Figure 3

Overlap among non-promoter-associated BEST predictions, DNase hypersensitive sites, and H3K27ac peaks in IMR90 cells. (a) The frequency of overlap (y-axis) is shown between BEST predictions (brown) and DHSs (x-axis; All DHS+), and DHSs that overlap H3K27ac peaks (x-axis; DHS+/H3K27ac+), relative to background expectation (black). Background regions are non-promoter-associated 2-kb windows randomly selected from the genome. P-values were calculated using the two-tailed chi-squared test; *Chi-squared test P-value < 0.00001. (b-d) Overlap between BEST predictions with LOD score > 2.5, DHSs, and H3K27ac peaks, in IMR90 cells is shown at three separate loci: (b) vacuole membrane protein 1 (VMP1) - non-promoter-associated BEST loci (black dashed boxes) are enriched for DHSs and H3K27ac, and depleted of H3K4me3; (c) primary transcript of microRNA let-7a-1 (Pri-let-7a-1) - a BEST locus (black dashed box) upstream of the promoter (green dashed box) lacks both H3K4me3 and H3K79me2 signal, indicating that it is highly unlikely to be an alternative promoter; and (d) La-related protein 1 (LARP1) - a BEST locus (black dashed box) positioned between the annotated promoter (red dashed box) and the likely active promoter (green black box) lacks both H3K4me3 and H3K79me2 peaks, indicating that it is highly unlikely to be an alternative promoter.