Figure 2.
Fetal-to-adult HSC transition is associated with chromatin accessibility signatures for Mk lineage priming. (A) Cell-sorting strategy for populations subjected to scATAC-seq. Post-sort reanalysis is shown for CD41– and CD41+ABM HSCs to indicate CD41 separation. (B) Aggregate scATAC-seq tracks show chromatin accessibility at the Itga2b locus of the sorted populations. Box highlights promoter region. (C) Itga2b promoter accessibility represented as percentage of single cells with detectable ATAC-seq signal within the promoter region. (D) UMAP visualization of single FL HSC CD41– (red = 2403 HSCs), ABM CD41– (blue = 2310 HSCs), ABM CD41+ (orange = 1123 HSCs), and MkPs (green = 2986 ABM MkPs). Magnified section shows combined ABM HSC cluster. (E) Slingshot pseudotime analysis44 based on PCA trajectory of the 10 000 most variable peaks. Each cell is represented as one dot. Accessibility analysis in panels F and I was performed on aggregate scATAC-seq data for the indicated samples. (F) Top enriched transcription factor–binding motifs for differentially accessible regions between ABM CD41– HSCs and FL CD41– HSCs. (G) UMAP visualization NFE2 motif accessibility enrichment across all samples at the single-cell level. Blue to yellow hues show relative accessibility. (H) Accessibility read coverage for previously published erythroid- and Mk-specific NFE2-binding sites defined per chromatin immunoprecipitation sequencing.47 Bar plots show maximum ATAC read coverage values for the indicated samples. (I) Top enriched transcription factor–binding motifs for differentially accessible regions between ABM CD41+ HSCs and ABM CD41– HSCs. (J) UMAP visualization of GATA1 motif accessibility enrichment across all samples at the single-cell level. Blue to yellow hues show relative accessibility. (K) Relative promoter accessibility of select Mk, erythroid, and shared lineage genes represented as the fraction of single cells with detectable scATAC-seq signal relative to the value of FL CD41– HSCs. FSC-A, forward scatter area.