Figure 3.

Predicted ncHAR enhancers and their tissues of activity. (a) We applied the EnhancerFinder enhancer prediction pipeline to the 2649 ncHARs; 773 were predicted to be developmental enhancers. Among this set, EnhancerFinder predicted 251 brain enhancers, 194 limb enhancers and 39 heart enhancers. (b) We compared the predicted fraction of enhancers and tissue-specific enhancers between the ncHARs, the genome-wide non-coding background, and a filtered set of non-coding conserved regions (mammalian phastCons elements). The ncHARs are dramatically enriched for predicted enhancer, brain enhancer, and limb enhancer activity compared with the genomic background; however, they are not significantly different from the non-coding conserved regions. Supporting these predictions, validated ncHAR developmental enhancers (table 2 and electronic supplementary material, table S4) show a strong enrichment for brain activity, though this may reflect biases in how they were selected for experimental analysis. The relative lack of heart enhancers may reflect the fact that this tissue follows an earlier developmental trajectory than brain and limb. (Online version in colour.)