Attema et al., have developed a ChIP variant that overcomes the limitation of standard protocols, that require a large number of cells (~5x108). Their method, termed miniChIP, allows the analysis of histone modifications in as low as ~50,000 cells. They applied their assay to analyze the epigenetic marks at lineage- specific genes in hematopoietic stem cells (HSC) for lineage commitment:
[This method is] amenable to the numbers of HSC and progenitors that can be reasonably obtained to high purity from adult mouse bone marrow [...]. We established the method on 50,000 cells through the systematic adjustment of formaldehyde cross-linking, sonication, preclearing, salt concentration and antibody immunoprecipitation conditions. [... Besides,] when used in conjunction with [...] carrier ChIP and Q2ChIP assays, [...] epigenetic analysis should be possible on extremely rare cells (i.e., 100) contained within primary tissues. Therefore, these newly described ChIP methods will serve as invaluable tools for the epigenetic analysis of primary cells in numerous developmental systems and neoplastic cell populations, including cancer stem cells, where cell numbers are limiting.
epigenetics
