PT - JOURNAL ARTICLE AU - Sarah Rennie AU - Maria Dalby AU - Marta Lloret-Llinares AU - Stylianos Bakoulis AU - Christian Dalager Vaagensø AU - Torben Heick Jensen AU - Robin Andersson TI - Transcription start site analysis reveals widespread divergent transcription in <em>D. melanogaster</em> and core promoter-encoded enhancer activities AID - 10.1101/221952 DP - 2017 Jan 01 TA - bioRxiv PG - 221952 4099 - http://biorxiv.org/content/early/2017/11/18/221952.short 4100 - http://biorxiv.org/content/early/2017/11/18/221952.full AB - Mammalian gene promoters and enhancers share many properties. They are composed of a unified promoter architecture of divergent transcripton initiation and gene promoters may exhibit enhancer function. However, it is currently unclear how expression strength of a regulatory element relates to its enhancer strength and if the unifying architecture is conserved across Metazoa. Here we investigate the transcription initiation landscape and its associated RNA decay in D. melanogaster. Surprisingly, we find that the vast majority of active gene-distal enhancers and a large fraction of gene promoters are divergently transcribed from two divergent core promoters. Moreover, we observe quantitative relationships between enhancer potential, expression level and core promoter strength, providing an explanation for indirectly related histone modifications that are reflecting expression levels. Lowly abundant unstable RNAs initiated from weak core promoters are key characteristics of gene-distal developmental enhancers, while the housekeeping enhancer strengths of gene promoters are directly echoing their expression strengths. The different layers of regulation mediated by gene-distal enhancers and gene promoters are also reflected in chromatin interaction data. Our results establish a unified promoter architecture of D. melanogaster regulatory elements that is universal across Metazoa, whose regulatory functions are related to their core promoter elements.