Unless you’ve been living under a rock, or maybe under a CpG island, then you’ve heard of 5-methylcytosine (5mC). 5mC is the normal cytosine nucleotide in DNA that has been modified by the addition of a methyl group to its 5th carbon. The role of this mark is so distinct that many consider 5mC to be the “5th base” of DNA. This methylation typically occurs at cytosine in CpG dinucleotides in vertebrates. CpG denotes 5’-cytosine-phosphodiester bond-guanine-3’ to be clear that the two nucleotides neighbour each other on the same strand of DNA. Since CpG is a simple palindromic sequence, it pairs with another CpG sequence on the complimentary strand. Typically, if one of these cytosines in methylated, both are (Robertson and Wolffe, 2000). This simple pattern allows 5mC to be faithfully passed through cell division with the help of DNA methyltransferases (DNMTs). De novo DNMTs establish 5mC at unmodified CpG sites. When DNA is replicated, the newly replicated stand does not carry the methyl mark. Maintenance DNMTs recognize these hemi-methylated CpG sites, and methylate the newly replicated stand.
5mC is a very important repressor of transcription in the genome. When present in promoters, 5mC is associated with stable, long-term transcriptional silencing. This may occur by either blocking positive transcription factors, or promoting the binding of negative ones. 5mC bind is bound by several classes of proteins that facilitate transcriptional repression. The MBD, SRA, and Kaiso and Kaiso-like protein families are three major groups that recognize methyl-CpG sites (Defossez and Stancheva, 2011).
Methylation of CpG islands also to has function relevance for gene expression. The accepted definition of is a region at least 200 bp long with greater than 50% GC content, and an observed-to-expected CpG ratio greater than 60% (Gardiner-Garden and Frommer, 1987). Methylation of CpG islands is associated with the repression of nearby genes (Deaton and Bird, 2011). It is also the key mechanism mediating genomic imprinting. Genomic imprinting is the process by which alleles are expressed in a parent-of-origin-specific manner. The imprinted copy of the allele is methylated and not expressed. This process is critical for normal development; abnormal imprinting leads to disorders such as Prader-Willi, Angelman, and Beckwith-Wiedemann syndrome (Butler, 2009).
DNA methylation has important roles in a dizzying number of processes and pathologies. Cytosine methylation is used by many organism to silence foreign DNA elements. For example, the human genome contains over 60% repetitive DNA, much of which is transposable sequences of viral origin that are kept inactive in part by DNA methylation (de Koning et al., 2011). 5mC is also crucial for cellular development and differentiation. Silencing of certain cell-type specific genes in creates differences in expression that differentiate once cell type from another.
Many aspects of the dogma of DNA methylation have been challenged in recent years. 5mC can actually have positive effects on transcription. Yu et al. (2013) found a series of genes that are activated by 3’ CpG islands during development. Methylation has also been shown to occur and have functional relevance at non-CpG sites. Up to 25% of 5mC in embryonic stem cells is at non-CpG cytosines. Non CpG 5mC is enriched in gene bodies, particularly the antisense strands of coding genes (Lister et al., 2009; Yu et al., 2013). The role of these marks remains unknown. Even though we know more about 5mC than any other epigenetic mark, it is clear that it plays a more complex role than we currently appreciate.
5mC Additional Reading
This review gives a comprehensive look at DNA methylation in the context of mammalian development. It gives a succinct summary of the enzymes governing 5mC catalysis and reading, genomic distribution, and various functions of 5mC.
This review touches on just about every aspect of DNA methylation. Current literature on methyl-metabolism, mechanism of gene repression, imprinting, CpG islands, demethylation and several other relevant topics are presented.
Reference List
- Butler, M.G. (2009). Genomic imprinting disorders in humans: a mini-review. J. Assist. Reprod. Genet. 26, 477-486.
- Deaton, A.M., and Bird, A. (2011). CpG islands and the regulation of transcription. Genes Dev. 25, 1010-1022.
- Defossez, P.A., and Stancheva, I. (2011). Biological functions of methyl-CpG-binding proteins. Prog. Mol. Biol. Transl. Sci. 101, 377-398.
- Gardiner-Garden, M., and Frommer, M. (1987). CpG islands in vertebrate genomes. J. Mol. Biol. 196, 261-282.
- de Koning, A.P., Gu, W., Castoe, T.A., Batzer, M.A., and Pollock, D.D. (2011). Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet. 7, e1002384.
- Lister, R., Pelizzola, M., Dowen, R.H., Hawkins, R.D., Hon, G., Tonti-Filippini, J., Nery, J.R., Lee, L., Ye, Z., Ngo, Q.M., et al. (2009). Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315-322.
- Robertson, K.D., and Wolffe, A.P. (2000). DNA methylation in health and disease. Nat. Rev. Genet. 1, 11-19.
- Yu, D.H., Ware, C., Waterland, R.A., Zhang, J., Chen, M.H., Gadkari, M., Kunde-Ramamoorthy, G., Nosavanh, L.M., and Shen, L. (2013). Developmentally programmed 3′ CpG island methylation confers tissue- and cell-type-specific transcriptional activation. Mol. Cell. Biol. 33, 1845-1858.
- Yu, D.H., Ware, C., Waterland, R.A., Zhang, J., Chen, M.H., Gadkari, M., Kunde-Ramamoorthy, G., Nosavanh, L.M., and Shen, L. (2013). Developmentally programmed 3′ CpG island methylation confers tissue- and cell-type-specific transcriptional activation. Mol. Cell. Biol. 33, 1845-1858.