DNMT3A regulates megakaryocyte-biased hematopoietic stem cell fate decisions [EM-Seq]

Hematopoietic stem cells (HSCs) are defined by their capacity to regenerate all main components of the peripheral blood, but individual HSCs exhibit a range of preferences for generating downstream cell types. Their propensities are thought to be epigenetically encoded, but no differential regulatory mechanisms have been identified. Here, we considered whether DNA methyltransferase 3A (DNMT3A) has a role in determining the differentiation choice of HSCs. We find that the most primitive megakaryocyte-biased HSCs depend most on DNMT3A for efficient hematopoietic regeneration, particularly of the lymphoid lineages. Reduced DNMT3A amplifies the biased HSC behavior. DNMT3A also regulates megakaryocyte and platelet output in part through DNA methylation at key megakaryocyte lineage loci. Together, our findings establish the role of epigenetic regulation in the fate of megakaryocyte-biased HSCs and their downstream progeny and suggest that the outcomes of DNMT3A-mutant clonal hematopoiesis and malignancies might vary depending on the identity of the HSC that acquires the mutation. To compare the genome-wide methylation patterns in WT and Dnmt3a+/– megakaryocyte-biased (Vwf+) and non-megakaryocyte-biased (Vwf-) HSCs: HSCs were sorted by FACS from mouse bone marrow using the markers Lineage–CD117+Sca1+CD150hiCD48lo and either Vwf-GFP+ or Vwf-GFP–. To obtain enough material, 3-4 mice were pooled per replicate.