In the last two decades researchers have been exerting a lot of efforts in attempt to find the answer coming up with a new term in the field of autoimmunity known as epigenetics. Epigenetics are defined as the mechanisms that contribute to stable changes of gene expression without a change in the primary nucleotide sequence. Epigenetic modifications might lead to over expression of some nucleotides with suppression of others and thats why they are the reason why an identical gene set within human bodies might display highly specific lineages and phenotypes despite being identical.
Research experts were able to identify three distinct forms of epigenetic modifications: DNA methylation, histone modifications and RNA interference. The understanding of each has effectively defined their relevance to gene expression in autoimmune disorders. Methylation means the addition of a methyl group (CH3) to DNA nucleotides from the methyl donor S-adenosyl methionine (SAM) by a family of enzymes called the DNA transferases. Such DNA alteration becomes relevant if it takes place within clusters of cytosine nucleotides called CpG islands or the high CpG density region of promoters. DNA methylation affects gene transcription in two ways: first, DNA methylation physically hinders binding of transcriptional proteins to the gene and second, methylated DNA recruits proteins known as methyl-CpG-binding domain proteins that facilitate formation of compact inactive chromatin or the silent chromatin. In such case it would be expected that the more the methylation of a specific gene nucleotide the lesser the expression of its respective gene