scAba-Seq
scAba-Seq
scABA-seq is a single-cell, genome-wide and strand-specific 5hmC sequencing technology, based on 5hmC glucosylation and glucosylation-dependent digestion of DNA.
Glucosylated DNA of individual cells is digested with AbaSI. Digested DNA is ligated to an adaptor containing a cell-specific barcode, Illumina 5′adaptor and a T7 promoter. Ligated DNA from different cells is pooled and amplified using in vitro transcription (IVT) mediated by T7 polymerase.
Pros:
- Determine strand-specific glucosylation in individual cells
Cons:
- Ambiguity might exist in 13 % of the cleaved molecules in the Aba-seq assay1
- Sequence bias in AbaSI activity2
- scAba-Seq: Mooijman D., Dey S. S., Boisset J. C., Crosetto N. and van Oudenaarden A. (2016) Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction. Nat Biotechnol advance online publication:
- 1. Serandour A. A., Avner S., Mahe E. A., Madigou T., Guibert S., et al. (2016) Single-CpG resolution mapping of 5-hydroxymethylcytosine by chemical labeling and exonuclease digestion identifies evolutionarily unconserved CpGs as TET targets. Genome Biol 17: 56
- 2. Sun Z., Dai N., Borgaro J. G., Quimby A., Sun D., et al. (2015) A sensitive approach to map genome-wide 5-hydroxymethylcytosine and 5-formylcytosine at single-base resolution. Mol Cell 57: 750-761