组蛋白去甲基化酶在发育和再生医学的研究

表观遗传学调控在器官发育以及再生医学中是重要的研究内容,而组蛋白的甲基化修饰属于表观遗传学调控机制之一并且成为近年来研究的热点内容。处于不同甲基化状态下的组蛋白,能影响多种分子对其的识别和结合,在转录起始、转录效率和转录后加工等多个层面调控相关基因的表达。而哺乳动物的器官发育与细胞重编程都与基因选择性表达密切相关,因此组蛋白甲基化状态在基因选择性表达中扮演着重要角色。本文概述了组蛋白去甲基化酶的分类以及组蛋白不同甲基化状态下对于基因的表达的调控,同时总结了组蛋白去甲基化酶在维持胚胎干细胞的多分化潜能和IPS细胞重编程效率方面的作用以及组蛋白去甲基化酶基因的缺失与相关器官发育的影响。最后探讨了组蛋白甲基化修饰酶在推动发育生物学与再生医学研究进展方面的潜能。     

m^6 A RNA甲基化修饰异常在肿瘤中的作用

N6-甲基腺嘌呤(N6-methyladenosine,m6A)是真核生物信使RNA(messenger RNA,mRNA)含量最多的化学修饰之一。m6A修饰主要由m6A甲基转移酶(methyltransferase)催化,m6A去甲基酶(demethylase)去除,并由m6A结合蛋白(binding protein)识别。它广泛参与调控mRNA剪接、加工、翻译和降解等生命周期的各个阶段,且与肥胖和肿瘤等多种疾病及异常的生理功能相关。近年的研究发现,肿瘤中m6A相关蛋白质(METTL3/14、WTAP、FTO、ALKBH5、YTHDFs)的异常表达,引发m6A甲基化的失调,调控致癌基因和抑癌基因的表达参与肿瘤的发生与发展,并与患者预后不良密切相关。随着RNA免疫沉淀测序技术与高通量测序技术和液相色谱等检测技术的快速发展,有关m6A在肿瘤发生发展中的作用机制研究的进展迅猛,靶向m6A也成为肿瘤临床治疗的新方向。本文重点对m6A RNA甲基化相关因子在癌症发生发展中的作用及机制进行综述,总结m6A RNA甲基化检测技术的最新进展,梳理现有文献报道的脱甲基酶抑制剂大黄酸、甲氯芬那酸2(meclofenamic acid2,MA2)和右旋羟戊二酸(R-2-hydroxyglutarate,R-2HG)等在肿瘤靶向治疗中的运用,为以m6A RNA甲基化为切入点的肿瘤防治研究提供思路与理论参考。     

哺乳动物DNA甲基化及其在体细胞诱导重编程中的作用

诱导多能干细胞(Induced pluripotent stem cell, iPS)技术提供了将终末分化的细胞逆转为多潜能干细胞的可能, 在干细胞基础理论研究和再生医学中具有重要意义。然而, 目前体细胞诱导重编程方法效率极低, 常发生不完全的重编程。研究表明, 在不完全重编程的细胞中存在体细胞的表观遗传记忆, 而DNA甲基化作为相对长期和稳定的表观遗传修饰, 是影响重编程效率和iPS细胞分化能力的重要因素之一。哺乳动物DNA甲基化是指胞嘧啶第五位碳原子上的甲基化修饰, 常发生于CpG位点。DNA甲基化能够调节体细胞特异基因和多能性基因的表达, 因此其在哺乳动物基因调控、胚胎发育和细胞重编程过程中发挥着重要作用。此外, 异常DNA甲基化可能导致iPS细胞基因印记的异常和X染色体的失活。文章重点围绕DNA甲基化的机制、分布特点、及其在体细胞诱导重编程中的作用进行了综述。     

