The FANTOM5 CAGE library collection6 enables the dissection of enhancer usage across cell types and tissues comprehensively sampled across the human body. Clustering based upon enhancer expression clearly grouped functionally-related samples together (Fig. 3c, and Supplementary Figs 18 and 19). While fetal and adult tissue often grouped together, two large fetal-specific clusters were identified: one brain-specific (pink) and one with diverse tissues (green). The fetal-brain cluster is associated with enhancers that are located close to known neural developmental genes, including NEUROG2, SCRT2, POU3F2 and MEF2C (Supplementary Fig. 18b), for which gene expression patterns correlate with enhancer RNA abundance across libraries, suggesting regulatory interaction (see below). The results corroborate the functional relevance of these enhancers for tissue-specific gene expression and suggest that they are an important part of the regulatory programs of cellular differentiation and organogenesis.
