Broadly Applicable Control Approaches Improve Accuracy of ChIP-Seq Data

Petrie, Meghan V.; He, Yiwei; Gan, Yan; Ostrow, Andrew Zachary; Aparicio, Oscar M.

doi:10.3390/ijms24119271

Open AccessArticle

Broadly Applicable Control Approaches Improve Accuracy of ChIP-Seq Data

by

Meghan V. Petrie

^†,

Yiwei He

^†

,

Yan Gan

,

Andrew Zachary Ostrow

and

Oscar M. Aparicio

^*

Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089, USA

^*

Author to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Int. J. Mol. Sci. 2023, 24(11), 9271; https://doi.org/10.3390/ijms24119271

Submission received: 25 April 2023 / Revised: 18 May 2023 / Accepted: 23 May 2023 / Published: 25 May 2023

(This article belongs to the Special Issue Protein and DNA Interaction)

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Abstract

Chromatin ImmunoPrecipitation (ChIP) is a widely used method for the analysis of protein–DNA interactions in vivo; however, ChIP has pitfalls, particularly false-positive signal enrichment that permeates the data. We have developed a new approach to control for non-specific enrichment in ChIP that involves the expression of a non-genome-binding protein targeted in the IP alongside the experimental target protein due to the sharing of epitope tags. ChIP of the protein provides a “sensor” for non-specific enrichment that can be used for the normalization of the experimental data, thereby correcting for non-specific signals and improving data quality as validated against known binding sites for several proteins that we tested, including Fkh1, Orc1, Mcm4, and Sir2. We also tested a DNA-binding mutant approach and showed that, when feasible, ChIP of a site-specific DNA-binding mutant of the target protein is likely an ideal control. These methods vastly improve our ChIP-seq results in S. cerevisiae and should be applicable in other systems.

Keywords: chromatin immunoprecipitation; controls; DNA-binding protein; genome; replication origins

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MDPI and ACS Style

Petrie, M.V.; He, Y.; Gan, Y.; Ostrow, A.Z.; Aparicio, O.M. Broadly Applicable Control Approaches Improve Accuracy of ChIP-Seq Data. Int. J. Mol. Sci. 2023, 24, 9271. https://doi.org/10.3390/ijms24119271

AMA Style

Petrie MV, He Y, Gan Y, Ostrow AZ, Aparicio OM. Broadly Applicable Control Approaches Improve Accuracy of ChIP-Seq Data. International Journal of Molecular Sciences. 2023; 24(11):9271. https://doi.org/10.3390/ijms24119271

Chicago/Turabian Style

Petrie, Meghan V., Yiwei He, Yan Gan, Andrew Zachary Ostrow, and Oscar M. Aparicio. 2023. "Broadly Applicable Control Approaches Improve Accuracy of ChIP-Seq Data" International Journal of Molecular Sciences 24, no. 11: 9271. https://doi.org/10.3390/ijms24119271

APA Style

Petrie, M. V., He, Y., Gan, Y., Ostrow, A. Z., & Aparicio, O. M. (2023). Broadly Applicable Control Approaches Improve Accuracy of ChIP-Seq Data. International Journal of Molecular Sciences, 24(11), 9271. https://doi.org/10.3390/ijms24119271

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Broadly Applicable Control Approaches Improve Accuracy of ChIP-Seq Data

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