Fig. 4.

Putative Nodal enhancers correspond to known functional enhancers in X. laevis and in mouse. (A) Genome browser shot of the gsc locus and its regulatory regions on xentro2 scaffold 185. Scale is shown at top. The gsc gene model is shown in purple. The ChIP-Seq read pile-up of Smad2/3 is shown in light green, with Nodal enhancer regions shown as black bars. ChIP-Seq read pileups are shown in orange for the putative enhancer histone marks H3K27ac (orange) and H3K4me1 (green), and the entire putative enhancer regions of H3K4me1/H3K27ac overlap for stage 10.5, stage 9, and SB431542-treated are shown as black lines. Note that the putative enhancer (H3K4me1/H3K27ac marked) regions are quite broad, while the region of Smad2/3 binding is narrow. The region corresponding to the published activin responsive element (ARE) for gsc in Xenopus laevis is shown in red, and the percent identity is indicated for the alignment of the X. laevis enhancer and orthologous X. tropicalis genomic coordinates. (B) Genome browser shot, putative enhancer regions, and known X. laevis enhancer position for eomesodermin on scaffold 26. ChIP-Seq data and X. laevis enhancer positions are marked as above. (C) Genome browser shot, putative enhancer regions, and known mouse enhancer position for pitx2 on scaffold 89. ChIP-Seq data and mouse enhancer positions are marked as above. (D) Genome browser shot, putative enhancer regions, and known mouse enhancer position for lefty on scaffold 719. (E) Genome browser shot, putative enhancer regions, and known mouse enhancer position for otx2 on scaffold 68.