Simplified ChIP-exo assays

Nature Communications
Matthew J RossiB Franklin Pugh

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.

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Citations

Jun 25, 2019·ELife·Michael P MeersSteven Henikoff
May 28, 2019·Genes & Development·Leighton Core, Karen Adelman
Jan 17, 2020·Molecular Microbiology·Rajesh BiswasBoris R Belitsky
May 1, 2020·NPJ Breast Cancer·Hanan S ElsarrajFariba Behbod
May 13, 2020·Biology Methods and Protocols·Christoph S BörlinJens Nielsen
Mar 28, 2020·Nature·Laura D GallegoAlwin Köhler
Dec 7, 2020·Molecular Systems Biology·Wim J de JongeFrank Cp Holstege
Oct 22, 2019·Trends in Biochemical Sciences·Sandipan Brahma, Steven Henikoff
Mar 6, 2021·Trends in Immunology·Jinyong Choi, Shane Crotty
Feb 13, 2021·NPJ Breast Cancer·Hanan S ElsarrajFariba Behbod
Mar 12, 2021·Nature·Matthew J RossiB Franklin Pugh
Mar 19, 2020·Molecular Cell·Ziyang HaoChuan He
May 23, 2021·Nature·B Franklin Pugh
Feb 24, 2021·Journal of Molecular Biology·Haining Chen, B Franklin Pugh
Mar 1, 2021·Journal of Molecular Biology·Roberta Dollinger, David S Gilmour
Jul 13, 2021·Bioinformatics·Anushua Biswas, Leelavati Narlikar

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Datasets Mentioned

BETA
GSE110681
GSE114606

Methods Mentioned

BETA
immunoprecipitation
ChIP-seq
ChIP-exo
ChIP
PCR
ChIPs
biopsies
electrophoresis

Software Mentioned

nexus
CircLigase
bwa
exo
mem
ChIP

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