MAB-seq
M.SssI Methylase-Assisted Bisulfite Sequencing
MAB-seq allows simultaneous and quantitative mapping of both 5fC and 5caC at single-base resolution (Wu et al., 2014). This method is complementary to caMAB-seq, a method for direct 5caC mapping.In this method, gDNA is treated with the bacterial CpG methyltransferase M.SssI, which methylates CpG dinucleotides. Next, bisulfite conversion of methylase-treated DNA leads to deamination of only 5fC and 5caC; originally unmodified CpGs are protected as 5mCpG. After sequencing, 5fC and 5caC are read as thymidine, while 5mC is read as cytosine.
Advantages:
- Can provide a quantitative measurement of the abundance of 5fC/5caC within CpG dyads.
Disadvantages:
- Unable to distinguish 5fC/5caC from unmodified C within a non-CpG context
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
Meldi K. M. and Figueroa M. E. Cytosine modifications in myeloid malignancies. Pharmacol Ther. 2015;152:42-53
References:
Aijo T., Huang Y., Mannerstrom H., Chavez L., Tsagaratou A., et al. A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways. Genome Biol. 2016;17:49
Neri F., Incarnato D., Krepelova A., Parlato C. and Oliviero S. Methylation-assisted bisulfite sequencing to simultaneously map 5fC and 5caC on a genome-wide scale for DNA demethylation analysis. Nat Protoc. 2016;11:1191-1205
Neri F., Incarnato D., Krepelova A., et al. Single-Base Resolution Analysis of 5-Formyl and 5-Carboxyl Cytosine Reveals Promoter DNA Methylation Dynamics. Cell Rep. 2015;10:674-683
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History: MAB-seq
Revision by sbrumpton on 2017-06-21 07:50:20 - Show/Hide
M.SssI Methylase-Assisted Bisulfite Sequencing
MAB-seq allows simultaneous and quantitative mapping of both 5fC and 5caC at single-base resolution (Wu et al., 2014). This method is complementary to caMAB-seq, a method for direct 5caC mapping.In this method, gDNA is treated with the bacterial CpG methyltransferase M.SssI, which methylates CpG dinucleotides. Next, bisulfite conversion of methylase-treated DNA leads to deamination of only 5fC and 5caC; originally unmodified CpGs are protected as 5mCpG. After sequencing, 5fC and 5caC are read as thymidine, while 5mC is read as cytosine.
Advantages:- Can provide a quantitative measurement of the abundance of 5fC/5caC within CpG dyads.
Disadvantages:- Unable to distinguish 5fC/5caC from unmodified C within a non-CpG context
Reagents:Illumina Library prep and Array Kit SelectorReviews:Meldi K. M. and Figueroa M. E. Cytosine modifications in myeloid malignancies. Pharmacol Ther. 2015;152:42-53References:Aijo T., Huang Y., Mannerstrom H., Chavez L., Tsagaratou A., et al. A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways. Genome Biol. 2016;17:49Neri F., Incarnato D., Krepelova A., Parlato C. and Oliviero S. Methylation-assisted bisulfite sequencing to simultaneously map 5fC and 5caC on a genome-wide scale for DNA demethylation analysis. Nat Protoc. 2016;11:1191-1205Neri F., Incarnato D., Krepelova A., et al. Single-Base Resolution Analysis of 5-Formyl and 5-Carboxyl Cytosine Reveals Promoter DNA Methylation Dynamics. Cell Rep. 2015;10:674-683