scChIX-seq infers dynamic relationships between histone modifications in single cells

Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing), to map multiple histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations: two repressive marks, two active marks, and an active plus a repressive mark. In mouse gastrulation, we find that cell type-specific regulation in active chromatin can be accompanied by stable heterochromatin landscapes that are shared across cell types. Applying scChIX-seq to two active marks during macrophage differentiation, we find H3K4me1 dynamics preceding H3K36me3. Modeling these dynamics enables integrated analysis of chromatin velocity during differentiation. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells. single-cell ChIC-seq data on bone marrow, mouse gastrulation, and macrophage in vitro differentiation