癌症相关的DNA甲基化连锁区域

DNA甲基化是重要的表观遗传标记之一,在转录调控中起直接作用。DNA甲基化的异常与癌症的发生发展密切相关。高通量测序使得在单碱基分辨率下检测全基因组的DNA甲基化水平成为可能。本文基于临近CpGs位点甲基化水平的相关性挖掘DNA甲基化连锁区域。结果发现DNA甲基化连锁区域的甲基化水平和模式在癌症中存在异常,而且显著富集到分化/发育相关的生物学功能。DNA甲基化连锁区域的挖掘有助于对具有生物学功能的表观遗传标记的进一步理解,有助于对癌症诊断的表观遗传标记的挖掘。     

DNA主动去甲基化的Science之路

DNA甲基化是一种非常重要的表观遗传调控方式,在基因印迹、X染色体失活、转座子与外源DNA的沉默及组织特异性基因的中发挥着重要的作用。在哺乳动物的配子发生过程及从受精到着床的早期胚胎发育阶段,基因组DNA发生大规模的主动去甲基化。但去甲基化的分子机制一直是表观遗传领域的谜题。2009年,Anjana Rao及其同事发现一种DNA双氧化酶TET蛋白能够将5-甲基胞嘧啶氧化成5-羟甲基胞嘧啶,这为DNA去甲基化的机制研究开拓了新的思路。在此基础上,徐国良实验室展开了深入研究,发现TET蛋白能够进一步将5-羟甲基胞嘧啶氧化成5-羧基胞嘧啶,并发现糖苷酶TDG能够特异性地识别并切除DNA中的5-羧基胞嘧啶,进而启动碱基切除修复途径完成DNA去甲基化,从而提出了氧化作用与碱基切除修复途径协同介导的DNA主动去甲基化机制。     

植物DNA甲基化作用机制的研究进展

DNA甲基化是表观遗传学的一种重要修饰形式,也是一种重要的基因表达调控机制。DNA甲基化的异常模式可导致植物生长发育异常。文中从植物DNA甲基化模式入手,对DNA甲基化在调控基因表达和维持基因组稳定性的分子功能、DNA甲基化在植物发育、参与植物对生物和非生物胁迫的反应等方面的相关研究进行回顾和总结,为深入了解DNA甲基化的作用机制并将DNA甲基化应用于植物新品种的培育和遗传改良研究提供一定的参考。     

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。     

利用拟南芥杂交组合研究siRNA与等位基因DNA甲基化调控中的联系

近年来,越来越多的实验结果表明,表观遗传因子,如DNA甲基化、小RNA、组蛋白修饰等在杂种优势形成中起到重要作用,然而对于这些表观遗传因子在F。中遗传调控方式的认识仍很有限．本实验室先前工作曾以拟南芥C24和Ler两种生态型及其正反交子一代为材料,运用新一代测序方法获得该杂交组合中DNA甲基化及小RNA单碱基分辨率的全基因组图谱．本文进一步对这批数据中的等位基因DNA甲基化水平进行分析,区分DNA甲基化遗传过程中的顺式与反式调控方式,并发现这两种调控方式均有重要的贡献．研究发现,siRNA与DNA甲基化的两种调控方式有密切联系,尤其在DNA甲基化的反式调控中,Fl中DNA甲基化变化程度越大,该区域内siRNA富集程度越强,二者可能存在某种调控机制．通过等位基因表观遗传组的分析研究杂交过程中DNA甲基化和小RNA遗传调控的规律,为更好地理解杂种优势机制提供了帮助．     

前列腺癌的DNA甲基化及其临床应用

目前认为恶性肿瘤的形成是遗传和表观遗传机制共同作用的结果。表观遗传机制包括DNA甲基化、组蛋白修饰和miRNA。DNA异常甲基化(高甲基化和低甲基化)是前列腺癌最具特征的表观遗传改变, 它能够导致基因组不稳定, 调控基因的异常表达, 在前列腺癌的形成和发展中起到重要作用。同时, DNA甲基化作为前列腺癌表观遗传研究的一个热点, 为临床前列腺癌的早期诊断、预后评估及药物治疗提供新的方法和途径。文章根据前列腺癌的DNA高甲基化和低甲基化的最新研究成果阐述了前列腺癌形成的表观遗传学机制, 并且讨论了它们在前列腺癌临床转化方面的最新研究进展。     

