This Small Business Innovation Research (SBIR) Phase I project proposes to develop a high-throughput, multi-analyte chromatin immunoprecipitation (ChIP) system. ChIP is a widely used technique among life science and biomedical researchers seeking map the specific DNA sequences that are bound by a DNA binding protein. Its use ranges from single gene analysis through to genome-wide applications that use next generation sequencing (NGS) technologies as readout. As envisioned, the proposed technology will transform the lengthy and cumbersome multi-day ChIP into a high throughput compatible single-day experiment. The technology will result in the insertion of oligonucleotides containing NGS platform-compatible tags and "bar-code" sequences into DNA fragments associated with the immunoprecipitating antibodies. Each antibody will be associated with a unique barcode that can also be used for direct DNA sequencing or PCR analysis. Feasibility of this approach will be achieved by systematic identification of optimal conditions for insertion of the bar-code containing oligonucleotides into chromatin, and then, with antibody-coupled oligonucleotides. Final validation will be performed at the genome scale using NGS to compare the genomic representation of the library produced by the novel method with that of traditional ChIP.
The broader impact/commercial potential of this project is far reaching. The life sciences research tools market is currently estimated at $42 billion, with the epigenetic sector experiencing high growth fueled by researchers purchasing commercial epigenetic products rather than spending the time and effort to develop them in-house, and by advances in NGS, which has accelerated genome-wide epigenetic analyses. Successful development of the high-throughput, multi-analyte ChIP 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 ChIP, which represents 20-25% of the epigenetic research tools market estimated at $175-245M in 2010. 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 on a genome wide scale.
This Small Business Innovation Research Phase 1project demonstrated proof of concept for the development of high throughput multi-analyte chromatin immunoprecipitation (ChIP). 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 regulated through chromatin-protein interactions with analysis ranging from single gene (using PCR) through to genome-wide (next generation sequencing (NGS)). As envisioned, the technology will transform the lengthy and cumbersome multi-day ChIP into a high throughput compatible single-day experiment. An immunoprecipitating antibody was 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 DNA at sites flanking antibody-bound chromatin fragments enabled direct detection (by PCR or NGS) of DNA fragments associated with the protein(s) of interest. As validation, NGS was used to compare the genomic representation of the library produced by the novel method with that of traditional ChIP. The Life Sciences research tool market is currently estimated at $42 billion, with the epigenetic sector enjoying high growth fueled by a shift by researchers to purchase commercial epigenetic products rather than spending the time and effort to develop them in-house made and by advances in NGS which has accelerated genome-wide epigenetic analyses. Successful development of the high throughput multi-analyte ChIP will have significant impact scientifically and commercially in the Life Sciences and Biomedical research arenas and in less than five years post-launch, it is projected to replace traditional ChIP, which represents 20-25% of the epigenetic research tools market estimated at $175-245M in 2010. The development of this novel ChIP method will be transformative, opening epigenetic analysis to virtually all researchers by elimination of technical barriers and by significantly reducing sample size requirements associated with traditional ChIP, with potential for enabling single cell epigenome analysis. Development of this technology which is based entirely on consumable reagents 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.
