A physical basis for quantitative ChIP-sequencing.

Autor:	Dickson BM; Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA. Electronic address: bradley.dickson@vai.org., Tiedemann RL; Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA., Chomiak AA; Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA., Cornett EM; Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA., Vaughan RM; Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA., Rothbart SB; Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA.
Jazyk:	angličtina
Zdroj:	The Journal of biological chemistry [J Biol Chem] 2020 Nov 20; Vol. 295 (47), pp. 15826-15837. Date of Electronic Publication: 2020 Sep 29.
DOI:	10.1074/jbc.RA120.015353
Abstrakt:	ChIP followed by next-generation sequencing (ChIP-Seq) is a key technique for mapping the distribution of histone posttranslational modifications (PTMs) and chromatin-associated factors across genomes. There is a perceived challenge to define a quantitative scale for ChIP-Seq data, and as such, several approaches making use of exogenous additives, or "spike-ins," have recently been developed. Herein, we report on the development of a quantitative, physical model defining ChIP-Seq. The quantitative scale on which ChIP-Seq results should be compared emerges from the model. To test the model and demonstrate the quantitative scale, we examine the impacts of an EZH2 inhibitor through the lens of ChIP-Seq. We report a significant increase in immunoprecipitation of presumed off-target histone PTMs after inhibitor treatment, a trend predicted by the model but contrary to spike-in-based indications. Our work also identifies a sensitivity issue in spike-in normalization that has not been considered in the literature, placing limitations on its utility and trustworthiness. We call our new approach the s ans-spike- i n method for q uantitative ChIP-sequencing (siQ-ChIP). A number of changes in community practice of ChIP-Seq, data reporting, and analysis are motivated by this work. Competing Interests: Conflict of interest—The authors declare that they have no conflicts of interest with the contents of this article. (© 2020 Dickson et al.)
Databáze:	MEDLINE
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