Fig. 2: Mapping and characterizing chondrogenic enhancers in limbs and trunk.

A Distribution of ATAC-seq and H3K27ac ChIP-seq signal over all accessible regions in EGFP+ and EGFP- cells from limbs and trunks. Two categories of regions are defined: accessible regions without H3K27ac enrichment (“inactive”) and accessible regions with H3K27ac enrichment in one of the studied conditions (“active”). B Distribution of ATAC-seq and H3K27ac ChIP-seq signal over the 2'704 chondrogenic enhancers identified in this work: accessible regions with differential H3K27ac coverage between EGFP+ and EGFP- cells ( ≥ 4-fold change coverage). C Tissue specificity of the 2'704 chondrogenic enhancers according to limb- and trunk-enrichment. Enrichment in limb or trunk is defined by difference in H3K27ac coverage ≥2-fold change in comparison to the counter-part tissue. D Boxplots showing the distribution of number of chondrogenic enhancers per TAD, split by two different TAD categories: TAD with chondrogenic enhancers and at least one protein-coding chondrogenic gene (chondroTADs n = 357, chondrogenic enhancers n = 1'363 (median=3) and chondrogenic genes n = 478) and TAD with chondrogenic enhancers but without any chondrogenic-specific gene (chondroEnhTADs n = 661, chondrogenic enhancers n = 1'315 (median=1)). Dots represent the number of chondrogenic enhancers contained in each TAD and some relevant examples are named based on the genes they encompass. Total number of TAD is 3'109, extracted from E14.5 mouse forelimb cartilage Hi-C²⁹. Boxes indicate the first and third quartiles, the whiskers indicate ±1.5 × interquartile range and the horizontal line within the boxes indicates the median. Statistical test used in D: Two-tailed Wilcoxon rank sum test, with a p-value of 4.68e⁻²³. ATAC-seq and H3K27ac coverages over 3 kb are centered at the corresponding merged ATAC-seq peaks located within a 75 bp window.