Promoter architecture and sex-specific gene expression in the microcrustacean <i>Daphnia pulex</i> revealed by large-scale profiling of 5′-mRNA ends

Abstract Large-scale TSS profiling produces a high-resolution, quantitative picture of transcription initiation and core promoter locations within a genome. However, application of TSS profiling to date has largely been restricted to a small set of prominent model systems. We sought to characterize the cis -regulatory landscape of the water flea Daphnia pulex, an emerging model arthropod that reproduces both asexually ( via parthenogenesis) and sexually ( via meiosis). We performed CAGE with RNA isolated from D. pulex within three developmental states: sexual females, asexual females, and males. Identified TSSs were utilized to generate a ‘Daphnia Promoter Atlas’-a catalog of active promoters across the surveyed states. We carried out de novo motif discovery using CAGE-defined TSSs and identified eight candidate core promoter motifs; this collection includes canonical promoter elements ( e.g . TATA, Initiator) in addition to others lacking obvious orthologs. A comparison of promoter activities found evidence for considerable state-specific differential gene expression between states. Our work represents the first global definition of transcription initiation and promoter architecture in crustaceans. The Daphnia Promoter Atlas presented here provides a valuable resource for comparative study of cis -regulatory regions in arthropods, as well as for investigations into the circuitries that underpin meiosis and parthenogenesis.