5-Метилцитозин: ДНК-ның өзгертілген негізі және геномдық белгілеушісі

Chemical compound which is a modified DNA base

5 Methylcytosine is a methylated form of the DNA base cytosine (C) that regulates gene transcription and takes several other biological roles. When cytosine is methylated, the DNA maintains the same sequence, but the expression of methylated genes can be altered (the study of this is part of the field of epigenetics). 5 Methylcytosine is incorporated in the nucleoside 5 methylcytidine. In 5 methylcytosine, a methyl group is attached to the 5th atom in the 6 atom ring, counting counterclockwise from the NH bonded nitrogen at the six o'clock position. This methyl group distinguishes 5 methylcytosine from cytosine.

While trying to isolate the bacterial toxin responsible for tuberculosis, W. G. Ruppel isolated a novel nucleic acid named tuberculinic acid in 1898 from Tubercle bacillus. The nucleic acid was found to be unusual, in that it contained in addition to thymine, guanine and cytosine, a methylated nucleotide. In 1925, Johnson and Coghill successfully detected a minor amount of a methylated cytosine derivative as a product of hydrolysis of tuberculinic acid with sulfuric acid. This report was severely criticized because their identification was based solely on the optical properties of the crystalline picrate, and other scientists failed to reproduce the same result. But its existence was ultimately proven in 1948, when Hotchkiss separated the nucleic acids of DNA from calf thymus using paper chromatography, by which he detected a unique methylated cytosine, quite distinct from conventional cytosine and uracil. After seven decades, it turned out that it is also a common feature in different RNA molecules, although the precise role is uncertain.

The NH2 group can be removed (deamination) from 5 methylcytosine to form thymine with use of reagents such as nitrous acid; cytosine deaminates to uracil (U) under similar conditions. 5 methylcytosine is resistant to deamination by bisulfite treatment, which deaminates cytosine residues. This property is often exploited to analyze DNA cytosine methylation patterns with bisulfite sequencing.

5mC marks are placed on genomic DNA via DNA methyltransferases (DNMTs). There are 5 DNMTs in humans: DNMT1, DNMT2, DNMT3A, DNMT3B, and DNMT3L, and in algae and fungi 3 more are present (DNMT4, DNMT5, and DNMT6). DNMT1 contains the replication foci targeting sequence (RFTS) and the CXXC domain which catalyze the addition of 5mC marks. RFTS directs DNMT1 to loci of DNA replication to assist in the maintenance of 5mC on daughter strands during DNA replication, whereas CXXC contains a zinc finger domain for de novo addition of methylation to the DNA. DNMT1 was found to be the predominant DNA methyltransferase in all human tissue. Primarily, DNMT3A and DNMT3B are responsible for de novo methylation, and DNMT1 maintains the 5mC mark after replication. Changes in the expression of DNMT results in aberrant methylation. Overexpression produces increased methylation, whereas disruption of the enzyme decreased levels of methylation. The oxidation occurs through the TET (Ten eleven translocation) family dioxygenases (TET enzymes) which can convert 5mC, 5hmC, and 5fC to their oxidized forms. However, the enzyme has the greatest preference for 5mC and the initial reaction rate for 5hmC and 5fC conversions with TET2 are 4.9 7.6 fold slower. TET requires Fe(II) as cofactor, and oxygen and α ketoglutarate (α KG) as substrates, and the latter substrate is generated from isocitrate by the enzyme isocitrate dehydrogenase (IDH). Cancer however can produce 2 hydroxyglutarate (2HG) which competes with α KG, reducing TET activity, and in turn reducing conversion of 5mC to 5hmC.

In cancer, DNA can become both overly methylated, termed hypermethylation, and under methylated, termed hypomethylation. CpG islands overlapping gene promoters are de novo methylated resulting in aberrant inactivation of genes normally associated with growth inhibition of tumors (an example of hypermethylation). Comparing tumor and normal tissue, the former had elevated levels of the methyltransferases DNMT1, DNMT3A, and mostly DNMT3B, all of which are associated with the abnormal levels of 5mC in cancer. The anticancer drug Cisplatin has been reported to react with 5mC.

"Epigenetic age" refers to the connection between chronological age and levels of DNA methylation in the genome. Coupling the levels of DNA methylation, in specific sets of CpGs called "clock CpGs", with algorithms that regress the typical levels of collective genome wide methylation at a given chronological age, allow for epigenetic age prediction. During youth (0–20 years old), changes in DNA methylation occur at a faster rate as development and growth progresses, and the changes begin to slow down at older ages. Multiple epigenetic age estimators exist. Horvath's clock measures a multi tissue set of 353 CpGs, half of which positively correlate with age, and the other half negatively, to estimate the epigenetic age. Hannum's clock utilizes adult blood samples to calculate age based on an orthogonal basis of 71 CpGs. Levine's clock, known as DNAm PhenoAge, depends on 513 CpGs and surpasses the other age estimators in predicting mortality and lifespan, yet displays bias with non blood tissues. There are reports of age estimators with the methylation state of only one CpG in the gene ELOVL2. Estimation of age allows for prediction lifespan through expectations of age related conditions that individuals may be subject to based on their 5mC methylation markers.