Methylation is the addition of a methyl group on to a molecule. This most often takes places at an oxygen atom forming a carbon-oxygen bond or at a carbon atom forming a carbon-carbon bond. Methylation is also important marine and soil microbiology with respect to bacteria and the methylation of mercury. Inorganic mercury (mercury without any carbon atoms attached) generally doesn't enter the food chain, however, methyl mercury is created in wetlands and then transported to the food-chain.
Today, the most common use of this word has is in relation to DNA and deactivation of various genes on the chromosome. The analogy to that is used is placing glue on the edge of a book to prevent the page from being read. This is often done in female mammals with the deactivation of one of the X chromosomes through methylation - the cell randomly picks one of the X chromosomes to turn off. This is known as X-chromosone mosaicism.
Methylation in DNA occurs on C base pairs
(though in simpler (bacteria and yeast) organisms, this occurs on A base pairs - though even that is too simple of a statement, most bacteria use patterns of tagged C and A base pairs to indicate its own DNA rather than that of DNA from a virus). Proteins indicating the deactivation of the gene then are attached to the DNA at the methyl groups. In addition to indicating that the gene is turned off, these proteins also act to help coil the DNA making genes in that area less available to be expressed.
The methyl groups are attached by an group of enzymes called methyltransferases. Mutations in the DNA that codes these enzymes have a wide range of genetic problems often in the form of abnormal immune systems (one example being ICF syndrome which stands for immunodeficiency, centromeric region instability, and facial anomalies). Laboratory mice engineered without the methyltransferase enzymes die before birth.
Methylation is an exception to Mendel's laws of genetics - that genes act the same no matter how they are transmitted. In 1910 an observation that the color of corn kernels was conveyed differently by the male or female set of genes - dark purple via egg, lavender by pollen. It is known known that in the pollen, the red gene is methylated. During the development of the kernel, the methyl tags are removed allowing the gene to be expressed.
Metalization is one of the factors in aging. Over time, methyl groups are placed in wrong spots and fall off of the right spots. Evidence also shows that improper methyl tags are a contributing factor to lupus. Abnormal methylation is also associated with cancers.
Difficulty in producing clones may be related to our inability to properly reset the state of a cell to that of a stem cell. Normally, the embryo removes all methyl groups from its DNA and then establishes a new set of methyl groups that match (the genes from the egg and sperm may not have had matching methylation patterns). This occurs at about 8 or 16 cells. The exception to this is a set of about 150 genes that are known as "imprinted genes" which are not stripped of the methylation pattern. This causes the embryo to only use some genes from the father, and
some genes from the mother. In a clone (even clones of the same individual), the methylation on the imprinted genes appear to be random. It appears that this disruption occurs in the culturing process that precedes cloning.