CHIP-on-chip, also known as genome-wide location analysis (LA), is a technique for isolation and identification of the DNA sequences occupied by specific DNA binding proteins in cells. CHIP-on-chip pairs Chromatin Immunoprecipitation (CHIP) with microarrays (chips) to analyze how regulatory proteins interact with the genome of living cells.

Previously, Chip-on-chip has helped to understand the evolution of complex diseases such as diabetes or cancer, and to gain insight into vital biological processes like cell proliferation, cell fate determination, oncogenesis, cell cycle, apoptosis, and neurogenesis.

Regulatory proteins bind to genomic DNA to control chromosome replication and gene activity, thereby functioning as switches in the regulatory circuitry of cells [1]. Carefully selected antibodies can be used to capture regulatory proteins and to precipitate the corresponding stretches of bound DNA [2]. Labelled DNA fragments can then be hybridized to complementary oligonucleotide probes on high-density DNA arrays to map the binding regions at the level of the DNA sequence [3].