Coupling Exonuclease Digestion with Selective Chemical Labeling forBase-resolution Mapping of 5-Hydroxymethylcytosine in Genomic DNA.

This protocol is designed to obtain base-resolution information on the level of 5-hydroxymethylcytosine (5hmC) in CpGs without the need for bisulfite modification. It relies on (i) the capture of hydroxymethylated sequences by a procedure known as 'selective chemical labeling' (see Szulwach et al., 2012 ) and (ii) the digestion of the captured DNA by exonucleases. After Illumina sequencing of the digested DNA fragments, an ad hoc bioinformatic pipeline extracts the information for further downstream analysis.