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

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

Angela R. Wu,^a Tiara L.A. Kawahara,^b Nicole A. Rapicavoli,^b Jan van Riggelen,^c Emelyn H. Shroff,^c Liwen Xu,^c Dean W. Felsher,^c Howard Y. Chang^bd and Stephen R. Quake^ad

Author affiliations

^a Department of Bioengineering, Stanford University, Stanford, CA 94305, United States of America
E-mail: quake@stanford.edu
Fax: (650) 736-1961
Tel: (650) 724-8890

^b Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California

^c Division of Medical Oncology, Departments of Medicine and Pathology, Stanford University School of Medicine, Stanford, California

^d Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789

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.

This article is part of the themed collection: Focus on USA

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Article information

DOI: https://doi.org/10.1039/C2LC21290K
Article type: Paper
Submitted: 23 Dec 2011
Accepted: 19 Mar 2012
First published: 08 May 2012

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Lab Chip, 2012,12, 2190-2198

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