Determining how proteins interact with DNA to regulate gene expression is essential for full understanding of many biological processes and disease states. Specific DNA-protein interaction sites can be isolated by chromatin immunoprecipitation (ChIP). Illumina combines whole-genome ChIP with massively parallel DNA sequencing to identify and quantify binding sites for DNA-associated proteins. Illumina’s ChIP-Seq protocol cost-effectively and precisely maps global binding sites for a protein of interest across the entire genome.

The ChIP process first enriches specific DNA-protein complexes using an antibody against a protein of interest. Oligonucleotide adapters are then added to the small stretches of DNA bound to these specific proteins. After size selection, the resulting ChIP DNA fragments are sequenced using cBot*, the Genome Analyzer, and Illumina Sequencing Reagents. Low sample input requirements minimize tedious immunoprecipitations while comprehensive mapping across the whole genome deliver data at one-tenth to one-thirtieth the cost of conventional tiling array (ChIP-chip) experiments. Most binding sites can be mapped using data generated in a single lane of one eight-lane flow cell.

*cBot carries out the same function as the Cluster Station

Highlights

• High-Quality Data: Positional resolution of mapped binding sites ± 5 bp
• Wide Dynamic Range: Robust quantification for determining binding specificities of varying strengths
• High Signal-to-Noise Ratio: Lower background than ChIP-chip, no cross hybridization
• Genome-Wide Analysis: Identifies any binding sites, not limited to array features or candidate sequences
• Low Starting Material Requirement: As little as 10 ng