Methylcytosine, deamination

Figure 8.3 5-Methylcytosine deamination to thymine in DNA. R Phosphodesoxyribose of the DNA backbone.

In mammalian genomes, some cytosine residues of the CpG (cytosines adjacent to guanines) sequences in DNA are methylated, forming 5-methylcytosine. Deamination of 5-methylcytosine, however, yields thymine, a normal base component of DNA. In single-stranded DNA, this is a challenging problem as cells are not able to determine that this thymine is abnormal. In double-stranded DNA, however, deamination of the 5-methylcytosine in a methylated C G base pair yields a T G mismatch. Cells are therefore able to distinguish the thymine in a T G mismatch as... 

Cannistraro VJ, Taylor J-S (2009) Acceleration of the 5-methylcytosine deamination in cyclobutane dimers by G and its implications for UV-induced C-to-T muataion hotspots. J Mol Biol 392 1145-1157... 

Not all mutagenesis in IS. coli is dependent on SOS-processing. Mutations may arise quite simply during DNA replication if a base is substituted by or converted to another, incorrect, base. Consider the consequence of oxidative deamination of the base 5-methylcytosine to thymine. Replication followed by daughter strand segregation will result in a G C base pair having been mutated to an A T base pair. Sites containing 5-methylcytosine are hotspots for G C to A T transitions in 12. coli (24). 

Morgan, H.D., Dean, W., Coker, H.A., Reik, W. and Petersen-Mahrt, S.K (2004) Activation-induced cytidine deaminase deaminates 5-methylcytosine in DNA and is expressed in pluripotent tissues implications for epigenetic reprogramming. The Journal of Bioh ad Chemistry, 279, 52353-52360. 

ROS can also deaminate 5-methylcytosine and cytosine to give thymine and uracil (Fig. 6.42). 

Base substitutions, either transitions or transversions, could occur as a result of replication of an altered template. This may be the result of the production of an altered base such as the formation of an adduct or chemically changed base, perhaps as a result of oxidative damage. For example, formation of 8-oxo-dG is the most common DNA lesion caused by oxidation and can be a promutagenic lesion as it can erroneously pair with adenosine during replication (Fig. 6.41). This means that the original base pair, G C, will become first 8-oxo-G A, then T A. Therefore, a G to T transversion has occurred. Another example is deamination of 5-methylcytosine to thymine (Fig. 6.42) at CpG sites, which results in G C to A T transitions. 

The deamination of 5-methylcytosine occurs more frequently than that of other bases but the product, thymine, is of course a normal base and therefore will not be recognized by the repair system (Fig. 6.42). This represents a major source of point mutations in DNA. 

CG doublets. The only modified base commonly found in eukaryotes is 5-methylcytosine,222/223 which upon deamination becomes thymine (Eq. 27-1). Most methylation occurs when C is followed by G. Usually 60-90% of all 5 -CG sequences (CpG sequences) in eukaryotic DNA are methylated. However, the fraction of methylated cytosine varies from almost zero for Drosophilia, Caenorhabditis, and Saccharomyces to as much as 30% in higher plants.224... 

S. Sun et al., Radical-mediated cytosine and S-methylcytosine hydrolytic deamination reactions. Int. J. Quantum Chem. 106, 1878-1894 (2006)... 

Answer Many C residues of CpG sequences in eukaryotic DNA are methylated at the 5 position to 5-methylcytosine. (About 5% of all C residues are methylated.) Spontaneous deamination of 5-methylcytosine yields thymine, T, and a G-T mismatch resulting from spontaneous deamination of 5-methylcytosine in a G=C base pair is one of the most common mismatches in eukaryotic cells. The specialized repair mechanism to convert G-T back to G=C is directed at this common class of mismatch. 

Another type of photochemical reaction involving a pyrimidine base is the addition of a molecule of water across the 5,6 double bond of C to yield a 5,6-dihydro-6-hydroxy derivative called the cytosine hydrate. The quantum yield for the formation of cytosine hydrates in UV-irradiated DNA is greater in single-stranded than in duplex-DNA (45). Hydrates of cytosine, deoxycytidine, CMP, or dCMP are unstable, readily reverting to the parent form by rehydration (45). However, their half-life is dramatically increased in DNA, and cytosine hydrate may be the major nondimer C photoproduct. Cytosine hydrate can undergo deamination and dehydration to yield uracil (1). The hydrate of 5-methylcytosine may undergo deamination to yield 5-thymine hydrate, which can convert to thymine upon dehydration (1). 

Ehrlich M, Zhang X-Y, Imander NM. Spontaneous deamination of cytosine and 5-methylcytosine residues in DNA and replacement of 5-methylcytosine residues with cytosine residues. Mutation Res. 1990 238 277-286. 

The distribution of CpG sequences in mammalian genomes is not uniform. The deamination of 5-methylcytosine produces thymine so CpG sequences are subject to mutation to TpG. Many CpG sequences have been converted... 

This formulation is confirmed by the fact that, on deamination, " it retains its tetranucleotide structure and pentabasicity, and hence contains no phosphoamide links. Bredereck and collaborators completely methylated thymonucleic acid, obtaining a product possessing seven A -methyl and three methoxyl groups to each four phosphorus atoms. On stepwise hydrolysis, this material gave 1,6-dimethyladenine, 1,6-di-methylcytosine, and 1-methylthymine. This confirms the previously-mentioned conclusion, that the sugar is attached to position 9 of the adenine and to position 3 of the pyrimidines. 

In human tumors, the pattern of p53 mutations is dominated by base transitions (C to T or G to A) at CpG dinucleotides (23% of all mutations). Although this type of mutation has been observed at 35 different codons, 90% of human CpG transitions are at one of six hotspot codons 175,213,245, 248, 273 and 282 (Fig. 3A) known to be important in maintaining p53 biological activity. CpG dinucleotides are sites of cytosine methylation, and deamination of 5-methylcytosine producing thymine is the most characteristic event generating spontaneous mutations in mammalian cells (Barker et... 

Shen J.C., Rideout W.M., Jones P.A. (1994). The rate of hydrolytic deamination of 5-methylcytosine in double stranded DNA. Nucleic Acids Res. 22 972-976. 

In several mammalian genomes, between 1% and 7% of C residues in DNA are methylated, and more than 90% of these have a G following them. Nearest-neighbor analysis done with a computer also reveals that the dinucleotide of highest frequency in the mammalian genomes is TG. An explanation of this phenomenon is that thymine residues can be the product of the spontaneous deamination of methylcytosine (Fig. 7-2). Corruption of the code by this means may not be detected by DNA repair mechanisms (Chap. 8), so such a change in a somatic cell will persist into the next generation derived from it. 

Several different DNA glycosylases are known to act on T G mismatches in DNA. The primary source of these mismatches is deamination of 5-methylcytosine (Duncan and Miller, 1980 Sved and Bird, 1990). 5-Methylcytosine is found in eukaryotes as an epigenetic modifier of chromatin structure and transcription, and in prokaryotes as the basis for self-protection from endogenous restriction enzymes. The human... 

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