ten-eleven-translocation protein,TET）家族,包括TET1、TET2、TET3,是调节DNA甲基化和去甲基化的重要酶类。TET酶是目前发现的调节DNA去甲基化（DNA demethylation）过程中最重要的酶。综述了TET酶在DNA去甲基化修饰中的作用机制,探讨了DNA去甲基化酶在生长发育和疾病中的关键作用,以期为今后表观遗传学的相关研究提供新思路。     

真核生物基因组DNA甲基化和去甲基化分析

DNA甲基化是真核生物的重要表观遗传修饰,如胞嘧啶C~5位甲基化5-甲基胞嘧啶(5mC)和腺嘌呤N~6位甲基化6-甲基腺嘌呤(6mA)。DNA 5mC可经Tet双加氧酶催化氧化形成5-羟甲基胞嘧啶(5hmC)、5-醛甲基胞嘧啶(5fC)和5-羧基胞嘧啶(5caC)。这些氧化产物不仅是去甲基化过程的中间体,而且也可能存在各自特有的表观调控功能。其中,5hmC异常可能和癌症相关,有可能成为疾病诊断的生物标志物。发展可靠、高灵敏和抗干扰能力强的DNA甲基化和去甲基化检测技术和方法至关重要,有助于理解甲基化和去甲基化的分子机制以及提高肿瘤的诊断水平。现针对DNA甲基化和去甲基化检测技术进行简要介绍。     

RNA甲基化修饰调控和规律

表观遗传学修饰包括DNA、RNA和蛋白质的化学修饰,基于非序列改变所致基因表达和功能水平变化。近年来,在DNA和蛋白质修饰基础上,可逆RNA甲基化修饰研究引领了第3次表观遗传学修饰研究的浪潮。RNA存在100余种化学修饰,甲基化是最主要的修饰形式。鉴定RNA甲基化修饰酶及研发其转录组水平高通量检测技术,是揭示RNA化学修饰调控基因表达和功能规律的基础。本文主要总结了近年来本课题组与合作团队及国内外同行在RNA甲基化表观转录组学研究中取得的主要前沿进展,包括发现了RNA去甲基酶、甲基转移酶和结合蛋白,揭示RNA甲基化修饰调控RNA加工代谢,及其调控正常生理和异常病理等重要生命进程。这些系列研究成果证明RNA甲基化修饰类似于DNA甲基化,具有可逆性,拓展了RNA甲基化表观转录组学研究新领域,完善了中心法则表观遗传学规律。     

RNA m6A修饰在肿瘤发展及免疫治疗中的研究进展

N6-甲基腺嘌呤(N6-methyladenosine,m⁶A)是指在腺苷的N6位置发生的甲基化修饰,是真核m RNA中最常见的表观遗传修饰方式。m⁶A甲基化的紊乱会导致基因转录和翻译过程异常,从而促进癌症的发生和发展。最近的研究表明,m⁶A甲基化不仅可以影响肿瘤的细胞增殖和抑制信号网络,还能调节肿瘤免疫原性。该研究聚焦于探讨m⁶A调节因子在调控肿瘤关键信号通路中的相关机制,并阐述了m⁶A表观遗传修饰调节免疫检查点的表达方式。这将为理解m⁶A表观遗传修饰在调节肿瘤免疫逃逸中的作用和机制提供一个新的思路。此外,该文还强调了基于m⁶A修饰的靶向联合免疫治疗策略的前景和发展方向,这有望提高免疫检查点抑制剂的治疗效果。     

植物DNA和mRNA中N6-甲基腺嘌呤的比较研究

DNA、RNA的甲基化作为重要的表观遗传标记,在真核生物多个细胞过程中发挥作用.DNA中的 N6-甲基腺嘌呤(N6-methyladenine in DNA,6mA)和 RNA 中的 N6-甲基腺嘌呤(N6-methyladenine inRNA,m6A)均为来自腺嘌呤第6位的甲基化修饰,在合成和功能上有相似性也有区别...     

Iron deficiency and its epigenetic effects on iron homeostasis

Iron deficiency is a common micronutrient deficiency associated with metabolic changes in the levels of iron regulatory proteins, hepcidin and ferroportin. Studies have associated dysregulation of iron homeostasis to other secondary and life-threatening diseases including anaemia, neurodegeneration and metabolic diseases. Iron deficiency plays a critical role in epigenetic regulation by affecting the Fe²⁺/α-ketoglutarate-dependent demethylating enzymes, Ten Eleven Translocase 1–3 (TET 1–3) and Jumonji-C (JmjC) histone demethylase, which are involved in epigenetic erasure of the methylation marks on both DNA and histone tails, respectively. In this review, studies involving epigenetic effects of iron deficiency associated with dysregulation of TET 1–3 and JmjC histone demethylase enzyme activities on hepcidin/ferroportin axis are discussed.     

