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Figure 4. Eomes, VegT, and Xbra Occupy the Same Genomic Recognition Sites and TGF-β Responsive Regulatory Elements(A) Developmental series of WMISHs for Eomes, VegT, and Xbra. cnh, chordoneural hinge; hm, head (prechordal) mesoderm; no, notochord; pnc, posterior wall of neurenteric canal; RB: Rohon-Beard cells; te, telencephalon. The scale bar represents 0.5 mm.(B) Gastrula-staged snapshot of Eomes, VegT, Xbra, and Smad2/Smad3 (Yoon et al., 2011) binding near Xbra and Xbra3.(C) Heat maps represent DNA occupancies of Smad2/Smad3, Eomes, VegT, and Xbra relative to all VegT-bound regions during gastrulation.(D) Histograms based on pairwise calculations of shortest distances between T-box TF and Smad2/Smad3 binding positions (FDR ≤ 1%) during gastrulation.(E) Metagene model shows DNA occupancy level of Eomes, VegT, Xbra, and Smad2/Smad3 relative to the start and end of nearest target genes.(F) Venn diagrams for Smad2/Smad3 binding positions overlapping (distance ≤ 100 bp) with the binding position of Eomes, VegT, and/or Xbra (FDR ≤ 1%).(G) Venn diagrams for Eomes, VegT, and Xbra target genes. The stringency was relaxed up to p ≤ 0.1 unless DNA occupancy was found equivalent to p ≤ 10−25 when comparing binding between two T-box TFs. DNA occupancies (p ≤ 10−25 + 10−25 < p ≤ 0.1 = total) detected as follows: Eomes (2407 + 1145 = 3552); VegT (3628 + 268 = 3896); Xbra (1379 + 1173 = 2552). The extent of overlap between genes targeted by different T-box TFs might be greater than indicated in brackets, because peaks (p ≤ 0.1) sometimes failed to be detected.See also Figure S5 and Table S1.

Image published in: Gentsch GE et al. (2013)

Image downloaded from an Open Access article in PubMed Central. © 2013 The Authors

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