Transcription factor TCF1 is indispensable for the epigenetic priming of EILPs toward distinct cell fates

Differentiation of Innate lymphoid cells (ILCs) from hematopoietic stem cells needs go through several progenitor stages defined by various cell surface markers. The progenitor populations at specific developmental stages may have multiple lineage potentials. However, it is not clear whether the multipotency of the progenitors are induced in situ by differentiation signals or are already predefined by epigenetic states. Here we report the profiling of genome-wide nucleosome position and chromatin accessibility simultaneously in ILC progenitors EILPs and ILCPs by single-cell MNase-Seq. We find that EILPs contain distinct sub-populations epigenetically primed toward either myeloid or ILC lineages, while ILCPs contain cells mainly primed for the ILC lineage at epigenetic level. We further demonstrate that the transcription factor TCF1 is indispensable for the epigenetic priming of lineage-defining sites (LDSs) for both myeloid lineages and ILC lineages at the EILP stage, and deletion of TCF1 results in the epigenetic priming that favors the myeloid lineages. Our results suggest that the multipotency of progenitor cells is defined by the existence of heterogeneous population of cells epigenetically primed for distinct downstream lineages, which are regulated by key transcription factors. We performed scMNase-seq for wild-type EILPs, ILCPs, and Tcf7-deficient EILPs to profile nucleosome positions and chromatin accessibility in single cells for each cell type. We performed DNase-seq and ChIC-seq of H3K4me3, H3K27ac, and H3K27me3 for ALPs, EILPs, ILCPs and Tcf7-deficient EILPs to profile chromatin accessibility and histone modifications in bulk cells for each cell condition. We performed ChIC-seq of TCF1 for EILPs and ILCPs to profile TCF1 binding in bulk cells for each cell type.