Developmental-stage-specific enhancers of Runx1. (A) UCSC genome browser tracks showing open chromatin signal for each of the populations. Tracks from E to IAC are cumulative scATAC-Seq signals (per-base unique fragment coverage) normalized by the number of cells in that population. Tracks for FL-HSC are bulk ATAC-Seq data from Chen et al.³⁹  Experimentally validated enhancers and E-Ps from Marsman et al³⁸  are shown in magenta. Enhancers and E-P links from Chen et al³⁹  are shown in dark green. E-P links were inferred based on linear regression on paired scRNA-scATAC meta cells (supplemental Methods). Placental mammal conservation by PhastCons score is shown as a gray track. For each of the inferred enhancers, we scanned for known motifs from CIS-BP database and grouped TFs from the same family having similar motifs. Motif hits of several previously reported early hematopoietic TFs are highlighted below the track. (B) Distribution of linear regression P values for predicted Runx1 enhancers. Highly significant peaks include the validated +23 and −371 enhancers. The most significant peak is ∼3.6 kb downstream of P1. (C) Coaccessibility of Runx1 P1 promoter and its predicted linked enhancers in each cell type. P values for coaccessibility in each cell type were computed using Fisher exact test with multiple testing correction. (D) Stage-specific chromatin accessibility of Runx1 −371 enhancer and Runx1 expression levels (z-score transformed). Each point in the scatter plot represents a paired ATAC-RNA meta cell in Figure 5A, with pooled RNA expression on the y-axis and pooled enhancer accessibility on the x-axis. A 2-dimensional density plot is superimposed on the scatter plot. (E) Coexpression of transcription factors that have binding motifs at Runx1 enhancers and whose expression precedes Runx1. Correlations were computed using gene expression matrix including conflux E, pre-HE, and HE cells. TFs with Pearson correlation with Runx1 <0.05 were removed. Hierarchical clustering was performed on the correlation matrix and a strong TF coexpression module was highlighted.