Protocol for double-crosslinking ChIP-seq to improve data quality and enhance detection of challenging chromatin targets

Chromatin factors drive genome function, yet many lack direct DNA-binding activity and cannot be conventionally profiled. Here, we present dxChIP-seq, a double-crosslinking chromatin immunoprecipitation sequencing (ChIP-seq) protocol that improves mapping of chromatin factors, including those that do not bind DNA directly, while enhancing signal-to-noise ratio. We describe steps for double-crosslinking, focused ultrasonication, immunoprecipitation, DNA purification, and library preparation. We then detail procedures for sequencing and analysis. This protocol is compatible with adherent cells and complex multicellular structures. For complete details on the use and execution of this protocol, please refer to Cacioppo et al.¹.