SBIR Phase II: High-Throughput Multi-Analyte Chromatin Immunoprecipitation (ChIP) Assay Development

This Small Business Innovation Research (SBIR) Phase II project proposes to develop a high-throughput, multi-analyte chromatin immunoprecipitation (ChIP) assay. ChIP is a widely used technique among life science and biomedical researchers seeking to understand how the epigenetic mechanism of histone post-translational modifications impacts the varied biological functions that are regulated through chromatin-protein interactions. Analysis ranges from single gene (using PCR) through to genome-wide (next generation sequencing (NGS)). As envisioned, the proposed technology will transform the lengthy and cumbersome multi-day ChIP into a high-throughput compatible single-day experiment. An antibody is linked to oligonucleotides containing NGS platform-compatible tags and "bar-code" sequences for simultaneous analysis of multiple DNA-protein interactions. The insertion of the oligonucleotides into chromatin at sites flanking antibody-bound chromatin fragments will enable direct detection (by PCR or NGS) of DNA fragments associated with the protein(s) of interest. Phase II efforts will focus on developing robust and reproducible methods for both antibody conjugation and technology validation with a panel of antibodies specific for varying classes of chromatin associating proteins, including histone and non-histone targets. DNA libraries produced by the novel method and that of traditional ChIP will be compared first by quantitative PCR for gene-specific analysis and subsequently genome-wide, by NGS. The broader impact/commercial potential of this project, if successful, will be the development of a high throughput multi-analyte ChIP assay that will have significant impact scientifically and commercially in the life sciences and biomedical research arenas. In less than five years post-launch, it is projected to replace traditional current ChIP methods, which represents 20-25% of the epigenetic research tools market estimated at $175-245M in 2010. The life sciences research tool market is currently estimated at $42 billion, with the epigenetic sector enjoying high growth fueled by a shift of researchers to purchase commercial epigenetic products rather than in-house made, and by advances in NGS, which has accelerated genome-wide epigenetic analyses. The development of this method will open epigenetic analysis to virtually all researchers by eliminating technical barriers and by significantly reducing sample size requirements associated with traditional ChIP, including a potential for single cell analysis. Development of this technology will spur the creation of additional novel technologies such as homogeneous ChIP for high-throughput screening, multi-analyte ChIP, and open the door for environmental, nutrition, and toxicology disciplines to study the epigenetic profiles of any eukaryotic organism a genome wide scale.