Combined bisulfite restriction analysis
Combined Bisulfite Restriction Analysis (or COBRA) is a molecular biology technique that allows for the sensitive quantification of DNA methylation levels at a specific genomic locus on a DNA sequence in a small sample of genomic DNA. The technique is a variation of bisulfite sequencing, and combines bisulfite conversion based polymerase chain reaction with restriction digestion. Originally developed to reliably handle minute amounts of genomic DNA from microdissected paraffin-embedded tissue samples, the technique has since seen widespread usage in cancer research and epigenetics studies. Procedure. Bisulfite Treatment. Genomic DNA of interest is treated with sodium  bisulfite, which introduces methylation-dependent sequence differences. During sodium bisulfite treatment, unmethylated cytosine residues are converted to uracil, while methylated cytosine residues are unaffected. PCR Amplification. Bisulfite treated DNA is then PCR amplified, resulting in cytosine residues at originally methylated positions, and thymine residues at originally unmethylated position (that were converted to uracil). Primers used during this step do not contain CpG sites (the common target of cytosine methylation), so the amplification process does not discriminate between templates based on methylation status. PCR products are purified to ensure complete digestion in the following step. Restriction Digest. The above steps lead  to the methylation dependent retention or loss of CpG-containing restriction enzyme sites, such as those for TaqI (TCGA) and BstUI (CGCG), depending on whether the cytosine residue was originally methylated or not, respectively. Due to the methylation-independent amplification in the above step, the resulting PCR products will be a mixed population of fragments that have lost or retained CpG-containing restriction enzyme sites, whose respective percentages will be directly correlated to the original level of DNA methylation in the sample DNA. PCR products are then treated with a restriction enzyme ("e.g." BstUI), which will only cleave sites that  were originally methylated (CGCG), while leaving sites that were originally unmethylated (TGTG). To ensure that all CpG sites are retained due to originally being methylated, and not a remnant of incomplete bisulfite conversion, a control digestion is performed, with enzymes such as Hsp92II which recognizes the sequence CATG, none of which should be remaining after bisulfite conversion (with the rare exception of non-CpG methylation) and thus no cleavage should occur if bisulfite conversion was complete. Quantification. The digested fragments are then separated by polyacrylamide gel electrophoresis with the expected appearance of bands corresponding to a single large undigested fragment , and multiple smaller bands corresponding to digested fragments. Quantitative amount of DNA in these bands can be determined with a device such as a phosphoimager, after which the methylation percentage of the original sample can be calculated by: Usage and Applications. COBRA has been used extensively in many research-based applications such as screening for DNA methylation changes at gene promoters in cancer studies, detecting altered methylation patterns at imprinted genes, and characterizing methylation patterns in the genome during development in mammals. In medicine, COBRA has been used as a tool to help diagnose human disease involving aberrant DNA methylation . Researchers utilized COBRA in conjunction with denaturing high performance liquid chromatography in the diagnosis of the genetic imprinting disorder Russell-Silver syndrome where of the imprinted gene H19 is responsible for the disorder in up to 50% of patients. Alternatives. In general, COBRA is often combined with other DNA methylation analyses and is frequently used in the initial screening of a loci of interest. If COBRA suggests altered methylation patterns, then more rigorous, labor-intensive techniques can be applied, such as bisulfite sequencing or MeDIP. Also PacBio sequencing can be used to detect DNA methylation.