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

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. Although ChIP-seq provides invaluable information on the fundamentals of health and disease, it also faces a frustrating challenge: its results are often seen as qualitative rather than quantitative, making interpretation difficult.

But, it turns out, ChIP-seq may have been quantitative from the start, according to a recent report selected as Editors’ Choice 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 further steps are needed to make it quantitative,” said Brad Dickson, Ph.D., a staff scientist at the Van Andel Institute and corresponding author of the study. “Our new approach provides a way to quantify results, thus making ChIP-seq more accurate while leaving standard protocols intact.”

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

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

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