After more than a decade, ChIP-seq may be quantitative after all

GRAND RAPIDS, Mich. (Nov. 20, 2020) — For more than a decade, scientists studying epigenetics have used a powerful method called ChIP-seq to map changes in proteins and other critical regulatory factors across the genome. While ChIP-seq provides invaluable insights into the underpinnings of health and disease, it also faces a frustrating challenge: its results are often viewed as qualitative rather than quantitative, making interpretation difficult.

But, it turns out, ChIP-seq may have been quantitative all along, according to a recent report selected as an Editors’ Pick by and featured on the cover of the Journal of Biological Chemistry.

“ChIP-seq is the backbone of epigenetics research. Our findings challenge the belief that additional steps are required to make it quantitative,” said Brad Dickson, Ph.D., a staff scientist at Van Andel Institute and the study’s corresponding author. “Our new approach provides a way to quantify results, thereby making ChIP-seq more precise, while leaving standard protocols untouched.”

Previous attempts to quantify ChIP-seq results have led to additional steps being added to the protocol, including the use of “spike-ins,” which are additives designed to normalize ChIP-seq results and reveal histone changes that otherwise may be obscured. These extra steps increase the complexity of experiments while also adding variables that could interfere with reproducibility. Importantly, the study also identifies a sensitivity issue in spike-in normalization that has not previously been discussed.

Using a predictive physical model, Dickson and his colleagues developed a novel approach called the sans-spike-in method for Quantitative ChIP-sequencing, or siQ-ChIP. It allows researchers to follow the standard ChIP-seq protocol, eliminating the need for spike-ins, and also outlines a set of common measurements that should be reported for all ChIP-seq experiments to ensure reproducibility as well as quantification.

By leveraging the binding reaction at the immunoprecipitation step, siQ-ChIP defines a physical scale for sequencing results that allows comparison between experiments. The quantitative scale is based on the binding isotherm of the immunoprecipitation products.

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Authors include Rochelle L. Tiedemann, Ph.D., Alison A. Chomiak, Ph.D., Robert M. Vaughan and Scott B. Rothbart, Ph.D., of Van Andel Institute; and Evan M. Cornett, Ph.D., of Indiana University School of Medicine. The Van Andel Institute Genomics Core and High-Performance Computing facility also supported this work.

Research reported in this publication was supported by Van Andel Institute; the National Institute of General Medical Sciences under award no. R35GM124736 (Rothbart); the National Cancer Institute of the National Institutes of Health under award no. F32CA225043 (Chomiak) and no. F99CA245821 (Vaughan); and the American Cancer Society-Michigan Research Fund under award no. PF-16-245-01-DMC (Tiedemann). The content is solely the responsibility of the authors and does not necessarily represent the official views of the granting organizations.

Van Andel Institute (VAI) is committed to improving the health and enhancing the lives of current and future generations through cutting edge biomedical research and innovative educational offerings. Established in Grand Rapids, Michigan, in 1996 by the Van Andel family, VAI is now home to more than 400 scientists, educators and support staff, who work with a growing number of national and international collaborators to foster discovery. The Institute’s scientists study the origins of cancer, Parkinson’s and other diseases and translate their findings into breakthrough prevention and treatment strategies. Our educators develop inquiry-based approaches for K-12 education to help students and teachers prepare the next generation of problem-solvers, while our Graduate School offers a rigorous, research-intensive Ph.D. program in molecular and cellular biology. Learn more at vai.org.