Nbn基因神经特异性敲除小鼠海马神经元发育的形态学研究

Nbn基因（又称Nbs1）是DNA断裂损伤修复和端粒长度调控的重要因子,其功能缺失不仅会导致DNA损伤修复异常,也会使端粒难以维持正常的稳定结构,从而影响小鼠中枢神经系统的发育,导致小头畸形、生长障碍、小脑萎缩以及共济失调等。本实验通过观察Nbn基因神经特异性敲除（Nbn-CNS-del）小鼠海马神经元发育的形态学变化,探讨Nbn基因在小鼠海马神经元发育中的作用,     

Tet双加氧酶在哺乳动物表观遗传调控中的作用

DNA甲基化作为一种重要的表观遗传修饰,在哺乳动物的生长发育过程中发挥着举足轻重的功能。DNA甲基化谱式并不是一成不变的,个体发育过程中甲基化谱式如何建立以及如何逆转从而实现基因时空特异性表达,一直是表观遗传领域的重大科学问题。课题以"干细胞全能性建立的表观遗传调控研究"为主要脉络,阐明了Tet双加氧酶介导的DNA去甲基化过程及其在细胞命运决定和哺乳动物发育中的功能。现将对项目启动五年来该课题的主要原创性工作进行综述。     

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。     

DNA甲基化与哺乳动物生殖

DNA甲基化是表观遗传水平基因表达调控的重要方式之一,对哺乳动物的生长发育具有重要作用。原始生殖细胞的甲基化水平、胚胎发育过程中甲基化的重排以及胎盘发育过程中异常甲基化都与生殖过程密切相关。男性不育、女性自然流产及辅助生殖技术(assisted reproductive technology,ART)的应用也与DNA甲基化有关,通过引起DNA甲基化变化从而影响表观遗传调控的变化。该文对DNA甲基化与哺乳动物生殖作一综述,并阐述DNA甲基化与男性不育、自然流产及ART过程的关系。     

Cooperative DNA and histone binding by Uhrf2 links the two major repressive epigenetic pathways

Gene expression is regulated by DNA as well as histone modifications but the crosstalk and mechanistic link between these epigenetic signals are still poorly understood. Here we investigate the multi-domain protein Uhrf2 that is similar to Uhrf1, an essential cofactor of maintenance DNA methylation. Binding assays demonstrate a cooperative interplay of Uhrf2 domains that induces preference for hemimethylated DNA, the substrate of maintenance methylation, and enhances binding to H3K9me3 heterochromatin marks. FRAP analyses revealed that localization and binding dynamics of Uhrf2 in vivo require an intact tandem Tudor domain and depend on H3K9 trimethylation but not on DNA methylation. Besides the cooperative DNA and histone binding that is characteristic for Uhrf2, we also found an opposite expression pattern of uhrf1 and uhrf2 during differentiation. While uhrf1 is mainly expressed in pluripotent stem cells, uhrf2 is upregulated during differentiation and highly expressed in differentiated mouse tissues. Ectopic expression of Uhrf2 in uhrf1(-/-) embryonic stem cells did not restore DNA methylation at major satellites indicating functional differences. We propose that the cooperative interplay of Uhrf2 domains may contribute to a tighter epigenetic control of gene expression in differentiated cells.     

Uhrf1 and Dnmt1 are required for development and maintenance of the zebrafish lens

DNA methylation is one of the key mechanisms underlying the epigenetic regulation of gene expression. During DNA replication, the methylation pattern of the parent strand is maintained on the replicated strand through the action of Dnmt1 (DNA Methyltransferase 1). In mammals, Dnmt1 is recruited to hemimethylated replication foci by Uhrf1 (Ubiquitin-like, Containing PHD and RING Finger Domains 1). Here we show that Uhrf1 is required for DNA methylation in vivo during zebrafish embryogenesis. Due in part to the early embryonic lethality of Dnmt1 and Uhrf1 knockout mice, roles for these proteins during lens development have yet to be reported. We show that zebrafish mutants in uhrf1 and dnmt1 have defects in lens development and maintenance. uhrf1 and dnmt1 are expressed in the lens epithelium, and in the absence of Uhrf1 or of catalytically active Dnmt1, lens epithelial cells have altered gene expression and reduced proliferation in both mutant backgrounds. This is correlated with a wave of apoptosis in the epithelial layer, which is followed by apoptosis and unraveling of secondary lens fibers. Despite these disruptions in the lens fiber region, lens fibers express appropriate differentiation markers. The results of lens transplant experiments demonstrate that Uhrf1 and Dnmt1 functions are required lens-autonomously, but perhaps not cell-autonomously, during lens development in zebrafish. These data provide the first evidence that Uhrf1 and Dnmt1 function is required for vertebrate lens development and maintenance.     

