DNA methylation and CpG islands Sample Clauses

DNA methylation and CpG islands. DNA methylation is a post-replication chemical modification which consists in the addition of a methyl group to the carbon-5 position of the cytosine pyrimidine ring. The reaction is catalysed by DNA methyltransferases (DNMT) and leads to the generation of 5-methylcytosine (5-mC) molecules (Figure 1.3.1.1.1). These can be further modified into 5-hydroxymethylcytosines (5hmc), through an oxidation reaction mediated by TET hydroxylases. In mammalian genomes, DNA methylation occurs almost exclusively at CpG positions (where “p” indicates the phosphodiester bond between cytosine and guanine). These CpG sites are underrepresented in the human genome as a result of the spontaneous deamination of 5-mC into thymidine. These events, which often escapes DNA repair mechanisms, result in the occurrence of C to T transitions during DNA replication. Therefore, germline CpG sites are likely to be lost over time, a notion that is supported by the large number of C/T SNPs reported in public databases. Previous studies have shown that isolated CpG nucleotides are mostly methylated, whereas cluster of CpG bases known as CpG islands (CGIs) are usually not modified. Importantly, the majority of CGIs map within gene promoters and first exons, where they are associated with transcription start sites. Intragenic and intergenic CGIs were until recently classified as “orphan CGIs”. However it is now recognised that the sites of these CGIs are likely to represent novel promoters, as they co-localise with open chromatin marks (see below) and can recruit RNA polymerase II to promote transcription. It has also been suggested that some orphan CGIs act as alternative promoters of nearby genes while others may initiate the transcription of non-coding RNAs (ncRNAs) (Xxxxxxxxxxx, Xxxxxxxxxx-Xxxxxxxxx et al. 2010). Several mechanisms have been proposed to explain what protects CGIs from DNA methylation. An attractive scenario is that methylation at CGIs is constantly removed by DNA demethylases through oxidation of 5-methylcytosine to 5- hydroxymethylcytosines by Tet1 enzyme. Another plausible explanation is that the occupancy of RNA polymerase II and the presence of H3K4me3 at CGI promoters would exclude DNMTs from sites of transcriptional initiation (Xxxxxxxxxxx, Xxxxxxxxxx- Xxxxxxxxx et al. 2010). Figure 1.3.1.1.1 Biochemical pathways for cytosine modification. DNA methyltransferase catalyses the transfer of a methyl group from S-adenosylmethionine to cytosine, leading to the production o...
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