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).
Methodologies to analyze bisulfite-treated DNA are continuously being developed.  To summarize these rapidly evolving methodologies, numerous review articles have been written.
The methodologies can be generally divided into strategies based on methylation-specific PCR (MSP) (Figure 4), and strategies employing polymerase chain reaction (PCR) performed under non-methylation-specific conditions (Figure 3).  Microarray-based methods use PCR based on non-methylation-specific conditions also.