High-throughput functional comparison of promoter and enhancer activities. Massively parallel reporter assay barcodes

Promoters initiate RNA synthesis, and enhancers stimulate promoter activity. Whether promoter and enhancer activities are encoded distinctly in DNA sequences is unknown. We compared the enhancer and promoter activities of 2,671 short (139 bp) genomic DNA fragments transduced into mouse neurons. We find that the same sequences typically encode both enhancer and promoter activities. However, gene promoters generate more promoter activity than distal enhancers, despite generating similar enhancer activity. Surprisingly, the greater promoter activity of gene promoters is not due to conventional core promoter elements or splicing signals. Instead, we find that particular transcription factor binding motifs are intrinsically biased toward the generation of promoter activity, while others are not. Our results suggest that specific complements of transcriptional activators endow gene promoters with stronger promoter activity than distal enhancers.