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Hunter AL, Adamson AD, Poolman TM, Grudzien M, Loudon ASI, Ray DW, Bechtold DA. HaloChIP-seq for Antibody-Independent Mapping of Mouse Transcription Factor Cistromes in vivo. Bio Protoc 2022; 12:e4460. [PMID: 35937930 PMCID: PMC9303821 DOI: 10.21769/bioprotoc.4460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/15/2022] [Accepted: 05/20/2022] [Indexed: 12/29/2022] Open
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 ® is a modified dehalogenase enzyme, which covalently binds synthetic ligands. This system can be used for imaging and purification of HaloTag ® fusion proteins, and has been used for ChIP in vitro . Here, we present a protocol for using the HaloTag ® system for ChIP in vivo , to map, with sensitivity and specificity, the cistrome of a dynamic mouse transcription factor expressed at its endogenous locus. Graphical abstract.
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Affiliation(s)
- Ann Louise Hunter
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Antony D. Adamson
- Genome Editing Unit, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Toryn M. Poolman
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 7LE, United Kingdom
| | - Magdalena Grudzien
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Andrew S. I. Loudon
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - David W. Ray
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 7LE, United Kingdom
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, United Kingdom
| | - David A. Bechtold
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
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Abstract
This protocol describes the injection of lentivirus into the perivitelline space of fertilized oocytes. Embryos usually survive lentiviral injection well because only the zona is pierced.
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