UHRF2 regulates local 5-methylcytosine and suppresses spontaneous seizures

The 5-methylcytosine (5mC) modification regulates multiple cellular processes and is faithfully maintained following DNA replication. In addition to DNA methyltransferase (DNMT) family proteins, ubiquitin-like PHD and ring finger domain-containing protein 1 (UHRF1) plays an important role in the maintenance of 5mC levels. Loss of UHRF1 abolishes 5mC in cells and leads to embryonic lethality in mice. Interestingly, UHRF1 has a paralog, UHRF2, that has similar sequence and domain architecture, but its biologic function is not clear. Here, we have generated Uhrf2 knockout mice and characterized the role of UHRF2 in vivo. Uhrf2 knockout mice are viable, but the adult mice develop frequent spontaneous seizures and display abnormal electrical activities in brain. Despite no global DNA methylation changes, 5mC levels are decreased at certain genomic loci in the brains of Uhrf2 knockout mice. Therefore, our study has revealed a unique role of UHRF2 in the maintenance of local 5mC levels in brain that is distinct from that of its paralog UHRF1.     

Usp7 and Uhrf1 control ubiquitination and stability of the maintenance DNA methyltransferase Dnmt1

In mammals Dnmt1 is the DNA methyltransferase chiefly responsible for maintaining genomic methylation patterns through DNA replication cycles, but how its maintenance activity is controlled is still not well understood. Interestingly, Uhrf1, a crucial cofactor for maintenance of DNA methylation by Dnmt1, is endowed with E3 ubiquitin ligase activity. Here, we show that both Dnmt1 and Uhrf1 coprecipitate with ubiquitin specific peptidase 7 (Usp7), a de-ubiquitinating enzyme. Overexpression of Uhrf1 and Usp7 resulted in opposite changes in the ubiquitination status and stability of Dnmt1. Our findings suggest that, by balancing Dnmt1 ubiquitination, Usp7 and Uhrf1 fine tune Dnmt1 stability.     

Folic acid and sodium butyrate prevent tumorigenesis in a mouse model of colorectal cancer

Colorectal cancer is a leading cause of morbidity and mortality worldwide, and its incidence has been increasing in recent years. The role of epigenetic modifications, including DNA methylation and histone modifications, has only recently been investigated. In this study, the effects of epigenetic agents such as folic acid (FA) and sodium butyrate (NaBu) on the development of colorectal cancer induced by 1,2-dimethylhydrazine (DMH) using ICR mice was examined. Of the mice treated in a chemopreventive manner with epigenetic agents, FA and NaBu, 15–50% developed colorectal cancer at 24 weeks compared with a 95% incidence of colorectal cancer in DMH-treated control mice. Folate deficiency can alter cytosine methylation in DNA leading to inappropriate activation of the proto-oncogene c-myc. We detected lower levels of p21WAF1 gene expression in colorectal cancer samples, as well as significantly lower levels of acetylated histone H3, compared with samples from corresponding normal colorectal mucosa. In contrast, administration of NaBu increased levels of p21WAF1 mRNA and p21WAF1 protein, and was associated with an accumulation of histone acetylation. In summary, our results show that FA and NaBu reduce the incidence of colorectal cancer induced by DMH-induced in ICR mice, and therefore we hypothesize that targeting epigenetic targets should be further investigated for the prevention of colorectal cancer in humans.     

