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Nucleic Acids Research Advance Access originally published online on January 17, 2008
Nucleic Acids Research 2008 36(3):e15; doi:10.1093/nar/gkm1158
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Nucleic Acids Research, 2008, Vol. 36, No. 3 e15
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

µChIP—a rapid micro chromatin immunoprecipitation assay for small cell samples and biopsies

John Arne Dahl and Philippe Collas*

Institute of Basic Medical Sciences, Department of Biochemistry, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway

*To whom correspondence should be addressed. Tel: +47 22851060; Fax: +47 22851058; Email: philippe.collas{at}medisin.uio.no

Received October 19, 2007. Revised December 13, 2007. Accepted December 14, 2007.

Chromatin immunoprecipitation (ChIP) is a powerful technique for studying protein–DNA interactions. Drawbacks of current ChIP assays however are a requirement for large cell numbers, which limits applicability of ChIP to rare cell samples, and/or lengthy procedures with limited applications. There are to date no protocols for fast and parallel ChIPs of post-translationally modified histones from small cell numbers or biopsies, and importantly, no protocol allowing for investigations of transcription factor binding in small cell numbers. We report here the development of a micro (µ) ChIP assay suitable for up to nine parallel quantitative ChIPs of modified histones or RNA polymerase II from a single batch of 1000 cells. µChIP can also be downscaled to monitor the association of one protein with multiple genomic sites in as few as 100 cells. µChIP is applicable to small fresh tissue biopsies, and a cross-link-while-thawing procedure makes the assay suitable for frozen biopsies. Using µChIP, we characterize transcriptionally permissive and repressive histone H3 modifications on developmentally regulated promoters in human embryonal carcinoma cells and in osteosarcoma biopsies. µChIP creates possibilities for multiple parallel and rapid transcription factor binding and epigenetic analyses of rare cell and tissue samples.


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