Fig. 2: Identification of gradients of chromatin activity in regional cis-regulatory elements (rCREs).

a Using the Hensen’s node as a landmark, HH5 avian embryos were divided into seven sections along the AP axis and subjected to ATAC-seq and CUT&RUN for H3K27AC. b Profiles of chromatin accessibility and H3K27AC enrichment of anterior and posterior rCRES (10,913 and 12,532 peaks, respectively) along the AP axis. Lines represent the average ATAC-seq and H3K27AC signal, while ribbons represent the standard deviation. The Spearman’s correlation coefficient represents the correlation between the mean ATAC-seq and H3K27AC CUT&RUN values (solid lines). Chromatin accessibility and H3K27AC enrichment are strongly correlated along the AP axis. Correlation assessed using a Pearson Correlation test. c In silico reconstruction of OTX2 gene expression alongside ATAC-seq profiles in the OTX2 locus. Note the gradients of accessibility that are formed from the anterior to the posterior regions of the embryo. Anterior peaks within 100 kb of the OTX2 transcription start site are shown for reference. Arrows highlight regions of chromatin accessibility that are not patterned. d In silico reconstruction of WNT5A gene expression alongside ATAC-seq profiles in the WNT5A locus. Posterior peaks within 100 kb of the WNT5A transcription start site are shown for reference. Accessibility profiles display a posterior to anterior gradient. Arrows highlight elements that are not patterned or with anterior-enriched accessibility. e Quantification of rCRE accessibility and H3K27AC enrichment in eight peaks in the OTX2 locus. Peaks correspond to those shown in panel (c). f Quantification of rCRE accessibility and H3K27AC enrichment in eight peaks in the WNT5A locus. Peaks correspond to those shown in panel (d). g Heatmap displaying variable motifs enriched along the AP axis as identified via Chromvar. Source data are provided as a Source Data file. AP anteroposterior, HH Hamburger Hamilton.