Transcriptional profiling reveals differential expression of a neuropeptide-like protein and pseudogenes in aryl hydrocarbon receptor-1 mutant Caenorhabditis elegans.
The aryl hydrocarbon receptor (AHR) functions in higher organisms in development, metabolism and toxic responses. Its Caenorhabditis elegans (C. elegans) ortholog, AHR-1, facilitates neuronal development, growth and movement. We investigated the effect of AHR mutation on the transcriptional profile of L4 stage C. elegans using RNA-seq and quantitative real time PCR in order to understand better AHR-1 function at the genomic level. Illumina HiSeq 2000 sequencing yielded 51.1, 61.2 and 54.0 million reads from wild-type controls, ahr-1(ia03) and ahr-1(ju145) mutants, respectively, providing detection of over 18,000 transcripts in each sample. Fourteen transcripts were over-expressed and 125 under-expressed in both ahr-1 mutants when compared to wild-type. Under-expressed genes included soluble guanylate cyclase (gcy) family genes, some of which were previously demonstrated to be regulated by AHR-1. A neuropeptide-like protein gene, nlp-20, and a F-box domain protein gene fbxa-192 and its pseudogenes fbxa-191 and fbxa-193 were also under-expressed. Conserved xenobiotic response elements were identified in the 5' flanking regions of some but not all of the gcy, nlp-20, and fbxa genes. These results extend previous studies demonstrating control of gcy family gene expression by AHR-1, and furthermore suggest a role of AHR-1 in regulation of a neuropeptide gene as well as pseudogenes.
Laboratory of Functional Genomics and Bioinformatics, A. I. Virtanen Institute for Molecular Sciences, Department of Neurobiology, University of Eastern Finland, Yliopistonranta 1, 70211 Kuopio, Finland. Electronic address: vuokko.aarnio@uef.fi.
Vuokko
V
Aarnio
Laboratory of Functional Genomics and Bioinformatics, A. I. Virtanen Institute for Molecular Sciences, Department of Neurobiology, University of Eastern Finland, Yliopistonranta 1, 70211 Kuopio, Finland. Electronic address: liisa.heikkinen@uef.fi.
Liisa
L
Heikkinen
Laboratory of Functional Genomics and Bioinformatics, A. I. Virtanen Institute for Molecular Sciences, Department of Neurobiology, University of Eastern Finland, Yliopistonranta 1, 70211 Kuopio, Finland. Electronic address: juhanip@student.uef.fi.
Juhani
J
Peltonen
Laboratory of Molecular Brain Research, A. I. Virtanen Institute for Molecular Sciences, Department of Neurobiology, University of Eastern Finland, Yliopistonranta 1, 70211 Kuopio, Finland. Electronic address: gundars.goldsteins@uef.fi.
Gundars
G
Goldsteins
Laboratory of Functional Genomics and Bioinformatics, A. I. Virtanen Institute for Molecular Sciences, Department of Neurobiology, University of Eastern Finland, Yliopistonranta 1, 70211 Kuopio, Finland. Electronic address: merja.lakso@uef.fi.
Merja
M
Lakso
Laboratory of Functional Genomics and Bioinformatics, A. I. Virtanen Institute for Molecular Sciences, Department of Neurobiology, University of Eastern Finland, Yliopistonranta 1, 70211 Kuopio, Finland. Electronic address: garry.wong@uef.fi.
Garry
G
Wong
D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000254:growth & development; D029742:Caenorhabditis elegans Proteins / Q000235:genetics*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D009154:Mutation; D009479:Neuropeptides / Q000235:genetics*; D011544:Pseudogenes; D018336:Receptors, Aryl Hydrocarbon / Q000235:genetics*
D029742:Caenorhabditis elegans Proteins; D009479:Neuropeptides; D018336:Receptors, Aryl Hydrocarbon
Aryl hydrocarbon receptor; C. elegans; Neuropeptide; Pseudogene; RNA-seq