专业背景：计算机科学 研究方向与兴趣: JavaEE-Web软件开发, 生物信息学, 数据挖掘与机器学习, 智能信息系统 目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学
摘要：
DNA甲基化是指生物体在DNA甲基转移酶(DNA methyltransferase，DNMT) 的催化下，以S-腺苷甲硫氨酸(SAM) 为甲基供体,将甲基转移到特定的碱基上的过程。 ......
DNA甲基化
DNA甲基化是指生物体在DNA甲基转移酶(DNA methyltransferase，DNMT) 的催化下，以S-腺苷甲硫氨酸(SAM) 为甲基供体,将甲基转移到特定的碱基上的过程。DNA甲基化可以发生在腺嘌呤的N -6位、胞嘧啶的N -4位、鸟嘌呤的N -7位或胞嘧啶的C-5位等。但在哺乳动物,DNA甲基化主要发生在5’-CpG-3’的C上.生成5-甲基胞嘧啶(5mC) 。反应如下：
图1 DNA甲基化
人类的CpG以两种形式存在，一种是分散于DNA 中，另一种是CpG结构高度聚集的CpG岛。在正常组织里，70 %～90 %的散在的CpG是被甲基修饰的,而CpG岛则是非甲基化的。
甲基化的作用
1．基因C →T突变
DNA 甲基化引起基因突变的机制主要是由于DMT催化反应形成。DMT可以加快C(胞嘧啶) 和5mC 脱氨,封闭U(尿嘧啶) 的修复,并且使U →T 改变,故DMT 促使CpG序列的C →T突变 。
图2： C突变成T
抑癌基因p53就是一个典型的例证。50% 实体瘤病人出现p53基因突变。突变中24% 是CpG 甲基化后脱氨引起的C→T 突变。
2 影响基因错配修复
DNA 错配修复系统(DNAmismatch repair system，MMR) 是指存在人类细胞中的一种修复DNA 碱基错配的安全保障体系，它是由一系列特异修复DNA碱基错配的酶分子组成。Ahujia 等研究发现MMR 缺陷时,CpG岛的甲基化增强,并认为MMR 与DNA 甲基化有关。在基因错配修复过程中甲基化具有导向识别作用,而在错配修复基因表达缺陷的原因中基因突变和基因启动子区的高甲基化是其主要原因 。
3．基因沉默
目前认为,甲基化影响基因表达的机制有下列几种： ①直接作用。基因的甲基化改变了基因的构型，影响DNA特异顺序与转录因子的结合,使基因不能转录； ②间接作用。基因5′端调控序列甲基化后与核内甲基化CG序列结合蛋白(methyl CG-binding p rotein)结合，阻止了转录因子与基因形成转录复合物； ③DNA去甲基化为基因的表达创造了一个良好的染色质环境。DNA去甲基化常与DNase I高敏感区同时出现,后者为基因活化的标志。
DNA 甲基转移酶有两种
1 DNMT1, 持续性DNA 甲基转移酶—— 作用于仅有一条链甲基化的DNA 双链, 使其完全甲基化, 可参与DNA 复制双链中的新合成链的甲基化,DNM T1 可能直接与HDAC (组蛋白去乙酰基转移酶) 联合作用阻断转录；
2 DNMT3a、DNM T3b从头甲基转移酶, 它们可甲基化CpG, 使其半甲基化, 继而全甲基化。从头甲基转移酶可能参与细胞生长分化调控, 其中DNM T3b在肿瘤基因甲基化中起重要作用。
DNA 去甲基化有两种方式
1、 被动途径: 由于核因子N F 粘附甲基化的DNA , 使粘附点附近的DNA不能被完全甲基化, 从而阻断DNM T1 的作用；
2 、主动途径：是由去甲基酶的作用, 将甲基集团移去的过程。在DNA 甲基化阻遏基因表达的过程中, 甲基化CpG 粘附蛋白起着重要作用。虽然甲基化DNA 可直接作用于甲基化敏感转录因子E2F、CREB、A P2、CM ycöM yn、N F2KB、Cmyb、Ets, 使它们失去结合DNA 的功能从而阻断转录, 但是, 甲基化CpG 粘附分子可作用于甲基化非敏感转录因子(SP1、CTF、YY1) ，使它们失活, 从而阻断转录。人们已发现5 种带有恒定的甲基化DNA 结合域(MBD ) 的甲基化CpG 粘附蛋白。其中M ECP2、MBD1、MBD2、MBD3 参与甲基化有关的转录阻遏；MBD1 有糖基转移酶活性；G 中移去，MBD4 基因的突变还与线粒体不稳定的肿瘤发生有关。在MBD2 缺陷的小鼠细胞中，不含M ECP1 复合物, 不能有效阻止甲基化基因的表达。这表明甲基化CpG 粘附蛋白在DNA 甲基化方式的选择，以及DNA 甲基化与组蛋白去乙酰化、染色质重组相互联系中的有重要作用。
DNA methylation
DNA methylation is universal in bacteria,plant, and animal. DNA methylation is a type of chemical modification of DNA that are stable over rounds of cell division but do not involve changes in the underlying DNA sequence of the organism. Chromatin and DNA modifications are two important features of Epigenetics and play a role in the process of cellular differentiation, allowing cells to stably maintain different characteristics despite containing the same genomic material. However, the DNA methylation level is dynamic over the course of development in multicellular organisms.
