Precise regulation of gene expression in time and space is required for development, differentiation and homeostasis in higher organisms1. Sequence elements within or near core promoter regions contribute to regulation2, but promoter-distal regulatory regions like enhancers are essential in the control of cell type specificity1. Enhancers were originally defined as remote elements that increase transcription independent of their orientation, position and distance to a promoter3. They were only recently found to initiate RNA polymerase II (RNAPII) transcription, producing so-called eRNAs4. Genomic locations of enhancers used by cells can be detected by mapping of chromatin marks and transcription factor binding sites from chromatin immunoprecipitation (ChIP) assays and DNase I hypersensitive sites (DHSs) (reviewed in ref. 1), but there has been no systematic analysis of enhancer usage in the large variety of cell types and tissues present in the human body. Using Cap Analysis of Gene Expression5 (CAGE), we show that enhancer activity can be detected through the presence of balanced bidirectional capped transcripts, enabling the identification of enhancers from small primary cell populations. Based upon the FANTOM5 CAGE expression atlas encompassing
