Multiplexed, single-cell profiling of histone modifications with SCEPTRE v1

Genome architecture and activity are tightly regulated during an organism’s development and function. Histone modifications are thought to contribute to this regulation by acting in combination to specify the activity states of individual genes. However, most methods used to profile these modifications either require a large number of cells or only target an individual histone modification at a time. This protocol uses the method Single Cell Evaluation of Post-TRanslational Epigenetic Encoding (SCEPTRE) to quantify immunolabeled H3K4me3 and H3K27me3 histone modifications at specific non-repetitive genomic loci in single cells using Expansion Microscopy. The protocol can be adapted to target alternative histone modifications or protein assemblies in other cell lines and for other genomic regions of interest. Reference: Woodworth,M.A., Ng,K.K.H., Halpern,A.R., Pease,N.A., Nguyen,P.H.B., Kueh,H.Y. and Vaughan,J.C. (2021) Multiplexed single-cell profiling of chromatin states at genomic loci by expansion microscopy. Nucleic Acids Research, 10.1093/nar/gkab423.