Epigenetics in Ocular Diseases

Epigenetics pertains to heritable alterations in gene expression that do not involve modification of the underlying genomic DNA sequence. Historically, the study of epigenetic mechanisms has focused on DNA methylation and histone modifications, but the concept of epigenetics has been more recently extended to include microRNAs as well. Epigenetic patterning is modified by environmental exposures and may be a mechanistic link between environmental risk factors and the development of disease. Epigenetic dysregulation has been associated with a variety of human diseases, including cancer, neurological disorders, and autoimmune diseases. In this review, we consider the role of epigenetics in common ocular diseases, with a particular focus on DNA methylation and microRNAs. DNA methylation is a critical regulator of gene expression in the eye and is necessary for the proper development and postmitotic survival of retinal neurons. Aberrant methylation patterns have been associated with age-related macular degeneration, susceptibility to oxidative stress, cataract, pterygium, and retinoblastoma. Changes in histone modifications have also been observed in experimental models of diabetic retinopathy and glaucoma. The expression levels of specific microRNAs have also been found to be altered in the context of ocular inflammation, retinal degeneration, pathological angiogenesis, diabetic retinopathy, and ocular neoplasms. Although the complete spectrum of epigenetic modifications remains to be more fully explored, it is clear that epigenetic dysregulation is an important contributor to common ocular diseases and may be a relevant therapeutic target.     

Chromatin remodeling and human disease

In the past few years, there has been a nascent convergence of scientific understanding of inherited human diseases with epigenetics. Identified epigenetic processes involved in human disease include covalent DNA modifications, covalent histone modifications, and histone relocation. Each of these processes influences chromatin structure and thereby regulates gene expression and DNA methylation, replication, recombination, and repair. The importance of these processes for nearly all aspects of normal growth and development is illustrated by the array of multi-system disorders and neoplasias caused by their dysregulation.     

Role of epigenetic reprogramming of host genes in bacterial pathogenesis

The genomes are regularly targeted by epigenetic regulatory mechanisms (DNA methylation, histone modifications, binding of regulatory proteins) in infected cells. In addition, proteins encoded by microbial genomes may disturb the action of a set of cellular promoters by interacting with the same epi-regulatory machinery. The outcome of this may result in epigenetic dysregulation and subsequent cellular dysfunctions that may manifest in or contribute to the development of pathological changes. How epigenetic methylation decorations on DNA and histones are started and established remains largely unknown. The inherited nature of these processes in regulation of genes suggests that they could play key roles in chronic diseases associated with microbial persistence; they might also explain so-called hit-and-run phenomena in infectious disease pathogenesis. Microbes infecting mammals may cause diseases by causing hyper-methylation of key cellular promoters at CpG di-nucleotides and may induce pathological changes by epigenetic reprogramming of host cells they are interacting with elucidation of the epigenetic consequences of microbe–host interactions may have important therapeutic implications because epigenetic processes can be reverted and elimination of microbes inducing patho-epigenetic changes may prevent disease development.     

γ-Glutamyl hydrolase modulation significantly influences global and gene-specific DNA methylation and gene expression in human colon and breast cancer cells

γ-Glutamyl hydrolase (GGH) plays an important role in folate homeostasis by catalyzing hydrolysis of polyglutamylated folate into monoglutamates. Polyglutamylated folates are better substrates for several enzymes involved in the generation of S-adenosylmethionine, the primary methyl group donor, and hence, GGH modulation may affect DNA methylation. DNA methylation is an important epigenetic determinant in gene expression, in the maintenance of DNA integrity and stability, and in chromatin modifications, and aberrant or dysregulation of DNA methylation has been mechanistically linked to the development of human diseases including cancer. Using a recently developed in vitro model of GGH modulation in HCT116 colon and MDA-MB-435 breast cancer cells, we investigated whether GGH modulation would affect global and gene-specific DNA methylation and whether these alterations were associated with significant gene expression changes. In both cell lines, GGH overexpression decreased global DNA methylation and DNA methyltransferase (DNMT) activity, while GGH inhibition increased global DNA methylation and DNMT activity. Epigenomic and gene expression analyses revealed that GGH modulation influenced CpG promoter DNA methylation and gene expression involved in important biological pathways including cell cycle, cellular development, and cellular growth and proliferation. Some of the observed altered gene expression appeared to be regulated by changes in CpG promoter DNA methylation. Our data suggest that the GGH modulation-induced changes in total intracellular folate concentrations and content of long-chain folylpolyglutamates are associated with functionally significant DNA methylation alterations in several important biological pathways.

Electronic supplementary material

The online version of this article (doi:10.1007/s12263-014-0444-0) contains supplementary material, which is available to authorized users.     

Preserving genome integrity and function: the DNA damage response and histone modifications

Modulation of chromatin templates in response to cellular cues, including DNA damage, relies heavily on the post-translation modification of histones. Numerous types of histone modifications including phosphorylation, methylation, acetylation, and ubiquitylation occur on specific histone residues in response to DNA damage. These histone marks regulate both the structure and function of chromatin, allowing for the transition between chromatin states that function in undamaged condition to those that occur in the presence of DNA damage. Histone modifications play well-recognized roles in sensing, processing, and repairing damaged DNA to ensure the integrity of genetic information and cellular homeostasis. This review highlights our current understanding of histone modifications as they relate to DNA damage responses (DDRs) and their involvement in genome maintenance, including the potential targeting of histone modification regulators in cancer, a disease that exhibits both epigenetic dysregulation and intrinsic DNA damage.