Unit

UNIT 21.9 Defining In Vivo Targets of Nuclear Proteins by Chromatin Immunoprecipitation and Microarray Analysis

  1. Zarmik Moqtaderi,
  2. Kevin Struhl

Published Online: 1 NOV 2004

DOI: 10.1002/0471142727.mb2109s68

Current Protocols in Molecular Biology

Current Protocols in Molecular Biology

How to Cite

Moqtaderi, Z. and Struhl, K. 2004. Defining In Vivo Targets of Nuclear Proteins by Chromatin Immunoprecipitation and Microarray Analysis. Current Protocols in Molecular Biology. 68:21.9:21.9.1–21.9.7.

Author Information

  1. Harvard Medical School, Boston, Massachusetts

Publication History

  1. Published Online: 1 NOV 2004
  2. Published Print: OCT 2004

Abstract

This unit describes the combination of chromatin immunoprecipitation (ChIP) with microarray hybridization to determine the genome-wide occupancy profile of a DNA-associated protein. After conventional ChIP, the immunoprecipitated material is amplified by a two-step process involving primer extension followed by PCR in the presence of a modified nucleotide. The amplified DNA is fluorescently labeled in a reaction that couples dye to the modified nucleotide, and the labeled sample is hybridized to a microarray representing a complete genome. This method allows the study of a protein's pattern of DNA association across an entire genome with no need for prior knowledge of potential DNA targets.

Keywords:

  • Chromatin immunoprecipitation;
  • ChIP;
  • microarray;
  • amplification;
  • PCR;
  • dye coupling;
  • protein-DNA interactions;
  • ChIP-chip;
  • ChIP-on-chip;
  • genome-wide location;
  • hybridization;
  • whole-genome analysis