DNA methylation disruption reshapes the hematopoietic differentiation landscape

Mutations in genes involved in DNA methylation (DNAme; e.g., TET2, DNMT3A), are frequently observed in hematological malignancies(1–3) and clonal hematopoiesis(4,5). Applying single-cell sequencing to murine hematopoietic stem and progenitor cells, we observed that these mutations disrupt hematopoietic differentiation, causing opposite shifts in the frequencies of erythroid vs. myelo-monocytic progenitors upon Tet2 or Dnmt3a loss. Notably, these shifts trace back to transcriptional priming skews in uncommitted hematopoietic stem cells (HSCs). To reconcile genome-wide DNAme changes with specific erythroid vs. myelo-monocytic skews, we provide evidence in support of differential sensitivity of transcription factors due to biases in CpG enrichment in their binding motif. Single-cell transcriptomes with targeted genotyping showed similar skews in transcriptional priming of DNMT3A-mutated human clonal hematopoiesis bone marrow progenitors. These data show that DNAme shapes the hematopoietic differentiation topography, and support a model in which genome-wide methylation changes are transduced to differentiation skews through biases in transcription factor binding-motif CpG enrichment.