oxBS-Seq

oxBS-Seq

Oxidative bisulfite sequencing (oxBS-Seq) differentiates between 5mC and 5hmC. With oxBS, 5hmC is oxidized to 5formylcytosine (5fC) with an oxidizing agent, while 5mC remains unchanged. Sodium bisulfite treatment of oxidized 5hmC results in its deamination to uracil which, upon sequencing, is read as a thymidine. Deep sequencing of oxBS-treated DNA and sequence comparison of treated vs. untreated can identify 5mC locations at base resolution.

Pros:

• CpG and non-CpG methylation throughout the genmoe is covered at single-base resolution
• 5mC dense and less dense in repeat regions are covered
• Method clearly differentiates between 5mC and 5hmC, precisely identifying 5mC

Cons:

• Bisulfite converts unmethylated cytosines to thymidines, reducing sequence complexity, which can make it difficult to create alignments
• SNPs where a cytosine is converted to thymidine will be missed upon bisulfite conversion
  

Methods Link:

• oxBS-Seq: Booth M. J., Branco M. R., Ficz G., Oxley D., Krueger F., et al. (2012) Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 336: 934-937

1. Booth M. J., Marsico G., Bachman M., Beraldi D. and Balasubramanian S. (2014) Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution. Nat Chem 6: 435-440
2. Booth M. J., Ost T. W., Beraldi D., Bell N. M., Branco M. R., et al. (2013) Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine. Nat Protoc 8: 1841-1851