Bisulfite sequencing

Bisulfite sequencing (also known as bisulphite sequencing) is the use of bisulfite treatment of DNA before routine sequencing to determine the pattern of methylation. DNA methylation was the first discovered epigenetic mark, and remains the most studied. In animals it predominantly involves the addition of a methyl group to the carbon-5 position of cytosine residues of the dinucleotide CpG, and is implicated in repression of transcriptional activity.Bisulfite sequencing applies routine sequencing methods on bisulfite-treated genomic DNA to determine methylation status at CpG dinucleotides. Other non-sequencing strategies are also employed to interrogate the methylation at specific loci or at a genome-wide level. All strategies assume that bisulfite-induced conversion of unmethylated cytosines to uracil is complete, and this serves as the basis of all subsequent techniques. Ideally, the method used would determine the methylation status separately for each allele. Alternative methods to bisulfite sequencing include Combined Bisulphite Restriction Analysis and methylated DNA immunoprecipitation (MeDIP).Bisulfite sequencing is used widely across mammalian genomes, however complications have arisen with the discovery of a new mammalian DNA modification 5-hydroxymethylcytosine. 5-Hydroxymethylcytosine converts to cytosine-5-methylsulfonate upon bisulfite treatment, which then reads as a C when sequenced. Therefore, bisulfite sequencing cannot discriminate between 5-methylcytosine and 5-hydroxymethylcytosine. This means that the output from bisulfite sequencing can no longer be defined as solely DNA methylation, as it is the composite of 5-methylcytosine and 5-hydroxymethylcytosine. The development of Tet-assisted bisulfite sequencing by Chuan He at the University of Chicago is now able to distinguish between the two modifications at single base resolution.The advances in bisulfite sequencing have led to the possibility of applying them at a genome-wide scale, where, previously, global measure of DNA methylation was feasible only using other techniques, such as Restriction landmark genomic scanning. The mapping of the human epigenome is seen by many scientists as the logical follow-up to the completion of the Human Genome Project. This epigenomic information will be important in understanding how the function of the genetic sequence is implemented and regulated. Since the epigenome is less stable than the genome, it is thought to be important in gene-environment interactions.5-Methylcytosine and 5-hydroxymethylcytosine both read as a C in bisulfite sequencing. Oxidative bisulfite sequencing is a method to discriminate between 5-methylcytosine and 5-hydroxymethylcytosine at single base resolution. The method employs a specific chemical oxidation of 5-hydroxymethylcytosine to 5-formylcytosine, which subsequently converts to uracil during bisulfite treatment. The only base that then reads as a C is 5‑methylcytosine, giving a map of the true methylation status in the DNA sample. Levels of 5‑hydroxymethylcytosine can also be quantified by measuring the difference between bisulfite and oxidative bisulfite sequencing.