ChEC-seq produces robust and specific maps of transcriptional regulators

Abstract

We previously introduced chromatin endogenous cleavage and high-throughput sequencing (ChEC-seq), which uses fusion of a chromatin-binding protein of interest to micrococcal nuclease (MNase) and high-throughput sequencing to generate genome-wide maps of factor binding. Here, we respond to concerns that have been raised about the specificity of the method relative to its negative control when a single long calcium incubation time is used. Through reanalysis of our previously published datasets, we show that short-duration ChEC-seq experiments provide robust, specific maps of transcriptional regulators across the budding yeast genome. Our analyses also confirm that consideration of MNase digestion kinetics is important for proper design and interpretation of ChEC-seq experiments.