Chromatin immunoprecipitation (ChIP) arguably represents the most powerful application of antibody technology to epigenetic research. It allows analysis of patterns of histone modification and non-histone protein distribution across genomic regions and underpins large scale epigenetic mapping projects. However, conventional ChIP generally requires at least 107 cells, which limits its applicability. To address this, we have developed a new protocol, CChIP, based on the use of carrier chromatin, that allows detailed and reproducible epigenetic analysis of as few as 100 cells. The procedure has been validated with primary mouse embryo material, but should be applicable to cells from various sources, including tissue biopsies and FACS-sorted cell populations. The protocol given here is for analysis of histone modifications in native, unfixed chromatin prepared by micrococcal nuclease digestion. CChIP will undoubtedly be applied to formaldehyde cross-linked chromatin, and thereby used to locate non-histone chromatin proteins, but the generally lower efficiency of precipitation with cross-linked chromatin is likely to increase the numbers of cell required.
University of Birmingham - Institute of Biomedical Research - The Medical School - Birmingham - B15 2TT, UK