Methylation sequencing
DNA methylation is a process by which methyl groups are added to the DNA molecule. Methylation can change the activity of a DNA segment without changing the sequence. When located in a gene promoter, DNA methylation typically acts to repress gene transcription.
(https://www.cincinnatichildrens.org/research/cores/pyrosequencing/services/methylation)
(http://www.epigentek.com/catalog/histone-modification.php)
Sequencing-based DNA methylation analysis help with epigenetic studies
Bisulfite sequencing exploits the difference in reactivity of cytosine and 5-methylcytosine with respect to bisulfite: cytosine is deaminated by bisulfite to form uracil (which reads as T when sequenced), whereas 5-methylcytosine is unreactive (i.e. reads as C). If two sequencing runs are done in parallel, one with bisulfite treatment and one without, the differences between the outputs of the two runs indicate methylated cytosines in the original sequence. This technique can also be used for dsDNA, since after treatment with bisulfite, the strands are no longer complementary and can be treated as ssDNA.
(http://www.atdbio.com/content/58/Next-generation-sequencing#Reversible-terminator-sequencing-Illumina)
5-Hydroxymethylcytosine, another important epigenetic modification, reacts with bisulfite to form cytosine-5-methylsulfonate (which reads as C when sequenced). This complicates matters somewhat, and means that bisulfite sequencing cannot be used as a true indicator of methylation in itself.
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