From raw materials to validated system

The construction of a genomic library and microarray to interpret systemic perturbations in Northern bobwhite

Arun Rawat, Kurt A. Gust, Youping Deng, Natàlia Garcia-Reyero, Michael J. Quinn, Mark S. Johnson, Karl J. Indest, Mohamed O. Elasri, Edward J. Perkins

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

The limited availability of genomic tools and data for nonmodel species impedes computational and systems biology approaches in nonmodel organisms. Here we describe the development, functional annotation, and utilization of genomic tools for the avian wildlife species Northern bobwhite (Colinus virginianus) to determine the molecular impacts of exposure to 2,6-dinitrotoluene (2,6-DNT), a field contaminant of military concern. Massively parallel pyrosequencing of a normalized multitissue library of Northern bobwhite cDNAs yielded 71,384 unique transcripts that were annotated with gene ontology (GO), pathway information, and protein domain analysis. Comparative genome analyses with model organisms revealed functional homologies in 8,825 unique Northern bobwhite genes that are orthologous to 48% of Gallus gallus protein-coding genes. Pathway analysis and GO enrichment of genes differentially expressed in livers of birds exposed for 60 days (d) to 10 and 60 mg/kg/d 2,6-DNT revealed several impacts validated by RT-qPCR including: prostaglandin pathway-mediated inflammation, increased expression of a heme synthesis pathway in response to anemia, and a shift in energy metabolism toward protein catabolism via inhibition of control points for glucose and lipid metabolic pathways, PCK1 and PPARGC1, respectively. This research effort provides the first comprehensive annotated gene library for Northern bobwhite. Transcript expression analysis provided insights into the metabolic perturbations underlying several observed toxicological phenotypes in a 2,6-DNT exposure case study. Furthermore, the systemic impact of dinitrotoluenes on liver function appears conserved across species as PPAR signaling is similarly affected in fathead minnow liver tissue after exposure to 2,4-DNT.

Original languageEnglish
Pages (from-to)219-235
Number of pages17
JournalPhysiological Genomics
Volume42
Issue number2
DOIs
Publication statusPublished - Jul 2010
Externally publishedYes

Fingerprint

2,6-dinitrotoluene
Colinus
Genomic Library
Gene Ontology
Liver
Cyprinidae
Peroxisome Proliferator-Activated Receptors
Systems Biology
Gene Expression Profiling
Metabolic Networks and Pathways
Computational Biology
Heme
Gene Library
Toxicology
Energy Metabolism
Genes
Prostaglandins
Birds
Anemia
Chickens

Keywords

  • Dinitrotoluenes
  • Energy metabolism
  • Gene orthologs
  • Next generation sequencing
  • Toxicogenomics

ASJC Scopus subject areas

  • Physiology
  • Genetics

Cite this

From raw materials to validated system : The construction of a genomic library and microarray to interpret systemic perturbations in Northern bobwhite. / Rawat, Arun; Gust, Kurt A.; Deng, Youping; Garcia-Reyero, Natàlia; Quinn, Michael J.; Johnson, Mark S.; Indest, Karl J.; Elasri, Mohamed O.; Perkins, Edward J.

In: Physiological Genomics, Vol. 42, No. 2, 07.2010, p. 219-235.

Research output: Contribution to journalArticle

Rawat, Arun ; Gust, Kurt A. ; Deng, Youping ; Garcia-Reyero, Natàlia ; Quinn, Michael J. ; Johnson, Mark S. ; Indest, Karl J. ; Elasri, Mohamed O. ; Perkins, Edward J. / From raw materials to validated system : The construction of a genomic library and microarray to interpret systemic perturbations in Northern bobwhite. In: Physiological Genomics. 2010 ; Vol. 42, No. 2. pp. 219-235.
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