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van Wijk MH, Riksen JAG, Elvin M, Poulin GB, