@article{3a85a44b6b4e463d9cbbade22580f2e0,
title = "HaloChIP-seq for Antibody-Independent Mapping of Mouse Transcription Factor Cistromes In Vivo",
abstract = "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{\textregistered} is a modified dehalogenase enzyme, which covalently binds synthetic ligands. This system can be used for imaging and purification of HaloTag{\textregistered} fusion proteins, and has been used for ChIP in vitro. Here, we present a protocol for using the HaloTag{\textregistered} system for ChIP in vivo, to map, with sensitivity and specificity, the cistrome of a dynamic mouse transcription factor expressed at its endogenous locus.",
keywords = "ChIP, Fusion protein, HaloTag{\textregistered}, NR1D1, Nuclear receptor, Tag",
author = "Hunter, {Ann Louise} and Antony Adamson and Toryn Poolman and Magdalena Grudzien and Andrew Loudon and David Ray and David Bechtold",
note = "Funding Information: This research was funded by the Biotechnology and Biological Sciences Research Council (BB/I018654/1 to D.A.B.), the Medical Research Council (Clinical Research Training Fellowship MR/N021479/1 to A.L.H.; MR/P00279X/1 to D.A.B.; MR/P011853/1 and MR/P023576/1 to D.W.R.), National Institute for Health Research Oxford Biomedical Research Centre, and the Wellcome Trust (107849/Z/15/Z, 107851/Z/15/Z). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. This protocol was derived from two original research papers (Hunter et al., 2020, 2021), the Promega HaloCHIPTM manufacturer{\textquoteright}s instructions, and the Active Motif High Sensitivity Chromatin Prep kit protocol, with adaptations for adipose tissue work informed by the publications of other groups (Haim et al., 2013; Castellano-Castillo et al., 2018). We acknowledge the core facilities at the University of Manchester: the Genome Editing Unit, the Genomic Publisher Copyright: {\textcopyright} 2022 E-Century Publishing Corporation. All rights reserved.",
year = "2022",
month = jul,
day = "5",
doi = "10.21769/BioProtoc.4460",
language = "English",
volume = "12",
journal = "Bio-protocol",
issn = "2331-8325",
publisher = "Bio-protocol LLC",
number = "13",
}