Extended Data Figure 7: Hierarchical clustering of 4C interactions.
From: Enhancer loops appear stable during development and are associated with paused polymerase
a, b, Based on the 92 viewpoints used for 4C in all three conditions (whole embryo 3–4 h, whole embryo 6–8 h and mesoderm 6–8 h). Hierarchical clustering of the quantitative 4C signal of all interactions (n = 1,389) (a) and the subset of interactions with promoters (n = 396) (b), across 3 conditions (whole embryo 3–4 h, whole embryo 6–8 h and mesoderm 6–8 h). The expression level of the corresponding gene is shown on the right hand side in b, using RNA-seq data from Graveley et al.9. Clustering was performed by Euclidean distance and Ward agglomeration method on the significant interaction regions defined at whole embryo 6–8 h using DESeq2 fit reference-normalized read counts. If the interacting region was associated with more than one promoter, expression for only one transcript is shown. Red horizontal bars indicate differential interactions. c, d, Hierarchical clustering of the quantitative 4C signal for all 140 differential interactions (c) and the subset of differential interactions at promoters (n = 39) with the expression level of the corresponding gene (d) across 3 conditions (whole embryo 3–4 h, whole embryo 6–8 h and mesoderm 6–8 h). Clustering was performed using Euclidean distance and Ward agglomeration method on the significant interaction regions defined at whole embryo 6–8 h. WE, whole embryo; MESO, mesoderm.
