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Artificial hematopoietic stem cells (HSCs) are considered the holy grail for blood cancer therapy because many patients cannot find matched bone marrow donors. However, this potential has not been fully realized due to limited knowledge of blood development in embryos. Hemogenic endothelium (HE) in the mouse embryo is known to generate all blood lineages, including HSCs. Yet the mechanisms that guide HE to become either short-term single lineage blood progenitors or true multilineage HSCs are still not well understood. To investigate this, single-cell, full-length transcriptomic data were analysed focusing on HE from three developmental paths: erythro-myeloid–primed HE in the yolk sac (YS) plexus, lympho-myeloid–primed HE in large YS arteries, and HSC-primed HE in the AGM region.
Conclusions: Notably, AGM-derived HE showed higher expression of genes involved in chromatin remodelling and RNA splicing. It also displayed isoform expression variability, dominant isoform switching, and isoform-based gene entropy switching. Using Nanopore long-read sequencing, AGM-specific splice variants of key stemness genes—including Runx1, Mecom, and Dnmt3b—were identified. Together, these findings suggest that alternative splicing plays an important role in HSC formation and provide new insight into lineage commitment within HE.