SBIR: Technology for Overcoming Bottlenecks in Chromatin Extraction from Challenging Biological Samples - PROJECT SUMMARY
The complex organization of chromatin (DNA with its associated nuclear proteins) is closely tied to the
regulation of gene expression, and evidence points to a central role for chromatin deregulation in tumor
development. A common analysis of chromatin regulatory protein localization is the chromatin
immunoprecipitation (ChIP) assay, which involves crosslinking of proteins to DNA, followed by chromatin
fragmentation, and then antibody mediated immunoprecipitation of the DNA fragments. Subsequent
quantification (quantitative PCR or Next Generation Sequencing) is usually performed. This assay is a key tool
for both industry and academic research studying cancer-related epigenetics
The challenge is that the formaldehyde crosslinks render the chromatin resistant to mechanical (i.e.
acoustic sonication) lysis, making current fragmentation techniques inefficient and time-consuming.
Furthermore, these techniques result in high sample-to-sample variability and require high-power, low-
throughput, and expensive sonication devices. Our customer discovery interviews have highlighted these pain
points; there is an urgent need for a higher quality and higher throughput method of chromatin fragmentation
before assays such as ChIP can be incorporated into cancer diagnostics applications.
Triangle Biotechnology recently developed a unique cavitation enhancing reagent (RapidShear) that
substantially improves the efficiency of acoustic fragmentation of genomic DNA. However, this reagent
formulation shows little to no improvement for chromatin fragmentation from fixed cells. To address the
aforementioned sample preparation challenges in the epigenetics space, we are developing a new reagent,
MegaShear, a more aggressive formulation for acoustic cavitation enhancement designed specifically for
chromatin processing. Preliminary studies indicated that MegaShear facilitates a substantial improvement in
chromatin fragmentation throughput, consistency, and yield. Validation and optimization of this technology will
alleviate a critical bottleneck in the ChIP workflow. MegaShear will enable a substantial leap in high quality
sample preparation throughput desired by large companies, as well as an increase in accessibility by enabling
the use of low-cost sonicators, desired by small academic labs.
With this SBIR, we will demonstrate proof of concept for MegaShear, validating the ability to produce
high quality chromatin with high consistency, reducing capital equipment cost, and substantially increasing
throughput. Success of this project will enable a novel commercial solution for addressing market pain
points in chromatin analysis.
