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Chromatin Affinity Purification

  • Ryoko Harada
  • Alain NepveuEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 809)

Abstract

Chromatin immunoprecipitation (ChIP) has become an essential assay in the field of transcriptional regulation. It is currently the most popular method to monitor the in vivo interaction between a protein and specific genomic sites. The method can also serve to identify novel transcriptional targets when the immunoprecipitated chromatin, sometimes called chipped DNA, is used either as a probe in hybridization experiments with microarrays of genomic DNA (ChIP-chip) or as template in DNA sequencing (ChIP-Seq). ChIP assays rely on the availability of good antibodies that can specifically and efficiently immunoprecipitate the protein under study even after cross-linking. However, good antibodies are not always available. To circumvent this problem, we have developed and validated the method of chromatin affinity purification (ChAP). The subsequent microarray analysis is then referred to as ChAP-chip. In brief, the protein under study is expressed together with two tags in order to allow the purification of chromatin by tandem affinity purification. To ensure that only true targets are identified, it is important to express the recombinant tagged-protein at physiological level. This requirement is not trivial as most expression vectors are designed to express proteins at high levels. We found most convenient to use an inducible retroviral vector in the absence of inducer and transactivator protein. We describe the procedure to generate cells stably expressing recombinant tagged-proteins at physiological level and then to purify the associated chromatin by affinity purification. Targets identified in this manner were validated in independent ChAP assays as well as in ChIP assays using antibodies against the endogenous protein.

Key words

Chromatin immunoprecipitation Affinity chromatography Tandem affinity purification Transcription factors Promoter Gene regulation Genome Genomic microarray 

Notes

Acknowledgments

We acknowledge the expert technical assistance of Ms. Ginette Bérubé and Mr. Lam Leduy in the preparation of retroviral vectors. This research was supported by grant #019389 from the Canadian Cancer Society to A.Nepveu.

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.The Rosalind and Morris Goodman Cancer Research CentreMcGill UniversityMontrealCanada
  2. 2.Departments of Biochemistry, Oncology, and Medicine, The Rosalind and Morris Goodman Cancer Research CentreMcGill UniversityMontrealCanada

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