title: Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex.
abstract: Large-scale transcription start site (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 Cap Analysis of Gene Expression (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," i.e., a catalog of active promoters across the surveyed states. Analysis of the distribution of promoters revealed evidence for widespread alternative promoter usage in D. pulex, in addition to a prominent fraction of compactly-arranged promoters in divergent orientations. 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 and 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 metazoans, as well as for investigations into the circuitries that underpin meiosis and parthenogenesis.
authors: Department of Biology, Indiana University, Bloomington, Indiana 47405 School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405 rtraborn@indiana.edu.
authors: R Taylor
authors: http://orcid.org/0000-0001-6249-8033
authors: RT
authors: Raborn
authors: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors: Ken
authors: http://orcid.org/0000-0003-4289-6637
authors: K
authors: Spitze
authors: Department of Biology, Indiana University, Bloomington, Indiana 47405 School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405.
authors: Volker P
authors: http://orcid.org/0000-0002-8055-7508
authors: VP
authors: Brendel
authors: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors: Michael
authors: M
authors: Lynch
mesh_terms: D000818:Animals; D003621:Daphnia / Q000235:genetics* / Q000254:growth & development; D005260:Female; D018507:Gene Expression Regulation, Developmental; D008297:Male; D008540:Meiosis / Q000235:genetics*; D010312:Parthenogenesis / Q000235:genetics; D011401:Promoter Regions, Genetic; D012727:Sex Characteristics; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
keywords: CAGE; Daphnia; cis-regulatory regions; meiosis; parthenogenesis; promoter architecture; transcription initiation