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。     

生殖细胞及早期胚胎基因组印记的表观调控

基因组印记是一种区别父母等位基因的表观遗传过程,可导致父源和母源基因特异性表达。印记是在配子发生过程中全基因组表观重编程时获得的,且在早期胚胎发育过程中得以维持。因此,在全基因组重编程过程中,对印记的识别和维持十分重要。本文概述了原始生殖细胞的印记清除、双亲原始生殖细胞的印记获得以及早期胚胎发育过程中印记维持的相关过程,并对在印记区域内保护印记基因免受全基因组DNA去甲基化的表观遗传因子的相关作用机制进行了讨论。     

Chromatin modification and epigenetic reprogramming in mammalian development

The developmental programme of embryogenesis is controlled by both genetic and epigenetic mechanisms. An emerging theme from recent studies is that the regulation of higher-order chromatin structures by DNA methylation and histone modification is crucial for genome reprogramming during early embryogenesis and gametogenesis, and for tissue-specific gene expression and global gene silencing. Disruptions to chromatin modification can lead to the dysregulation of developmental processes, such as X-chromosome inactivation and genomic imprinting, and to various diseases. Understanding the process of epigenetic reprogramming in development is important for studies of cloning and the clinical application of stem-cell therapy.     

DNA methylation dynamics in human induced pluripotent stem cells

Indeed human induced pluripotent stem cells (hiPSCs) are considered to be powerful tools in regenerative medicine. To enable the use of hiPSCs in the field of regenerative medicine, it is necessary to understand the mechanisms of reprogramming during the transformation of somatic cells into hiPSCs. Genome-wide epigenetic modification constitutes a critical event in the generation of iPSCs. In other words, to analyze epigenetic changes in iPSCs means to elucidate reprogramming processes. We have established a large number of hiPSCs derived from various human tissues and have obtained their DNA methylation profiles. Comparison analyses indicated that the epigenetic patterns of various hiPSCs, irrespective of their source tissue, were very similar to one another and were similar to those of human embryonic stem cells (hESCs). However, the profiles of hiPSCs and hESCs exhibited epigenetic differences, which were caused by random aberrant hypermethylation at early passages. Interestingly, continuous passaging of the hiPSCs diminished the differences between DNA methylation profiles of hiPSCs and hESCs. The number of aberrant DNA methylation regions may thus represent a useful epigenetic index for evaluating hiPSCs in the context of therapeutic applications.     

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。     

系统性红斑狼疮患者PBMCs差异表达基因m6A修饰的生物信息学分析

采用生物信息学方法,通过公共数据库,分析系统性红斑狼疮(SLE)N6-甲基腺苷(m6A)修饰谱系。基于公共数据建立SLE m6A传修饰表达谱,分析m6A相关的DEGs在SLE中的潜在作用;利用ADEx数据库获取DEGs,利用m6A GEO数据集(GSE173312),分析获取SLE m6A修饰谱;用DAVID对m6A DEGs进行GO/Pathway注释分析。在SLE患者中,m6A组分写入器RBM15B和擦除酶FTO的表达下调,阅读器IGFBP3的表达上调。SLE m6A修饰谱包括181个基因,其中123个基因的表达上调,58个基因的表达下调。这些基因主要参与了细胞凋亡和细胞周期通路、I型干扰素信号通路,DNA复制和B细胞MHC II分子调节等生物学过程。SLE患者的PBMCs细胞m6A修饰存在异常,并可能参与疾病的发生和发展。     

N~6 -methyl-adenosine (m ~6A) in RNA: An Old Modification with A Novel Epigenetic Function

