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Automated High-throughput ChIP-seq Workflow using Covaris Adaptive Focused Acoustics (AFA) System for Accelerated Epigenetic Drug Screening
Jonathan Young1, Tianyao Xu1, Eugenio Daviso2, Jim Laugharn2, Hamid Khoja2 & Alon Goren1,#1 Department of Medicine, University of California San Diego, La Jolla, CA USA2 Covaris Inc. Woburn, MA# Correspondence should be addressed to email@example.com.
Mapping the epigenomic landscape is essential for understanding gene regulatory mechanisms during cell fate changes, disease onset and progression, and during treatment response. Such epigenomic mapping holds huge potential for identification of biomarkers and targets for therapy in general, and epigenetic targets in particular. However, most existing ChIP-sequencing (ChIP-seq) workflows are very time-consuming, difficulty to optimize and standardize for different input material and across different laboratories, and involve many manual steps which makes it inefficient for high throughput screening approaches.
To overcome these issues, we combined our validated automated ChIP-seq (Busby et al., Epigenetics & Chromatin, 2016) with the Covaris Adaptive Focused Acoustics (AFA) technology to streamline and significantly reduce the overall workflow time for ChIP-seq. In our study, we tested the ability of AFA to enhance the binding kinetics of antibody-epitope association, improve signal-to-noise ratios, and decrease total processing time. We evaluated a range of epitopes including major histone modifications such as H3K4me3 which is associated with open chromatin and forms narrow peaks, H3K27me3 which is linked to repressed chromatin and binds to wide regions, and H3K27ac associated with open chromatin, and both wide enhancer loci as well as narrow promoter regions. Additionally, we studied the capacity of the AFA to augment the IP step of DNA associated proteins such as CTCF and validated our test conditions using two cell types. Furthermore, we validate each of our test conditions using a variety of cell types. Our preliminary results demonstrate that AFA expedites the immunoprecipitation process to an hour or less while also improving the signal to noise ratio in ChIP-seq, and has the potential to be accelerate similar drug discovery workflows that are based on an immunoprecipitation step, such as MeDIP-seq.
Altogether, we have developed a novel use of AFA for accelerated IP that allows enhancing and simplifying ChIP-seq processes. As the process can be performed in a 96 well plate format and thus integrated into other automated workflows, we expect this key advancement would be highly useful for both research, clinical diagnostic applications and discovery pipelines for epigenetics drugs.