MeDIPchip

MeDIPchip is a genome-wide DNA methylation profiling technique that combines methylated DNA immunoprecipitation (MeDIP) with microarray analysis. It enables the detection of methylated regions across the genome by enriching for 5-methylcytosine-containing DNA fragments and interrogating them on a microarray.

In typical workflows, genomic DNA is sheared to fragments of roughly 200–1000 base pairs. The fragments are incubated with an antibody against 5-methylcytosine to immunoprecipitate methylated DNA, which is then purified. The enriched DNA is labeled and hybridized to tiling or promoter-specific microarrays, while input DNA or unmethylated controls are processed in parallel to provide a reference. After hybridization and washing, the microarray is scanned, and data are analyzed to identify regions with enrichment relative to the reference, indicating methylation.

Data analysis involves normalization, background subtraction, and peak calling to determine methylated loci. Comparisons between samples can reveal differential methylation patterns associated with development, tissue types, or disease states.

Applications of MeDIPchip include mapping genome-wide methylation landscapes, assessing promoter and CpG island methylation, and studying epigenetic regulation in development, cancer, imprinting, and aging. It has also been used to compare methylation between normal and diseased tissues or to identify differentially methylated regions.

Limitations include its relatively limited resolution, constrained by DNA fragment size and microarray design, and semi-quantitative readouts that are less precise than sequencing-based approaches. Bias toward densely methylated regions and potential cross-hybridization can affect accuracy. MeDIPchip was widely used before sequencing-based methods (such as MeDIP-seq) became common, offering higher resolution and broader coverage.