DNA methylation is a form of DNA chemical modification

  • DNA methylation is a form of DNA chemical modification that can change genetic performance without changing the DNA sequence. The so-called DNA methylation refers to the covalent bonding of a methyl group to the 5th carbon position of the cytosine of the genome CpG dinucleotide under the action of DNA methyltransferase. A large number of studies have shown that DNA methylation can cause changes in chromatin structure, DNA conformation, DNA stability, and the way in which DNA interacts with proteins, thereby controlling gene expression.







    DNA methylation is one of the earliest discovered and most studied epigenetic regulation mechanisms. In a broad sense, DNA methylation means that specific bases in the DNA sequence are catalyzed by DNA methyltransferase (DNMT) to S-adenosyl methionine (SAM). As a methyl donor, a chemical modification process in which a methyl group is obtained by covalent bonding. This DNA methylation modification can occur at the C-5 position of cytosine, the N-6 position of adenine and the N-7 position of guanine. The DNA methylation involved in general research mainly refers to the methylation process of the 5th carbon atom on the cytosine in the CpG dinucleotide, and the product is called 5-methylcytosine (5-mC) , Is the main form of DNA methylation in eukaryotes such as plants and animals, and it is also the only form of mammalian DNA methylation found. As a relatively stable modification state, DNA methylation can be inherited to the new generation DNA along with the DNA replication process under the action of DNA methyltransferase, which is an important epigenetic mechanism.


    Enzyme classification

    The methylation pattern of DNA in the genome is achieved by DNA methyltransferase. DNA methylases are divided into two categories, namely maintenance DNA methyltransferase (Dnmtl or maintenance methylase) and de novo methylase. According to sequence homology and function, eukaryotic DNA methyltransferases are divided into 4 categories: Dnmtl/METl, Dnmt2, CMTs and Dn-mt3. DnmtliiMET1 enzymes are involved in the maintenance of CG sequence methylation. CMTs enzymes are only found in plants. The main feature is that their catalytic regions T and IV embed the main chromosome region and specifically maintain the methylation of the CG sequence. Dnmt: Three types of enzymes have been identified in mice, humans and zebrafish. Dnmt3a and Dnmt3b are highly expressed in undifferentiated embryonic stem cells, but the expression level is very low in somatic cells. Their main function is de novo methylation, but they also play a role in maintaining methylation and are responsible for the methylation of repetitive sequences.



    There are two types of DNA methylation reactions. One is that the two strands of DNA that are not methylated are methylated, which is called de novo methylation (denovo methylation); the other is that one strand of double-stranded DNA is already methylated, and the other is not methylated. The grouped chain is methylated, this type is called maintenance methylation.



    Because the Dnmtl and Dnmt3 gene families have no specificity for the CpG dinucleotide sequence, people have proposed a mechanism for DNA methyltransferase to find the target site. First, methyltransferases are not equally close to all chromosomal regions. Proteins with chromosome remodeling and DNA helicase activity can regulate DNA methylation in mammalian cells, such as the two members of the SNF2 family ATRX and Lsh; secondly, accessory factors (proteins, RNA, etc.) can recruit DNA methyltransferases In the specific genome sequence or chromosome structure, such as pRB protein can interact with Dnmtl and recruit it to the highly methylated heterochromatin region in the late S phase.

    DNA methylation is a normal and common modification method in eukaryotic cells, and it is also the main epigenetic form of mammalian gene expression regulation. Although the nucleotide sequence and composition of DNA are not changed after DNA methylation, gene expression is affected. Although there are many ways of methylation modification, the base of the modified site can be the N-6 position of adenine, the N-4 position of cytosine, the N-7 position of guanine and the C-5 position of cytosine. , They are respectively catalyzed by different DNA methylases, but most of them occur on CpG islands in the promoter region of genes. During DNA methylation, cytosine protrudes from the DNA double helix and enters the crack that can be combined with the enzyme. Under the catalysis of cytosine methyltransferase, the active methyl group is transferred from S-adenosylmethionine to At the 5-position of cytosine, 5-methylcytosine (5-MC) is formed. Methylation in the promoter region of a gene can lead to transcriptional silence.

    The DNA methylation level of mammals has a significant change during the lifetime: in the first few cleavages of the fertilized egg, the demethylase removes almost all the methylation markers inherited from the parental generation on the DNA molecule; in the embryo implantation in the uterus At this time, a new type of methylation spreads throughout the genome, and constructive methylases make DNA re-establish a new methylation pattern. Once a new methylation pattern is established in the cell, it will maintain the methylation enzyme The "maintenance of methylation" format transmits the new DNA methylation pattern to all daughter cells' DNA molecules. This explains that genetic imprinting is not a mutation, nor is it a permanent change. The imprint is reversible. It only lasts during the life of the individual. When the gametes of the next generation of individuals are formed, the old genetic imprint is eliminated and a new genetic imprint occurs. It can be seen that one of the molecular mechanisms of genetic imprinting may be DNA methylation. In the study of genetic imprinting and tumors, it was also found that the tumor suppressor gene P16 was inactivated by methylation, and demethylation could restore the original characteristics of the gene. Abnormal methylation may be one of the important causes of tumors. It shows that the modification of DNA methylation has a wide range of effects.

    Methylated DNA can be demethylated. The demethylation of DNA is regulated by the fragments within the gene and the factors bound to it. There are two hypotheses that can explain the molecular mechanism of DNA demethylation. One hypothesis is associated with DNA semi-reserved replication, which is passive demethylation. If the methylated DNA is not methylated after semi-reserved replication, the DNA is in a state of hemimethylation. If the semi-methylated DNA undergoes DNA semi-reserved replication again, the DNA methylation activity is still inhibited , 50% of the cells are in a hemimethylated state. The second hypothesis has nothing to do with semi-reserved copying and is an active process. DNA demethylation is catalyzed by DNA demethylase. DNA demethylation is a reaction that removes methylated bases under the action of DNA glycosidase, which is equivalent to the repair reaction of damaged DNA catalyzed by glycosidase and abasic nuclease digestion coupling. 5-methylcytosine glycosylase is a candidate demethylase in vivo. In addition, methylated CpG binding proteins such as MBD2 also have demethylase activity.

    During cell development, various epigenetic phenomena do not exist in isolation but are closely related. The phenomenon of DNA methylation and histone methylation co-regulating gene expression was first confirmed in Neurospora crassa. Further biochemical studies showed that DNA methylation is regulated by histone methylation. Studies on mammals have found that DNA methylation is the basis for the establishment and maintenance of other epigenetic phenomena. For example, DNA methylation sites can recruit complexes with inhibitory functions such as histone deacetylases, while eliminating Remove the histone acetylation mark near the site. Some studies also believe that DNA methylation is regulated by histone modification, and it is reported that histone modification H3K9me can promote the process of DNA methylation.


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