Optimized protocols for chromatin immunoprecipitation of exogenously expressed epitope-tagged proteins

STAR Protoc. 2023 Mar 17;4(1):102050. doi: 10.1016/j.xpro.2023.102050. Epub 2023 Jan 21.

Abstract

Chromatin immunoprecipitation (ChIP) assay is widely used for investigating the interaction between DNA and DNA-binding proteins such as transcription factors, co-factors, or chromatin-associated proteins. However, a successful ChIP assay largely depends on the quality of a ChIP-grade primary antibody. In cases where specific antibodies are unavailable or with low binding affinity, here, we describe a tailored protocol to achieve robust and reproducible chromatin binding by expressing an exogenous epitope-tagged protein in cells, followed by ChIP assays using a tag-specific antibody. For complete details on the use and execution of this protocol, please refer to Fang et al. (2021)1 and Kidder et al. (2011).2.

Keywords: Cell Biology; Genomics; Molecular Biology; RNAseq.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, N.I.H., Extramural

MeSH terms

  • Antibodies / metabolism
  • Chromatin / genetics
  • Chromatin Immunoprecipitation / methods
  • DNA-Binding Proteins* / genetics
  • Epitopes
  • Transcription Factors* / genetics

Substances

  • Epitopes
  • Transcription Factors
  • DNA-Binding Proteins
  • Antibodies
  • Chromatin