Aba-seq
AbaSI Coupled with Sequencing
Aba-seq is a method for high-resolution mapping of the 5hmC methylome that provides sensitive detection of 5hmC at low-occupancy regions (Sun et al., 2013). The method relies on the unique property of the restriction enzyme AbaSI to recognize glucosylated 5hmC with high specificity, compared to 5mC and C. A single-cell variation, scAba-seq, is also available (Mooijman et al., 2016). A related method uses PvuRts1I to overcome the sequence bias in AbaSI (Sun et al., 2015)
Advantages:
- Covers CpG and non-CpG methylation throughout the genome at single-base resolution
- Covers 5mC in dense and less dense repeat regions
- Clearly differentiates between 5mC and 5hmC
Disadvantages:
- Ambiguity can exist in 13% of the cleaved molecules in the Aba-seq assay (Serandour et al., 2016)
- Sequence bias in AbaSI activity (Sun et al., 2015)
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
Plongthongkum N., Diep D. H. and Zhang K. Advances in the profiling of DNA modifications: cytosine methylation and beyond. Nat Rev Genet. 2014;15:647-661
References:
Sun Z., Terragni J., Borgaro J. G., et al. High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells. Cell Rep. 2013;3:567-576