A highly parallel, automated platform enabling individual or sequential ChIP of histone marks and transcription factors

Abstract

Despite its popularity, chromatin immunoprecipitation followed by sequencing (ChIP-seq) remains a tedious (>2d), manually intensive, low-sensitivity and low-throughput approach. Here, we combine principles of microengineering, surface chemistry and molecular biology to address the major limitations of standard ChIP-seq. The resulting approach, FloChIP, automates and miniaturizes ChIP in a beadless fashion while facilitating the downstream library preparation process through on-chip chromatin tagmentation. FloChIP is fast (<2h), has a wide dynamic range (from 106 to 500 cells), is high-throughput (up to 64 parallel, antibody- or sample-multiplexed experiments) and is compatible with both histone mark and transcription factor ChIP. In addition, FloChIPs interconnected design allows for straightforward chromatin re-immunoprecipitation, thus constituting the first example of a microfluidic sequential ChIP-seq system. Finally, we demonstrate FloChIPs high-throughput capacity by performing ChIP-seq of the transcription factor MEF2A in 32 distinct human lymphoblastoid cell lines, providing novel insights into the main factors driving collaborative DNA binding of MEF2A and into its role in B-cell-specific gene regulation. Together, our results validate FloChIP as a flexible and reproducible automated solution for individual or sequential ChIP-seq.