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All Things Ch IP: Ch IP-Chip, Ch IP-Seq, Ch IP-PCR

Epigenetic Regulation and Epigenomics

  1. Jason M. Rizzo,
  2. Michael J. Buck

Published Online: 10 OCT 2011

DOI: 10.1002/3527600906.mcb.201100007

Reviews in Cell Biology and Molecular Medicine

Reviews in Cell Biology and Molecular Medicine

How to Cite

Rizzo, J. M. and Buck, M. J. 2011. All Things Ch IP: Ch IP-Chip, Ch IP-Seq, Ch IP-PCR . Reviews in Cell Biology and Molecular Medicine. .

Author Information

  1. State University of New York at Buffalo, Department of Biochemistry and the Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York, USA

Publication History

  1. Published Online: 10 OCT 2011

Abstract

Chromatin immunoprecipitation (ChIP) has long been a valuable tool for scientists seeking to study in vivo protein–DNA interactions. Beginning with the pioneering efforts of Solomon et al., successful applications of the ChIP protocol have spanned multiple model systems across a wide breadth of biological disciplines. ChIP is a technique whereby a protein of interest is selectively immunoprecipitated from a chromatin preparation to determine the DNA sequences associated with it. While a relatively simple experiment conceptually, the ChIP protocol is notorious for the variance it can produce. Additionally, the availability of multiple assays for analyzing the protein-associated DNA that ChIP collects can confound even the most experienced researcher, particularly in choosing, designing or analyzing a given assay of ChIP DNA. The aim of this chapter is to aid the experience of a ChIP user by outlining ways to design, control and analyze ChIP experiments to enhance data quality and interpretation.

Keywords:

  • Antigen;
  • Chromatin;
  • Chromatin immunoprecipitation (ChIP);
  • ChIP-chip;
  • ChIP-Seq;
  • Epitope;
  • Immunoprecipitation (IP);
  • IP enrichment;
  • Micrococcal nuclease (MNase);
  • Sonication