High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation

Abstract

Chromatin immunoprecipitation (ChIP) is an assay for interrogating protein–DNA interactions that is increasingly being used for drug target discovery and screening applications. Currently the complexity of the protocol and the amount of hands-on time required for this assay limits its use to low throughput applications; furthermore, variability in antibody quality poses an additional obstacle in scaling up ChIP for large scale screening purposes. To address these challenges, we report HTChIP, an automated microfluidic-based platform for performing high-throughput ChIP screening measurements of 16 different targets simultaneously, with potential for further scale-up. From chromatin to analyzable PCR results only takes one day using HTChIP, as compared to several days up to one week for conventional protocols. HTChIP can also be used to test multiple antibodies and select the best performer for downstream ChIP applications, saving time and reagent costs of unsuccessful ChIP assays as a result of poor antibody quality. We performed a series of characterization assays to demonstrate that HTChIP can rapidly and accurately evaluate the epigenetic states of a cell, and that it is sensitive enough to detect the changes in the epigenetic state induced by a cytokine stimulant over a fine temporal resolution. With these results, we believe that HTChIP can introduce large improvements in routine ChIP, antibody screening, and drug screening efficiency, and further facilitate the use of ChIP as a valuable tool for research and discovery.

Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond

“…40 HTChIP is an extremely effective tool that uses a microfluidic device to simultaneously process 16 distinct biological samples. Thus using the microfluidic device, complex protocols with multiple components can be streamlined in a systematic manner.…”

Chromatin immunoprecipitation in microfluidic droplets: towards fast and cheap analyses

“…Wu et al developed an automated microfluidic-based platform to perform 16 assays simultaneously using only 10 000 cells for each experiment, by achieving increased chromatin yield during the immunoprecipitation steps. This integrated approach offers greater sensitivity than conventional procedures 16 . Geng et al developed an assay that permits the analysis of histone modifications from as few as 50 cells by using magnetic beads in a microfluidic chamber 17 .…”

Droplet-Based Microfluidics: Enabling Impact on Drug Discovery

“…76 Other recent efforts in this area include the functional screening of hybridoma cells for the release of antibodies inhibiting a drug target at a screening rate of 300,000 cell clones per day 77 and chromatin immunoprecipitation on a chip to select for antibodies against specific proteins. 78 In 2007, Maerkl and Quake 79 introduced the MITOMI (Mechanically Induced Trapping of Molecular Interactions) platform (see Fig. 2).…”