HaloChIP-seq for Antibody-Independent Mapping of Mouse Transcription Factor Cistromes in vivo

Chromatin immunoprecipitation (ChIP) maps, on a genome-wide scale, transcription factor binding sites, and the distribution of other chromatin-associated proteins and their modifications. As such, it provides valuable insights into mechanisms of gene regulation. However, successful ChIP experiments are dependent on the availability of a high-quality antibody against the target of interest. Using antibodies with poor sensitivity and specificity can yield misleading results. This can be partly circumvented by using epitope-tagged systems (e.g., HA, Myc, His), but these approaches are still antibody-dependent. HaloTag (R) is a modified dehalogenase enzyme, which covalently binds synthetic ligands. This system can be used for imaging and purification of HaloTag (R) fusion proteins, and has been used for ChIP in vitro. Here, we present a protocol for using the HaloTag (R) system for ChIP in vivo, to map, with sensitivity and specificity, the cistrome of a dynamic mouse transcription factor expressed at its endogenous locus.

Automated summary

Chromatin immunoprecipitation (ChIP) maps enable the identification of transcription factor binding sites and chromatin-associated proteins, providing valuable insights into gene regulation mechanisms. The success of ChIP experiments relies on the availability of high-quality antibodies. The HaloTag(R) system, a modified enzyme, can be used for ChIP to accurately map the cistrome of dynamic mouse transcription factors in vivo.