ATAC-sequencing analysis shows that loss of RUNX1 R233/R237 methylation changes the epigenomic signature of LT-HSCs to a poised progenitor state. (A) A volcano plot showing the difference of chromatin accessibility between Runx1^+/+ and Runx1^KTAMK/KTAMK LT-HSCs. Each dot represents one ATAC-sequencing peak. Peaks with |log₂ fold change| > 1 and false discovery rate <0.05 are shown in red (n = 2 mice; 7-8 weeks old). (B) Representative ATAC-sequencing plots showing the chromatin accessibility in control (blue) and Runx1^KTAMK/KTAMK (red) LT-HSCs. The upper plot around the Aldh1a1 gene locus shows the higher peaks in the promoter region (blue box) of control LT-HSCs. In contrast, the Rag1, Rag2 (middle), and Ccnd1 (lower) promoters (red box) have higher peaks in Runx1^KTAMK/KTAMK LT-HSCs. (C) De novo motif discovery shows that the sequence TGTGGTTT was enriched in the regions with higher chromatin accessibility in control LT-HSCs compared with Runx1^KTAMK/KTAMK LT-HSCs (upper). This sequence almost completely matches the known RUNX1 motif (lower). (D) ATAC-sequencing reads of control (blue) and Runx1^KTAMK/KTAMK (red) LT-HSCs across LT-HSC–specific (left) or MPP-specific (red) ChIP-sequencing peak regions for H3K27Ac (left) and H3K4me1 (right).