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Methylation of DNA - A small percentage of cystine residues are methylated in many eukaryotic organisms, mainly in CPG sequences. The degree of methylation of DNA is related to silencing of a gene. Genes that are dormant at one stage of development but active in another are usually less methylated.

The essential function of m5cyt is to modify protein DNA interaction. Methylation itself may not prevent transcription, but rather may be a signal for transcriptional inactivity. Further interest has been generated in the role of methylation in controlling gene expression by the discovery of Z-DNA and the fact that Z-DNA can be stabilized by methylation.

This observation has led to a model of transcriptional regulation based on alternative DNA structure sequence that could exist as B-DNA while being transcribed. If the gene is to be silenced, (turned off) the CPG sequences are converted to stable Z-DNA by methylation which then blocks transcription.

Methylation can exist in three states, methylated, half methylated and fully methylated. After DNA replication, a half methylated site is quickly converted to a fully methylated site. Symmetrical methylation occurs on both strands with the help of methylase enzyme acting only on a half­ methylated site.

Methylated sites would remain methylated, unmethylated sites would remain unmethylated. The complex secondary and tertiary folding of eukaryotic chromosomes probably involves specific protein DNA interactions, which could be influenced by the distribution of m5cyt in the DNA.

The high methylation of centromeric regions suggests a possible role in the mitosis and chromosome sorting.