Fig. 2. HMGN1 promotes chromatin accessibility and confers stem cell and leukemia-associated transcriptional and chromatin phenotypes.

a Schematic of the experimental approach for ATAC-seq, RNA-seq, Mint-ChIP chromatin profiling, and TMT proteomics during myeloid differentiation. b Gene set enrichment analysis (GSEA) of RNA-seq in undifferentiated wild-type and HMGN1-OE progenitors showing enrichment of the Brown_myeloid_cell_development_up gene set in wild-type cells. Heatmap shows mean expression of the leading edge genes from the gene set in GSEA in biological duplicates of wild-type and HMGN1-OE cells at the indicated time points, expressed as log2 fold change (FC) relative to WT_0h. c GSEA of wild-type and HMGN1-OE progenitors showing enrichment of genes in the Eppert_LSC_signature gene set in HMGN1-OE cells. Heatmap of leading edge genes as in panel b. d Heatmap of expression of Hox cluster genes in wild-type and HMGN1-OE cells during differentiation, expressed as in panel b. e Chromatin accessibility tracks representing distance from nearest peak center of all differential peaks in ATAC-seq (left), and metagene plots of ATAC-seq differential peaks and all shared peaks in wild-type and HMGN1-OE cells (right, n = 3 biologically independent replicates). f Gene tracks showing ATAC-seq reads at the HoxA7 and HoxA9 loci at baseline and 96 h in wild-type and HMGN1-OE progenitors (top). Heatmap of ATAC-seq signals at HoxA and HoxB genes in wild-type and HMGN1-OE progenitors, expressed as log2 FC relative to the mean WT_0h value (bottom). g Metagene profiles of H3K27 acetylation surrounding promoters in wild-type and HMGN1-OE cells at 0 and 96 h of differentiation (left). H3K27ac levels were also measured by western blotting (middle) and by intracellular flow cytometry (right, normalized to WT 0 h, n = 3 biological replicates, genotypes compared by two-sided t test). Data are presented as mean values ± SD. Source data are provided as a Source Data file.