A Nuclear factor I-X mediated regulatory network governs the balance of hematopoietic stem and progenitor cells during hematopoiesis

The transcription factor (TF), nuclear factor I-X (NFIX), is a positive regulator of hematopoietic stem and progenitor cell (HSPC) transplantation. Nfix-deficient HSPC exhibit a severe loss of repopulating activity, increased apoptosis and a loss of colony forming potential. However, the underlying mechanism remains elusive. Here, we performed cellular indexing of transcriptomes and epitopes by high-throughput sequencing (CITE-seq) on Nfix-deficient HSPC and observed loss of long-term hematopoietic stem cells (LT-HSC) and an accumulation of megakaryocyte and myelo-erythroid progenitors. The genome-wide binding profile of NFIX in primitive murine hematopoietic cells revealed its co-localization with other hematopoietic TFs such as PU.1. We confirmed the physical interaction between NFIX and PU.1 and unveiled that the two TFs co-occupy super-enhancers and regulate genes implicated in cellular respiration and hematopoietic differentiation. Our data support a model in which NFIX collaborates with PU.1 at super-enhancers to promote the differentiation of hematopoietic progenitors. Overall design: scRNA-seq of NFIX WT and KO bone marrow cells, NFIX,PU.1 CHIP-seq, ATAC-seq, and H3K27ac ChIP-seq in HPC5 cells.