Fig. 4

Peaks shared between HSCs and unipotent cell types are primarily non-promoter and are enriched for known cell type-specific transcription factors. a Schematic for how the unipotent lineage peaks exclusively intersected with HSC peaks were generated. Peaks were compared using HOMER mergePeaks.pl tool using peak-lists from the 6 cell types assayed. The resulting 5 overlapping peak-lists contained shared peaks between HSCs and only the unipotent cell type of interest (but not present in any of the other four lineages). The five exclusive pairwise comparisons (e.g., HSC/MkP only, HSC/EP, etc.) were used for panels b–h. b MkPs have the highest peak overlap with HSCs. The number of unipotent lineage peaks that were uniquely intersected with HSCs was divided by the total number of peaks for each mature cell type. MkPs had the highest percentage of HSC overlap (12.2%), followed by B cells (9.2%), GMs (3.4%), T cells (2.4%), then EPs (2.2%). c Peaks exclusively shared between each unipotent cell type and HSCs were significantly enriched in the non-promoter regions of the genome. The shared peak-lists described in a were annotated using HOMER annotatePeaks.pl function and filtered as promoter (± 500 bp from TSS), and non-promoter (< -500 bp and >  + 500 bp from TSS). The number of promoter and non-promoter peaks was divided by the total number of peaks for each cell type. For all cell types, less than 20% of peaks were promoter peaks, with MkPs with the highest (16.4%) and GMs with the lowest (5.3%) percentage. This is a significant (< 0.001) difference compared to the normal distribution of promoter peaks (35–61%) for each cell type assayed. ***p-value of < .001. d–h Unipotent lineage peaks exclusively intersected with HSC peaks displayed enrichment of motifs for transcription factors with known roles in lineage differentiation. Motifs were found using HOMER findMotifsGenome.pl function, with a background file containing the combined peak-lists of the other 4 cell types. The top 10 results, as ranked by p-value from the known_motifs.html output, are shown. d In MkP/HSC peaks, Gata family peaks made up 5 of the top 10 hits, followed by ERG, Runx1, and fusions EWS:FL1 and EWS:ERG. e EP/HSC-enriched motifs also contained Gata factors, as well as the combination Gata:SCL motif and the known beta-globin locus control binder NFE2 and its paralog NFE2L2. f GM/HSCs had CEBPa and PU.1 motifs as top hits, along with ETS transcription factor binding sites. g B cell/HSC-enriched motifs had CTCF with CTCFL (BORIS) as the top two hits. B cells/HSC peaks also had E2A motifs enriched, as well as Ascl2, Slug, and ZEB1/2. h Tcf7 motif was the top hit for T cell/HSC-shared peaks, along with CTCF and Tbx5/6. Similar to the B-cell/HSC list, the T-cell/HSC list was also enriched for E2A motifs