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 CAGEdefined 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 statespecific 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.

Thermal tolerance in the keystone species Daphnia magna—a candidate gene and an outlier analysis approach

“…AnxB11 is involved in lipid transport, whereas DamVTG1 encodes the egg yolk precursor protein vitellogenin, which has been shown to be upregulated in asexual females of Daphnia pulex as compared to sexual, resting‐egg bearing females (Raborn et al . ). The downregulation of vitellogenin documented in this study might thus be indicative of a switch from asexual to sexual reproduction and in the induction of dormant eggs under heat stress.…”

A comprehensive epigenomic analysis of phenotypically distinguishable, genetically identical female and male Daphnia pulex

“…Previous studies have investigated differences in the expression levels of genes between female and male Daphnia (in D. pulex, D. magna and D. galeata) [1,[24][25][26]. Our study differs from previous published work as in addition to investigate differences in expression at the gene level, we also investigated changes in expression at the transcriptome level identifying variation in alternative splicing and usage of alternative start and stop sites.…”

“…The genetically identical male and female Daphnia have a variety of morphological and behavioural differences, including lipid metabolism, mortality, and body size [17][18][19][20][21][22][23]. Previous studies have investigated gene expression differences between female and male Daphnia in several species [1,[24][25][26]. Despite differences in analysis techniques and quality of reference genomes these studies have identified substantial overlap in genes with sex-biased expression [26].…”

YeasTSS: An Integrative Web Database of Yeast Transcription Start Sites

“…For examples, they can be used for precisely determining 5’ boundary and the 5’untranslated region (5’UTR) of protein-coding genes, improving genome annotation, inference the locations of core promoters, identification of novel genes, core promoter elements, and other motifs associated with transcription (2). In addition, because most genes have multiple core promoters that have distinct activities in response to environmental cues or in different types of cells (2–5), quantitative TSS maps obtained from various growth conditions in a species are important for studying regulated control of transcription initiation and inferring gene regulatory network.…”

“…The high-resolution quantitative TSS maps in many organisms significantly improve our understanding of the complex and highly dynamic nature of transcription initiation landscape in eukaryotes (2–5). These studies revealed that most eukaryotic genes contain multiple core promoters which are differentially used among different tissues or developmental stages or in response to environmental cues (2,3,5,17). The selection and activity of core promoters are precisely regulated to ensure that a correct transcript is produced at an appropriate level in different tissues, developmental stages, or growth conditions.…”