Aba-Seq
Aba-Seq
Aba-seq is a method for high-resolution mapping of the 5hmC methylome that provides sensitive detection of 5hmC at low-occupancy regions. 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 available1. A related method uses PvuRts1I to overcome the sequence bias in AbaSI2.
Pros:
- 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
Cons:
- Ambiguity can exist in 13% of the cleaved molecules in the Aba-seq assay3
- Sequence bias in AbaSI activity4
- Aba-Seq: Sun Z., Terragni J., Borgaro J. G., Liu Y., Yu L., et al. (2013) High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells. Cell Rep 3: 567-576
- 1. Mooijman D., Dey S. S., Boisset J. C., Crosetto N. and van Oudenaarden A. Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction. Nat Biotechnol. 2016;34:852-856
- 2. Sun Z., Dai N., Borgaro J. G., et al. A sensitive approach to map genome-wide 5-hydroxymethylcytosine and 5-formylcytosine at single-base resolution. Mol Cell. 2015;57:750-761
- 3. Serandour A. A., Avner S., Mahe E. A., et al. Single-CpG resolution mapping of 5-hydroxymethylcytosine by chemical labeling and exonuclease digestion identifies evolutionarily unconserved CpGs as TET targets. Genome Biol. 2016;17:56
- 4. Sun Z., Dai N., Borgaro J. G., et al. A sensitive approach to map genome-wide 5-hydroxymethylcytosine and 5-formylcytosine at single-base resolution. Mol Cell. 2015;57:750-761