Non-germ Line Restoration of Genomic Imprinting for a Small Subset of Imprinted Genes in Ubiquitin-like PHD and RING Finger Domain-Containing 1 (Uhrf1) Null Mouse Embryonic Stem Cells

The underlying mechanism for the establishment and maintenance of differential DNA methylation in imprinted genes is largely unknown. Previous studies using Dnmt1 knock-out embryonic stem (ES) cells demonstrated that, although re-expression of DNMT1 restored DNA methylation in the non-imprinted regions, the methylation patterns of imprinted genes could be restored only through germ line passage. Knock-out of Uhrf1, an accessory factor essential for DNMT1-mediated DNA methylation, in mouse ES cells also led to impaired global DNA methylation and loss of genomic imprinting. Here, we demonstrate that, although re-expression of UHRF1 in Uhrf1^−/− ES cells restored DNA methylation for the bulk genome but not for most of the imprinted genes, it did rescue DNA methylation for the imprinted H19, Nnat, and Dlk1 genes. Analysis of histone modifications at the differential methylated regions of the imprinted genes by ChIP assays revealed that for the imprinted genes whose DNA methylation could be restored upon re-expression of UHRF1, the active histone markers (especially H3K4me3) were maintained at considerably low levels, and low levels were maintained even in Uhrf1^−/− ES cells. In contrast, for the imprinted genes whose DNA methylation could not be restored upon UHRF1 re-expression, the active histone markers (especially H3K4me3) were relatively high and became even higher in Uhrf1^−/− ES cells. Our study thus supports a role for histone modifications in determining the establishment of imprinting-related DNA methylation and demonstrates that mouse ES cells can be a valuable model for mechanistic study of the establishment and maintenance of differential DNA methylation in imprinted genes.     

Agglomerates of aberrant DNA methylation are associated with toxicant-induced malignant transformation

Epigenetic dysfunction is a known contributor in carcinogenesis, and is emerging as a mechanism involved in toxicant-induced malignant transformation for environmental carcinogens such as arsenicals or cadmium. In addition to aberrant DNA methylation of single genes, another manifestation of epigenetic dysfunction in cancer is agglomerative DNA methylation, which can participate in long-range epigenetic silencing that targets many neighboring genes and has been shown to occur in several types of clinical cancers. Using in vitro model systems of toxicant-induced malignant transformation, we found hundreds of aberrant DNA methylation events that emerge during malignant transformation, some of which occur in an agglomerative fashion. In an arsenite-transformed prostate epithelial cell line, the protocadherin (PCDH), HOXC and HOXD gene family clusters are targeted for agglomerative DNA methylation. The agglomerative DNA methylation changes induced by arsenicals appear to be common and clinically relevant events, since they occur in other human cancer cell lines and models of malignant transformation, as well as clinical cancer specimens. Aberrant DNA methylation in general occurred more often within histone H3 lysine-27 trimethylation stem cell domains. We found a striking association between enrichment of histone H3 lysine-9 trimethylation stem cell domains and toxicant-induced agglomerative DNA methylation, suggesting these epigenetic modifications may become aberrantly linked during malignant transformation. In summary, we found an association between toxicant-induced malignant transformation and agglomerative DNA methylation, which lends further support to the hypothesis that epigenetic dysfunction plays an important role in toxicant-induced malignant transformation.     

Agglomerates of aberrant DNA methylation are associated with toxicant-induced malignant transformation

Epigenetic dysfunction is a known contributor in carcinogenesis, and is emerging as a mechanism involved in toxicant-induced malignant transformation for environmental carcinogens such as arsenicals or cadmium. In addition to aberrant DNA methylation of single genes, another manifestation of epigenetic dysfunction in cancer is agglomerative DNA methylation, which can participate in long-range epigenetic silencing that targets many neighboring genes and has been shown to occur in several types of clinical cancers. Using in vitro model systems of toxicant-induced malignant transformation, we found hundreds of aberrant DNA methylation events that emerge during malignant transformation, some of which occur in an agglomerative fashion. In an arsenite-transformed prostate epithelial cell line, the protocadherin (PCDH), HOXC and HOXD gene family clusters are targeted for agglomerative DNA methylation. The agglomerative DNA methylation changes induced by arsenicals appear to be common and clinically relevant events, since they occur in other human cancer cell lines and models of malignant transformation, as well as clinical cancer specimens. Aberrant DNA methylation in general occurred more often within histone H3 lysine-27 trimethylation stem cell domains. We found a striking association between enrichment of histone H3 lysine-9 trimethylation stem cell domains and toxicant-induced agglomerative DNA methylation, suggesting these epigenetic modifications may become aberrantly linked during malignant transformation. In summary, we found an association between toxicant-induced malignant transformation and agglomerative DNA methylation, which lends further support to the hypothesis that epigenetic dysfunction plays an important role in toxicant-induced malignant transformation.