Simplified ChIP-exo assays

Matthew J. Rossi, William K. M. Lai and B. Franklin Pugh ()
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Matthew J. Rossi: The Pennsylvania State University
William K. M. Lai: The Pennsylvania State University
B. Franklin Pugh: The Pennsylvania State University

Nature Communications, 2018, vol. 9, issue 1, 1-13

Abstract: Abstract ChIP-seq and ChIP-exo identify where proteins bind along any genome in vivo. Although ChIP-seq is widely adopted in academic research, it has inherently high noise. In contrast, ChIP-exo has relatively low noise and achieves near-base pair resolution. Consequently, and unlike other genomic assays, ChIP-exo provides structural information on genome-wide binding proteins. Construction of ChIP-exo libraries is technically difficult. Here we describe greatly simplified ChIP-exo methods, each with use-specific advantages. This is achieved through assay optimization and use of Tn5 tagmentation and/or single-stranded DNA ligation. Greater library yields, lower processing time, and lower costs are achieved. In comparing assays, we reveal substantial limitations in other ChIP-based assays. Importantly, the new ChIP-exo assays allow high-resolution detection of some protein-DNA interactions in organs and in as few as 27,000 cells. It is suitable for high-throughput parallelization. The simplicity of ChIP-exo now makes it a highly appropriate substitute for ChIP-seq, and for broader adoption.

Date: 2018
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DOI: 10.1038/s41467-018-05265-7

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