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

Riccardo Dainese, Vincent Gardeux, Gerard Llimos, Daniel Alpern, Jia Yuan Jiang, Antonio Carlos Alves Meireles-Filho, Bart Deplancke

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

Despite its popularity, chromatin immunoprecipitation followed by sequencing (ChIP-seq) remains a tedious (>2 d), 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 technology, FloChIP, automates and miniaturizes ChIP in a beadless fashion while facilitating the downstream library preparation process through on-chip chromatin tagmentation. FloChIP is fast (<2 h), has a wide dynamic range (from 106 to 500 cells), is scalable and parallelized, and supports antibody- or sample-multiplexed ChIP on both histone marks and transcription factors. In addition, FloChIP's interconnected design allows for straightforward chromatin reimmunoprecipitation, which allows this technology to also act as a microfluidic sequential ChIP-seq system. Finally, we ran FloChIP for the transcription factor MEF2A in 32 distinct human lymphoblastoid cell lines, providing 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.

Original languageEnglish (US)
Pages (from-to)13828-13838
Number of pages11
JournalProceedings of the National Academy of Sciences of the United States of America
Volume117
Issue number24
DOIs
StatePublished - Jun 16 2020
Externally publishedYes

Keywords

  • ChIP-seq
  • Epigenetics
  • Microfluidics
  • Transcription factor

ASJC Scopus subject areas

  • General

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