A quick and quantitative chromatin immunoprecipitation assay for small cell samples

Chromatin immunoprecipitation (ChIP) is to date a technique of choice for studying protein-DNA interactions. ChIP has been used for mapping the location of modified histones on DNA, often in relation to transcription or differentiation. A drawback of current ChIP protocols, however, is the requirement for large cell numbers, which limits the applicability of ChIP to rare cell samples. The procedure is also tedious and time consuming. We systematically evaluated and modified critical steps in the ChIP procedure to develop a quick and quantitative ChIP assay, referred to as Q(2)ChIP, suitable for up to 1,000 histone immunoprecipitations or 100 transcription factor immunoprecipitations from as few as 100,000 cells under cross-linking conditions. Analysis of the precipitated DNA by real time PCR enables quantification of the relative amount of a specific histone modification or transcription factor associated with a specific locus. This communication describes all steps of the Q(2)ChIP procedure as it is carried out in our laboratory.