2cChIP-seq: an efficient and reliable method for epigenomic profiling of small cell numbers and single cells [single-cell 2cChIP-seq]

We developed a new technique by supplementing carrier materials of both chemically modified mimics with epigenetic marks and dUTP-containing DNA fragments during ChIP procedures (thereafter referred to as 2cChIP-seq), dramatically improving immunoprecipitation efficiency and reducing sample loss. Using this strategy, we generated high-quality epigenomic profiles of histone modifications or DNA methylation in 10–1,000 cells. Moreover, 2cChIP-seq reliably captured genomic regions with histone modification at single-cell level. Lastly, we characterized the methylome of differentiated female germline stem cells (FGSCs) with this approach. Through comparing the DNA methylation patterns of the undifferentiated and differentiated FGSCs, we observed a particular DNA methylation signature potentially involved in differentiation of mouse germline stem cells. Hence, we provided a reliable and robust epigenomic profiling approach for small cell numbers and single cells. Overall design: Based on Tn5 transposition of chromatin, 2cChIP-seq was applied to profile H3K4me3 histone modifications in single-cell E14_ESC.