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. Author manuscript; available in PMC: 2015 Jul 28.
Published in final edited form as: Dev Biol. 2014 Sep 6;395(1):38–49. doi: 10.1016/j.ydbio.2014.08.034

Fig. 3.

Fig. 3

Identification of putative Nodal enhancers in blastula and gastrula. (A) Identification of regions bound by Smad2/3 and genes associated with these regions at stage 8, 9 and 10.5. The number of genes associated with Smad2/3 bound regions is further classified into those whose expression was detected by 3SEQ. (B) Venn diagrams comparing regions bound by Smad2/3 at stages 9 and 10.5 (left) and the genes that are associated to Smad2/3 binding at stages 9 and 10.5 (right). (C) Box plot representation of transcript abundance of genes associated with a Smad2/3 bound region (blue) and those that are not associated with a Smad2/3 bound region (green) at stage 9 (293 expressed genes associated with Smad2/3 binding vs. 6555 not associated) and stage 10.5 (404 genes vs. 6645 not associated). (D) Venn diagrams demonstrating the overlap between regions bound by Smad2/3 and regions bound by both H3K4me1 and H3K27ac at stages 9 and 10.5. (E) DAVID analysis of genes associated with Smad2/3, H3K4me1 and H3K27ac bound regions (Nodal enhancers) at stage 9 (orange), stage 10.5 (dark green) and genes associated only with Smad2/3 bound regions at stage 9 (yellow) and stage 10.5 (light green).