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

View ORCID ProfileR. Taylor Raborn, View ORCID ProfileKen Spitze, View ORCID ProfileVolker P. Brendel, Michael Lynch
doi: https://doi.org/10.1101/047894
R. Taylor Raborn
1Department of Biology, Indiana University
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  • For correspondence: rtraborn@indiana.edu
Ken Spitze
1Department of Biology, Indiana University
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Volker P. Brendel
1Department of Biology, Indiana University
2School of Informatics and Computing, Indiana University
3These authors jointly supervised this work.April 20, 2016
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Michael Lynch
1Department of Biology, Indiana University
3These authors jointly supervised this work.April 20, 2016
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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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 28, 2016.
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Promoter architecture and sex-specific gene expression in the microcrustacean Daphnia pulex revealed by large-scale profiling of 5′-mRNA ends
R. Taylor Raborn, Ken Spitze, Volker P. Brendel, Michael Lynch
bioRxiv 047894; doi: https://doi.org/10.1101/047894
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Promoter architecture and sex-specific gene expression in the microcrustacean Daphnia pulex revealed by large-scale profiling of 5′-mRNA ends
R. Taylor Raborn, Ken Spitze, Volker P. Brendel, Michael Lynch
bioRxiv 047894; doi: https://doi.org/10.1101/047894

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