PT - JOURNAL ARTICLE AU - Michael P. Meers AU - Karen Adelman AU - Robert J. Duronio AU - Brian D. Strahl AU - Daniel J. McKay AU - A. Gregory Matera TI - Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in <em>Drosophila melanogaster</em> AID - 10.1101/165639 DP - 2017 Jan 01 TA - bioRxiv PG - 165639 4099 - http://biorxiv.org/content/early/2017/07/19/165639.short 4100 - http://biorxiv.org/content/early/2017/07/19/165639.full AB - High-resolution transcription start site (TSS) mapping in D. melanogaster embryos and cell lines has revealed a rich and detailed landscape of both cis-and trans-regulatory elements and factors. However, TSS profiling has not been investigated in an orthogonal in vivo setting. Here, we present a comprehensive dataset that links TSS dynamics with nucleosome occupancy and gene expression at unprecedented sequencing depth in the wandering third instar larva, a developmental stage characterized by large-scale shifts in transcriptional programs in preparation for metamorphosis. The data recapitulate major regulatory classes of TSSs, based on peak width, promoter-proximal polymerase pausing, and cis-regulatory element density. We confirm the paucity of divergent transcription units in D. melanogaster, but also identify notable exceptions. Furthermore, we identify thousands of novel initiation events occurring at unannotated TSSs that can be classified into functional categories by their local density of histone modifications. Interestingly, a sub-class of these unannotated TSSs overlaps with functionally validated enhancer elements, consistent with a regulatory role for “enhancer RNAs” in defining transcriptional programs important for animal development. We conclude that high-depth TSS mapping is a powerful strategy for identifying and characterizing low-abundance and/or low stability RNAs.