Chromatin accessibility profiles of Smc3 haploinsufficiency. (A) Global chromatin accessibility assessed by ATAC-seq (top row). Overall THS density was analyzed genome wide and found in promoter regions (±1 kb of annotated RefSeq TSS) and enhancer sites (>1 kb from annotated TSS). All plots were generated using a LOESS curve through the mean of duplicate ATAC-seq measurements. Analysis was also performed on THSs of unchanged and down-regulated genes (middle and bottom rows). THSs included in analysis were within 30 kb of annotated TSSs of either unchanged or down-regulated genes. (B) ATAC-seq peak density was quantified within a 200-bp window of gene TSSs in 1-kb bins (top left). A highlighted 60-kb region immediately surrounding the TSSs is shown in the bottom left panel (* represents individual bins with P < 0.005, Student’s t test). The value for each bin is the mean of replicate samples with a fitted LOESS curve. Enhancer-only THS density is shown in the top right panel, whereas promoter-only peaks are shown in the bottom right panel. (C) Cumulative THS enhancer and promoter peaks counting outwards from TSSs. (D) Chromatin accessibility of the unchanged gene locus Galc and the down-regulated gene locus Atp1b2. (E) Genome-wide chromatin accessibility at THSs as measured by ATAC-seq in each genotype. Plotted is the mean ATAC-seq signal at all THSs genome wide. (F) Transcription factor motif site enrichment in ATAC-seq peaks gained and lost in Smc3Δ/+ Flt3-ITD cells compared with Smc3fl/+. (G) GSEA using RNA-seq data from each genotype compared with Smc3fl/+ controls and a human HSC STAT5 target gene set. (H) Chromatin accessibility of the Stat5 target gene Socs2 showing potentiation of Stat5 signaling at specific regulatory elements. Shown are ATAC-seq profiles of the entire locus for each genotype. Stat5 motifs are found within each labeled regulatory element (sequence highlighted in red).
