Genome-wide identification of TAL1's functional targets: Insights into its mechanisms of action in primary erythroid cells

Detection of ChIP-seq peaks in Tal1^WT/WT and Tal1^RER/RER samples. (A) Outline of the experimental strategy. (B) Venn diagram showing that the peaks identified in material isolated from Tal1^RER/RER Ter119⁻ fetal liver cells (594 peaks, in orange circle) are a subset of the peaks identified in material isolated from Tal1^WT/WT cells (2994 peaks, in blue circle). Below, the peaks are divided into three categories: “WT only” when not detected in the Tal1^RER/RER sample; “0.1–0.8” or “0.8–1.8” according to the ratio of intensity between Tal1^RER/RER and the corresponding Tal1^WT/WT peaks. (C) TAL1 ChIP-seq peaks are displayed on two genomic loci (on chromosomes 8 and 7, top track) on GBrowse. For both sets of samples (Tal1^WT/WT and Tal1^RER/RER), the sequencing reads, identified as peaks, are mapped onto the chromosome view along with their coordinates and visualized along the sequence in GBrowse. The peaks exclusively detected from the wild-type sample (Tal1^WT/WT Peaks) are labeled “WT only.” All the peaks detected from the mutant population (Tal1^RER/RER Peaks) correspond to genomic locations also identified as peaks in the wild-type population. For those peaks, the ratio of intensity between wild-type and mutant samples is shown (RER/WT ratios 0.1–0.8 or 0.8–1.8). (D) The distribution of the 594 peaks detected in the Tal1^RER/RER sample (RER/WT ratios 0.1–0.8 and 0.8–1.8) is compared with that of their corresponding peaks (i.e., detected at the same position) in the Tal1^WT/WT sample, according to their intensities. The “WT only” peaks are not shown. (E) Genomic distribution in percentages of the Tal1^WT/WT peaks with respect to gene loci. In gray, exons; position of intron 1 is shown; thin lines on either side of the locus represent upstream and downstream flanking sequences; the arrow shows position of the transcription start site (TSS). (F) Distribution in percentages of the Tal1^WT/WT peaks as a whole (All peaks) and after fractionation according to their requirement for direct DNA-binding activity (WT only, ratios 0.1–0.8 or 0.8–1.8), with respect to the three main genomic locations, as indicated on the graph.