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| Status |
Public on Sep 19, 2014 |
| Title |
Differential gene expression in ahr-1 mutants compared to wild-type C. elegans |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The aryl hydrocarbon receptor (AHR) functions in higher organisims 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 an 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.
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| Overall design |
One sample was created from each of the following strains: wild-type N2, ahr-1(ia03) mutant and ahr-1(ju145) mutant. In data analysis, each mutant sample was individually compared to the wild-type sample to find differentially expressed genes.
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| Contributor(s) |
Aarnio V, Heikkinen L, Peltonen J, Goldsteins G, Lakso M, Wong G, Antoschechkin I, Sternberg P |
| Citation(s) |
24463456 |
| Submission date |
Sep 18, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Vuokko Aarnio |
| E-mail(s) |
vuokko.aarnio@uef.fi
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| Organization name |
University of Eastern Finland
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| Department |
A. I. Virtanen Institute, Department of Neurobiology
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| Street address |
P. O. Box 1627
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| City |
Kuopio |
| ZIP/Postal code |
70211 |
| Country |
Finland |
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| Platforms (1) |
| GPL13657 |
Illumina HiSeq 2000 (Caenorhabditis elegans) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA261420 |
| SRA |
SRP047293 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE61537_ahr-1ia03vsWild-type.xls.gz |
3.0 Mb |
(ftp)(http) |
XLS |
| GSE61537_ahr-1ju145vsWild-type.xls.gz |
3.1 Mb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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