Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia

Katina I. Spanier, Mieke Jansen, Ellen Decaestecker, Gert Huselmans, Dorthe Becker, John Colbourne, Luisa Orsini, Luc De Meester, Stein Aerts

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)
241 Downloads (Pure)

Abstract

Ecological genomics aims to understand the functional association between environmental gradients and the genes underlying adaptive traits. Many genes that are identified by genome-wide screening in ecologically relevant species lack functional annotations. Although gene functions can be inferred from sequence homology, such approaches have limited power. Here, we introduce ecological regulatory genomics by presenting an ontology-free gene prioritization method. Specifically, our method combines transcriptome profiling with high-throughput cis-regulatory sequence analysis in the water fleas Daphnia pulex and Daphnia magna. It screens coexpressed genes for overrepresented DNA motifs that serve as transcription factor binding sites, thereby providing insight into conserved transcription factors and gene regulatory networks shaping the expression profile. We first validated our method, called Daphnia-cisTarget, on a D. pulex heat shock data set, which revealed a network driven by the heat shock factor. Next, we performed RNA-Seq in D. magna exposed to the cyanobacterium Microcystis aeruginosa. Daphnia-cisTarget identified coregulated gene networks that associate with the moulting cycle and potentially regulate life history changes in growth rate and age at maturity. These networks are predicted to be regulated by evolutionary conserved transcription factors such as the homologues of Drosophila Shavenbaby and Grainyhead, nuclear receptors, and a GATA family member. In conclusion, our approach allows prioritising candidate genes in Daphnia without bias towards prior knowledge about functional gene annotation and represents an important step towards exploring the molecular mechanisms of ecological responses in organisms with poorly annotated genomes.
Original languageEnglish
Pages (from-to)1821-1842
JournalGenome Biology and Evolution
Volume9
Issue number6
Early online date14 Jul 2017
DOIs
Publication statusE-pub ahead of print - 14 Jul 2017

Keywords

  • cis-regulation
  • omics data integration
  • prioritization
  • crustacea endocrine signaling
  • functional enrichment
  • motif discovery

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