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. 2018 Jun 18;7:e36144. doi: 10.7554/eLife.36144

Figure 2. Genomic TALE occupancy is continuously and dynamically associated with the TALE GRN during embryogenesis.

See also Figure 2—figure supplement 1. (A) Representative UCSC browser tracks illustrating Prep binding at the hoxb1a and mafba loci in 3.5 and 12hpf embryos. (B) Graph showing the distribution of Prep3.5hpf and Prep12hpf binding sites relative to TSSs. (C) Venn diagram illustrating co-localization of Prep peaks in 3.5hpf and 12hpf embryos. Two peaks are considered to co-localize if their summits are within 50 bp. (D) Chart illustrating percent of Prep12hpf-only peaks found at various distances from Prep3.5hpf peaks. (E) GO term enrichment for Prep3.5hpf and Prep12hpf-only peaks identified by GREAT using the nearest gene within 5 or 30 kb association rule. In the case of GO terms associated with genes within 30 kb, only select categories are presented, a full list of GO terms is available in Supplementary file 3. FDR = Binomial False Discovery Rate. (F) Graph showing percent of TALE GRN genes (p-adj ≤0.01, fold-change ≥1.5) associated (≤5 or 30 kb) with Prep3.5hpf and Prep12hpf-only peaks. p-values for enrichment above a random set of genes were calculated using the Pearson correlation test.

Figure 2.

Figure 2—figure supplement 1. Analysis of TALE binding in zebrafish embryos.

Figure 2—figure supplement 1.

(A) Expression levels of maternal and paternal prep1 and pbx2 transcripts during early zebrafish embryogenesis (from [Harvey et al., 2013]). Until 3.5hpf, transcripts from the paternal allele (which requires zygotic activation) are not detected, demonstrating that only maternal prep and pbx transcripts are present prior to this time point. (B) RT-PCR analysis on 0–1.25hpf, 3.5hpf and 9hpf zebrafish embryos demonstrating that prep1.1, prep1.2, pbx2 and pbx4 transcripts are maternally deposited. (C) Density plot illustrating the distance between each Prep12hpf-only peak and its nearest Prep3.5hpf peak. Peaks located >100 kb from a Prep3.5hpf peak are not shown (of 16,500 Prep12hpf-only peaks, 2,138 [13%] are located at >100 kb). p=1.85 E-11 (Chi-square comparison to shuffled peaks).