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Structural and functional features of the 5-methylcytosine distribution in the eukaryotic genome

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Abstract

DNA methylation is an integral part of the mechanism of a remodeling and modification of the chromatin structure. The global complex net of chromatin modification and remodeling reactions is still to be determined, and studies of the mechanisms controlling the epigenetic processes of histone modification and DNA methylation are in their infancy. Cytosine methylation occurs predominantly in CpG sequences of the eukaryotic genome, and it also takes place at symmetric CpHpG and nonsymmetric CpHpH sites (where H is A, T, or C). The modification efficiency of the three types of DNA methylation sites depends on their genomic localization. Different regions of the eukaryotic genome are remarkable for their methylation features: CpG-islands, CpG-island shores, differentially methylated regions of imprinted genes, and regions of nonalternative site-specific modification. The three canonical sites (CpG, CpHpG, and CpHpH) differ in DNA methylation efficiency depending on their nucleotide context. An epigenetic code of DNA methylation can be assumed with context differences playing a specific functional role. The review summarizes the main up-to-date data on the structural and functional features of site-specific cytosine methylation in eukaryotic genomes. Pathogenesis-related alterations in the methylation pattern of the eukaryotic genome are considered.

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Abbreviations

MTase:

DNA-methyltransferase

C5-MTase:

DNA-(cytosine-5-)-methyltransferase

AdoMet:

S-adenosyl-L-methionine

RLGS:

restriction-marked scanning of genome

DMR:

regions of differentiated methylation of DNA

T-DMR:

tissue specific differentially methylated areas of DNA

C-DMR:

oncospecific differentially methylated areas of DNA

CAM (Crassulean acid metabolism):

Crassula type metabolism of organic acids of plant

siRNA:

short interferencing RNA

H:

A, T, or C

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  1. Pushchino Branch, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russia

    O. V. Dyachenko, T. V. Shevchuk & Ya. I. Buryanov

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Original Russian Text © O.V. Dyachenko, T.V. Shevchuk, Ya.I. Buryanov, 2010, published in Molekulyarnaya Biologiya, 2010, Vol. 44, No. 2, pp. 195–210.

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Dyachenko, O.V., Shevchuk, T.V. & Buryanov, Y.I. Structural and functional features of the 5-methylcytosine distribution in the eukaryotic genome. Mol Biol 44, 171–185 (2010). https://doi.org/10.1134/S0026893310020019

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