In prokaryotic organisms, DNA methylation occurs at the number 5 carbon of the cytosine pyrimidine ring and the number 6 nitrogen of the adenine purine ring. However, in eukaryotic organisms DNA methylation occurs only at the number 5 carbon of the cytosine pyrimidine ring. In mammalian, DNA methylation occurs most at the number 5 carbon of the cytosine of a CpG dinucleotide. CpG dinucleotide is only 1% in human genome, which is great fewer than expected.
Between 70-80% of all CpGs are methylated. Unmethylated CpGs are grouped in clusters called "CpG islands" that are present in the 5' regulatory regions of many genes. In many disease processes such as cancer, gene promoter CpG islands acquire abnormal hypermethylation, which results in heritable transcriptional silencing. DNA methylation may impact the transcription of genes in two ways. First, the methylation of DNA may itself physically impede the binding of transcriptional proteins to the gene, thus blocking transcription. Second, and likely more important, methylated DNA may be bound by proteins known as Methyl-CpG-binding domain proteins (MBDs). MBD proteins then recruit additional proteins to the locus, such as histone deacetylases and other chromatin remodelling proteins that can modify histones, thereby forming compact, inactive chromatin termed silent chromatin. This link between DNA methylation and chromatin structure is very important. In particular, loss of Methyl-CpG-binding Protein 2 (MeCP2) has been implicated in Rett syndrome and Methyl-CpG binding domain protein 2 (MBD2) mediates the transcriptional silencing of hypermethylated genes in cancer.
DNA methylation
In humans, the process of DNA methylation is carried out by three enzymes, DNA methyltransferase 1, 3a, and 3b (DNMT1, DNMT3a, DNMT3b). It is thought that DNMT3a and DNMT3b are the de novo methyltransferases that set up DNA methylation patterns early in development. DNMT1 is the proposed maintenance methyltransferase that is responsible for copying DNA methylation patterns to the daughter strands during DNA replication. DNMT3L is a protein that is homologous to the other DNMT3s but has no catalytic activity. Instead, DNMT3L assists the de novo methyltransferases by increasing their ability to bind to DNA and stimulating their activity. Finally, DNMT2 has been identified as an "enigmatic" DNA methyltransferase homolog, containing all 10 sequence motifs common to all DNA methyltransferases; however, DNMT2 does not methylate DNA but instead methylates a small RNA. (see the left)
Since many tumor suppressor genes are silenced by DNA methylation during carcinogenesis, there have been attempts to re-express these genes by inhibiting the DNMTs. 5-aza-2'-deoxycytidine (decitabine) is a nucleoside analog that inhibits DNMTs by trapping them in a covalent complex on DNA by preventing the β-elimination step of catalysis, thus resulting in the enzymes' degradation. However, for decitabine to be active, it must be incorporated into the genome of the cell, but this can cause mutations in the daughter cells if the cell does not die. Additionally, decitabine is toxic to the bone marrow, which limits the size of its therapeutic window. These pitfalls have led to the development of antisense RNA therapies that target the DNMTs by degrading their mRNAs and preventing their translation. However, it is currently unclear if targeting DNMT1 alone is sufficient to reactivate tumor suppressor genes silenced by DNA methylation. (see the below)
Expression control
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