Method for accurate epigenome profiling using a few hundred cells and its applications

Difficulties to accurately map epigenomes in a few cells sorted or dissected from tissues have hampered our understanding of how chromatin modification regulates development and diseases. Despite recent progress, all reported chromatin-immunoprecipitation-based deep sequencing (ChIP-seq) methods have not achieved high quality mapping of rare cell populations. We report Recovery via Protection (RP)-ChIP-seq and favored amplification RP-ChIP-seq (FARP-ChIP-seq) for as few as 500 cells with superior quality compared to all reported techniques to date. FARP-ChIP-seq accurately mapped histone H3 lysine 4 trimethylation (H3K4me3) and H3K27me3 in long-term hematopoietic stem cells (LT-HSCs), short-term HSCs (ST-HSCs), and multi-potent progenitors (MPPs) sorted from one mouse. These high quality datasets not only implicate genes involved in HSC differentiation but also demonstrate a general lack of H3K4me3/H3K27me3 bivalency on hematopoietic genes in HSCs. Thus the method offers accurate mapping for fewest cells. two H3K4me3 replications for mESC, two to three replications of H3K4me3 and H3K27me3 for LT-HSC, ST-HSC and MPP, 2 replicates of H3K4me3 for young and old lens