N6 -methyl-adenosine (m6A) is one of the most common and abundant modifications on RNA molecules present in eukaryotes. However, the biological significance of m6A methylation remains largely unknown. Several independent lines of evidence suggest that the dynamic regulation of m6A may have a profound impact on gene expression regulation. The m6A modification is catalyzed by an unidentified methyltransferase complex containing at least one subunit methyltransferase like 3 (METTL3). m6A modification on messenger RNAs (mRNAs) mainly occurs in the exonic regions and 3’-untranslated region (3’-UTR) as revealed by high-throughput m6A-seq. One significant advance in m6A research is the recent discovery of the first two m6A RNA demethylases fat mass and obesity-associated (FTO) gene and ALKBH5, which catalyze m6A demethylation in an a-ketoglutarate (a-KG)-and Fe2+-dependent manner. Recent studies in model organisms demonstrate that METTL3, FTO and ALKBH5 play important roles in many biological processes, ranging from development and metabolism to fertility. Moreover, perturbation of activities of these enzymes leads to the disturbed expression of thousands of genes at the cellular level, implicating a regulatory role of m6A in RNA metabolism. Given the vital roles of DNA and histone methylations in epigenetic regulation of basic life processes in mammals, the dynamic and reversible chemical m6A modification on RNA may also serve as a novel epigenetic marker of profound biological significances.     

High resolution methylation analysis of the HoxA5 regulatory region in different somatic tissues of laboratory mouse during development

Homeobox genes encode a group of DNA binding regulatory proteins whose key function occurs in the spatial-temporal organization of genome during embryonic development and differentiation. The role of these Hox genes during ontogenesis makes it an important model for research. HoxA5 is a member of Hox gene family playing a central role during axial body patterning and morphogenesis. DNA modification studies have shown that the function of Hox genes is partly governed by the methylation-mediated gene expression regulation. Therefore the study aimed to investigate the role of epigenetic events in regulation of tissue-specific expression pattern of HoxA5 gene during mammalian development. The methodology adopted were sodium bisulfite genomic DNA sequencing, quantitative real-time PCR and chromatin-immunoprecipitation (ChIP). Methylation profiling of HoxA5 gene promoter shows higher methylation in adult as compared to fetus in various somatic tissues of mouse being highest in adult spleen. However q-PCR results show higher expression during fetal stages being highest in fetal intestine followed by brain, liver and spleen. These results clearly indicate a strict correlation between DNA methylation and tissue-specific gene expression. The findings of chromatin-immunoprecipitation (ChIP) have also reinforced that epigenetic event like DNA methylation plays important role in the regulation of tissue specific expression of HoxA5.     

METTL14 suppresses pyroptosis and diabetic cardiomyopathy by downregulating TINCR lncRNA

N6-methyladenosine (m6A) is one of the most important epigenetic regulation of RNAs, such as lncRNAs. However, the underlying regulatory mechanism of m6A in diabetic cardiomyopathy (DCM) is very limited. In this study, we sought to define the role of METTL14-mediated m6A modification in pyroptosis and DCM progression. DCM rat model was established and qRT-PCR, western blot, and immunohistochemistry (IHC) were used to detect the expression of METTL14 and TINCR. Gain-and-loss functional experiments were performed to define the role of METTL14-TINCR-NLRP3 axis in pyroptosis and DCM. RNA pulldown and RNA immunoprecipitation (RIP) assays were carried out to verify the underlying interaction. Our results showed that pyroptosis was tightly involved in DCM progression. METTL14 was downregulated in cardiomyocytes and hear tissues of DCM rat tissues. Functionally, METTL14 suppressed pyroptosis and DCM via downregulating lncRNA TINCR, which further decreased the expression of key pyroptosis-related protein, NLRP3. Mechanistically, METTL14 increased m6A methylation level of TINCR gene, resulting in its downregulation. Moreover, the m6A reader protein YTHDF2 was essential for m6A methylation and mediated the degradation of TINCR. Finally, TINCR positively regulated NLRP3 by increasing its mRNA stability. To conclude, our work revealed the novel role of METTL14-mediated m6A methylation and lncRNA regulation in pyroptosis and DCM, which could help extend our understanding the epigenetic regulation of pyroptosis in DCM progression.Subject terms: Cardiomyopathies, Endocrine system and metabolic diseases