Fig. 1: Sequential activation of the HoxD gene cluster upon Wnt signaling.
From: Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos
a, Various stembryonic stages were used for the timecourse with the pulse of Wnt agonist in red. b, Timecourse of H3K27ac ChIP–seq over the entire HoxD locus. Genomic coordinates are on top, and the positions of C-DOM and T-DOM are shown in red and green, respectively, at the bottom. The quantification of the H3K27ac signals within the colored vertical columns is in Extended Data Fig. 1. Acetylation peaks at the Mtx and Lnp promoters are indicated. I and II point to the acetylation peaks used in Extended Data Fig. 1. c, Magnification of the HoxD cluster showing the progressive anterior to posterior spreading of H3K27ac. The start of robust coverage in the anterior part is counterbalanced by a decrease in the weaker acetylation initially detected in posterior regions (black arrows in b and c). d, Heatmap of H3K27ac ChIP–seq coverage over the HoxD cluster at various timepoints. Squares represent 10-kb DNA segments. e, Heatmap of FPKM values of Hoxd genes transcripts over time (average of two replicates). The dashed region around Hoxd9 at 96 h in c–e highlights the increased activation in all subsequent stages when compared to Hoxd4. Genomic coordinates for c and d—chr2:74667374–74767842.
