Single-cell analysis of chromatin silencing programs in development and tumor progression

Single-cell analysis has become a powerful approach for the molecular characterization of complex tissues. Methods for quantifying gene expression and chromatin accessibility2 of single cells are now well-established, but analysis of chromatin regions with specific histone modifications has been technically challenging. Here, we adapt the recently published CUT&Tag method3 to scalable single-cell platforms to profile chromatin landscapes in single cells (scCUT&Tag) from complex tissues. We focus on profiling Polycomb Group (PcG) silenced regions marked by H3K27 trimethylation (H3K27me3) in single cells as an orthogonal approach to chromatin accessibility for identifying cell states. We show that scCUT&Tag profiling of H3K27me3 distinguishes cell types in human blood and allows the generation of cell-type-specific PcG landscapes from heterogeneous tissues. Furthermore, we use scCUT&Tag to profile H3K27me3 in a brain tumor patient before and after treatment, identifying cell types in the tumor microenvironment and heterogeneity in PcG activity in the primary sample and after treatment. Overall design: We used Cleavage under targets and Tagmentation (Cut-and-Tag), a chromatin profiling strategy in which antibody-targeted controlled integration of DNA sequencing adapters produce libraries in nuclei. The resulting nuclei were isolated either by a microwell approach (Takara's iCell8) or by a microfluidic approach (10x Genomic's GEM) where unique barcodes are added, followed by paired-end sequencing.