Chromatin openness at enhancer and promoter sites in RXRα;RXRβ-deficient LT-HSCs. (A) Heat map of assay for transposase-accessible chromatin with sequencing (ATAC-seq) signals located in transcription start site (TSS) flanking regions (±1 kb) in 5-month-old Vav^Cre+Rxrab^fl/fl and WT LT-HSCs and MPPs. (B) HOMER known motif analysis of ATAC-seq peaks. The top panels shows transcription factor motifs enriched in WT LT-HSCs relative to the background of Vav^Cre+Rxrab^fl/fl LT-HSC peaks. The bottom panel shows transcription factor motifs enriched in Vav^Cre+Rxrab^fl/fl LT-HSCs relative to the background of WT LT-HSC peaks. (C) Peak annotations identified in an overlap analysis between the open promoter and enhancer regions in LT-HSCs identified in the ATAC-seq experiment (defined by genomic distribution; see also supplemental Figure 8A), and regions marked by high H3K4me3 and H3K27Ac, and ±1 kb from TSS (putative promoters), high H3K4me1 and H3K27Ac, and >1 kb and <−1 kb from the TSS (putative active enhancers), and high H3K4me1 but no H3K27Ac, and >1 kb and <−1 kb from the TSS (putative poised enhancers). (D) University of California, Santa Cruz (UCSC) genome browser track examples of active enhancers (vertical gray highlights) and promoters (vertical blue highlights) within loci that overlap RXRα CUT&RUNseq and ATAC-seq peaks.