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Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia

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 fr...

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Autores principales: Spanier, Katina I., Jansen, Mieke, Decaestecker, Ellen, Hulselmans, Gert, Becker, Dörthe, Colbourne, John K., Orsini, Luisa, De Meester, Luc, Aerts, Stein
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5569996/
https://www.ncbi.nlm.nih.gov/pubmed/28854641
http://dx.doi.org/10.1093/gbe/evx127
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author Spanier, Katina I.
Jansen, Mieke
Decaestecker, Ellen
Hulselmans, Gert
Becker, Dörthe
Colbourne, John K.
Orsini, Luisa
De Meester, Luc
Aerts, Stein
author_facet Spanier, Katina I.
Jansen, Mieke
Decaestecker, Ellen
Hulselmans, Gert
Becker, Dörthe
Colbourne, John K.
Orsini, Luisa
De Meester, Luc
Aerts, Stein
author_sort Spanier, Katina I.
collection PubMed
description 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.
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spelling pubmed-55699962017-08-29 Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia Spanier, Katina I. Jansen, Mieke Decaestecker, Ellen Hulselmans, Gert Becker, Dörthe Colbourne, John K. Orsini, Luisa De Meester, Luc Aerts, Stein Genome Biol Evol Research Article 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. Oxford University Press 2017-07-14 /pmc/articles/PMC5569996/ /pubmed/28854641 http://dx.doi.org/10.1093/gbe/evx127 Text en © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Research Article
Spanier, Katina I.
Jansen, Mieke
Decaestecker, Ellen
Hulselmans, Gert
Becker, Dörthe
Colbourne, John K.
Orsini, Luisa
De Meester, Luc
Aerts, Stein
Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia
title Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia
title_full Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia
title_fullStr Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia
title_full_unstemmed Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia
title_short Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia
title_sort conserved transcription factors steer growth-related genomic programs in daphnia
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5569996/
https://www.ncbi.nlm.nih.gov/pubmed/28854641
http://dx.doi.org/10.1093/gbe/evx127
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