Tracking chromatin structure changes by single-cell multi-epigenomics with RNA polymerase II binding profiles

Transcription factor-bound chromatin structures regulate cell lineages in multicellular organisms. Single-cell epigenomics has the potential to reveal lineage determination on chromatin structure, but the methodology is still in development. Here, we develop single-cell combinatorial-indexing multi-target Chromatin Integration Labeling followed by sequencing (sci-mtChIL-seq) as a single-cell multi-epigenomics approach, which enables simultaneous single-cell analysis of both RNA polymerase II binding to chromatin and epigenomic factors such as transcription factors/histones. We apply sci-mtChIL-seq to analyze the binding dynamics of skeletal-muscle-specific transcription factor MyoD during mouse embryonic myogenesis. Based on RNA polymerase II-bound gene profiles, single-cells are efficiently classified into myogenic-clusters and ordered pseudotemporally. MyoD exhibits genome-wide binding in the muscle-progenitor-cell population, but in myocytes, this transitions toward enrichment in muscle-specific genes on active chromatin. Thus, sci-mtChIL-seq can be a powerful tool to analyze epigenomic dynamics in cell fate determination.