Fig. 1

Schematic outline of the MB-seq and MRB-seq experiment. a Schematic drawing of MB-seq approach. Genomic DNA was randomly fragmented to 100–300 bp and ligated to AluI-linkers with a methylated AluI recognition site close to the T-overhang. The ligated-fragments were captured using methylcytosine antibody, then treated with sodium bisulfite and converted to double stranded DNA by amplification using biotin labelled AluI primers. The AluI-linker was digested and removed by streptavidin coupled beads. The linker-removed sequence was added 3’end A-tailing, then ligated to Illumina multiplexing adaptors following PCR amplification using Illumina paired-end PCR primers. The PCR products of 230–250 bases in length were size-selected on a gel and sequenced on the Illumina platform. b Schematic drawing of MRB-seq approach. Repetitive DNA elements were removed using Cot-1 DNA after MeDIP (based on the MB-seq approach). Cot-1 DNA was labelled with biotin and coupled with streptavidin, and the streptavidin-biotin-Cot-1 DNA was hybridized to enriched methylated DNA fragments via MeDIP to remove repeat fragments. The methylated fragments obtained (single/low copy DNA fragments) were then subjected to sodium bisulfite treatment, PCR amplification, AluI digestion and sequencing library preparation, as per MB-seq