Epigenetics, the study of inheritable mechanisms that regulate gene expression, has clinical ramifications from cancer to autoimmune disorders to psychiatric pathologies. The main tool to study epigenetics is chromatin immunoprecipitation (ChIP), which probes the relationship between DNA and its structural nucleosome-forming histone proteins. Standard benchtop ChIP has three major drawbacks: (1) it requires a large input volume of cells, (2) it is very time consuming and work intensive, and (3) it is low throughput. Digital microfluidic biochips (DMFB) have proven to be successful at utilizing small volumes of reagents and samples to perform high throughput bioanalyses and assays of macromolecules. Their ease of configurability, automation, and high sensitivity make them an ideal platform for ChIP adaptation, addressing the three biggest issues facing epigenetic study and workflow. Herein, we demonstrate the first step towards ChIP implementation on a DMFB by detecting specifically modified nucleosomes, the building blocks of chromatin, in a nucleosome immunoprecipitation assay. Using magnetic beads to capture the nucleosomes with magnetic fields generated by embedded current wires and fluorescent conjugated antibodies for detection, this DMFB system allows complete on-chip isolation and detection without the need for external magnets or specialized fluoroscopy equipment. This assay design can be adapted to probe for multiple specific nucleosome modifications, thus establishing a rapid screening method for antibody specificity and sensitivity. Most importantly, this novel confirmatory checkpoint, currently unavailable when running ChIP, ensures that the target analyte has been isolated prior to intensive downstream analyses such as PCR and sequencing.