Transcriptional plasticity, priming and commitment in hematopoietic lineages [CRISP-seq]

Differentiation of adult hematopoietic stem cells (HSC) constantly produces the cell types of the blood and immune system. The dynamics of this process and the hierarchy of downstream oligopotent stem cell differentiation remain controversial. Here we dissect hematopoietic progenitor populations in a minimally biased fashion using extensive single cell sampling from murine bone marrow. We characterize the HSC population, define its quiescent transcriptional program and validate it with label retaining assays and cytokine mediated stimulations. Analysis of initial HSC commitment defines marked bifurcation of erythroid/megakaryocytic cells from myeloid/lymphoid lineages. Unexpectedly, we find states that mix transcription of pre-myeloid and pre-lymphoid genes. This suggests a model in which more than one differentiation trajectory can link HSC to several cell types. Dendritic cells are thus linked with both monocyte and lymphocyte precursors. Our data support a model of hematopoiesis balancing relaxation of an HSC quiescent state, gradual bifurcations and trans-differentiation. Cas9-GFP LSK cells were infected with BFP+ lentiviral guide RNAs and transplanted into irradiated mice. Both mRNA content and matched lentiviral transcribed barcodes were extracted and sequenced in different batches on an Illumina NextSeq