MeDIP

MeDIP stands for methylated DNA immunoprecipitation, a method used to map DNA methylation across genomes by capturing methylated DNA fragments with antibodies against 5-methylcytosine (5mC). Genomic DNA is sheared into fragments, typically a few hundred base pairs in length, then incubated with anti-5mC antibodies to form immune complexes that are captured on protein A/G beads. After washing, the methylated DNA is eluted and analyzed by either MeDIP-chip (microarray) or MeDIP-seq (high-throughput sequencing). The approach yields genome-wide profiles of relative methylation density, with enrichment signals marking methylated regions, but it does not provide single-base resolution and is biased toward CpG-dense regions.

Applications include surveying genome-wide methylation patterns in development, tissue- and disease-specific epigenetics, imprinting, cancer, and comparative methylome studies. Data analysis involves aligning sequencing reads to a reference genome, calling enriched regions (peaks) against an appropriate control (input DNA), and comparing samples to infer methylation differences. Important caveats include limited resolution set by fragment size, potential antibody cross-reactivity with other cytosine modifications (e.g., 5-hydroxymethylcytosine), and the inability to distinguish methylation density at individual nucleotides. Quantitative interpretation is relative rather than absolute; comparisons require careful normalization.

MeDIP is commonly contrasted with bisulfite-based methods that provide single-base resolution and with MBD-based capture approaches. It remains a cost-effective, scalable option for genome-wide methylation profiling when high-resolution data are not required.