Unit

UNIT 21.3 Chromatin Immunoprecipitation for Determining the Association of Proteins with Specific Genomic Sequences In Vivo

  1. Oscar Aparicio1,
  2. Joseph V. Geisberg2,
  3. Edward Sekinger2,
  4. Annie Yang2,
  5. Zarmik Moqtaderi2,
  6. Kevin Struhl2

Published Online: 1 FEB 2005

DOI: 10.1002/0471142727.mb2103s69

Current Protocols in Molecular Biology

Current Protocols in Molecular Biology

How to Cite

Aparicio, O., Geisberg, J. V., Sekinger, E., Yang, A., Moqtaderi, Z. and Struhl, K. 2005. Chromatin Immunoprecipitation for Determining the Association of Proteins with Specific Genomic Sequences In Vivo. Current Protocols in Molecular Biology. 69:21.3:21.3.1–21.3.33.

Author Information

  1. 1

    University of Southern California, Los Angeles, California

  2. 2

    Harvard Medical School, Boston, Massachusetts

Publication History

  1. Published Online: 1 FEB 2005
  2. Published Print: JAN 2005

Abstract

Chromatin immunoprecipitation (ChIP) is a powerful and widely applied technique for detecting the association of individual proteins with specific genomic regions in vivo. Live cells are treated with formaldehyde to generate protein-protein and protein-DNA cross-links between molecules that are in close proximity on the chromatin template in vivo. DNA sequences that cross-link with a given protein are selectively enriched, and reversal of the formaldehyde cross-linking permits recovery and quantitative analysis of the immunoprecipitated DNA. As formaldehyde inactivates cellular enzymes essentially immediately upon addition to cells, ChIP provides snapshots of protein-protein and protein-DNA interactions at a particular time point, and hence is useful for kinetic analysis of events occurring on chromosomal sequences in vivo. In addition, ChIP can be combined with microarray technology to identify the location of specific proteins on a genome-wide basis. Basic Protocol 1 in this unit describes the ChIP procedure for Saccharomyces cerevisiae; Basic Protocol 2 describes the corresponding steps for mammalian cells.