Fig. 1: Runx1 resides within a topologically associating domain (TAD) in undifferentiated cells.

a Schematic of the Runx1 locus on mouse chromosome 16, with Runx1 proximal (P2) and distal (P1) promoters, exons, and adjacent gene desert labeled. Previously identified enhancers are indicated by red circles that are numbered according to the distance (in kb) from the Runx1 start codon in exon 1^{13,15,16,17,19,20,21,128,127,129}. b Schematic of seven-day differentiation protocol with cytokines and markers used for isolation of cells by FACS indicated. EHT = endothelial-to-hematopoietic transition. DNaseI-seq data in mESC was previously published⁴². c Bright-field images of different stages of in vitro differentiation. Colonies of hemogenic endothelial (HE) cells are outlined with dashed yellow lines and clusters of emerging hematopoietic progenitors are indicated by hollow white arrowheads. Scale bars = 200 µm. Representative images are shown. Experiments were performed more than ten times with similar results. d Principal component analysis (PCA) of individual poly(A) minus RNA-seq replicates colored by cell type. e Plot of normalized counts of lineage marker gene expression across differentiation. Undifferentiated n = 2, mesoderm n = 3, hematopoietic n = 4. f PCA of individual Tiled-C replicates colored by cell type. g Tiled-C matrix at 2 kb resolution for undifferentiated mESCs. Matrix is a merge of three independent replicates (n = 3). Interactions are visualized with a threshold at the 94th percentile. Runx1 promoters (P1 and P2), neighboring genes, the adjacent gene desert, and approximate location of the 1.1 Mb Runx1 TAD are labeled. Publicly available CTCF ChIP-seq in E14 mESCs⁴⁰ was reanalyzed and the orientation of CTCF motifs identified de novo under CTCF peaks is indicated. Previously published enhancer regions are indicated and numbered according to their distance from the Runx1 start codon in exon 1. Enhancer regions that are accessible in undifferentiated cells are shown as red bars and enhancers that did not overlap DNaseI-seq⁴² peaks are identified by gray bars.