MeDIP-Seq/DIP-Seq

MeDIP-Seq/DIP-Seq

Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) or DNA immunoprecipitation sequencing (DIP-Seq) is commonly used to study 5mC or 5hmC modification. Specific antibodies can be used to study cytosine modifications. If using 5mC-specific antibodies, methylated DNA is isolated from genomic DNA via immunoprecipitation. Anti-5mC antibodies are incubated with fragmented genomic DNA and precipitated, followed by DNA purification and sequencing. Deep sequencing provides greater genome coverage, representing the majority of immunoprecipitated methylated DNA.

Pros:
  • Covers CpG and non-CpG 5mC throughout the genome
  • 5mC in dense, less dense, and repeat regions are covered
  • Antibody-based selection is independent of sequence and does not enrich for 5hmC due to antibody specificity
Cons:
  • Base-pair resolution is lower (~150 bp) as opposed to single base resolution
  • Antibody specificity and selectivity must be tested to avoid nonspecific interaction
  • Antibody-based selection is biased towards hypermethylated regions