Proximity of induced genes to GATA1-occupied DNA segments. (A) The cumulative distribution of the distance from the TSS of each gene in a response category to the nearest GATA1-occupied DNA segment (GATA1 OS) is shown in each panel, with the y-axis showing the fraction of genes whose nearest GATA1 OS is within the designated distance. The color of each distribution line is distinctive for each response category (purple for all responsive genes, red for up-regulated, blue for down-regulated, and gray for nonresponsive genes). The distributions of distances from the GATA1 OSs to the TSS of responsive genes are shown in the bottom panel, with the gray lines for 1000 iterations of random selection of TSSs from 2616 nonresponsive genes. (B) GATA1 occupancy signals near the TSSs. The distribution of raw GATA1 ChIP-seq signals (mean number of ChIP-seq tags in 100-bp windows) is graphed as a function of distance on either side of the TSS of genes in three response categories. DNA upstream of the TSS is given a negative value for the distance from the TSS. All the genes in a designated category were first centered by the TSS and then windows were extended along each side of TSS up to 3 kb. (C) Preferred locations of GATA1-occupied segments with respect to genes. The bar graph presents the fraction of genes in each response category that has at least one GATA1 OS in the indicated subregion of a gene. These subregions are segments around the TSS (−5 kb from the TSS to the end of the first exon), the first intron, the remaining exons and introns, and 5 kb past the poly(A) addition site. (D) An example of newly discovered GATA1 OSs close to the TSS of the GATA1-incuded gene Aqp8. Tracks are as in Fig. 1B.
