Identification of accessible regions in APL cells. (A) Overview of the accessible regions at the SPI1and TAL1 genes in NB4 cells identified by NA-seq using Nlalll and Hpall. (B) Enrichment of DNaseI hotspots within the NA-seq dataset. Enrichment was computed with a lowered threshold and different distances from the middle of the regions defined by NA-seq (see supplemental Methods). The number of overlapping regions for every size window are indicated. (C-D) Enrichment plots of NA-seq regions within a window of ± 5 kb of DNaseI-defined accessible regions in NB4 cells. Inset pie charts: The percentage of NA-seq regions that overlap with the DNAseI dataset. (C) HpaII data. (D) NlaIII data. (E) Genomic distribution of the unique and DNaseI hotspots overlapping NA-seq regions. Accessible sites were examined for their presence in promoter (−500 bp up to 100 bp downstream of transcription start site), gene body (intron and exon), or intergenic (everything else) regions. Analysis was performed using “Genomatix” tool for annotation and statistics, whereby 1.8% of the human genome consists of promoters, 44% gene bodies, and 54% intergenic regions. (F) Intensity plot showing tag enrichment from 2 biologic replicates within ± 5 kb windows from the center of the NA-seq regions that do not overlap with the DNaseI hotspots (left). The same number of random regions was plotted as control (right).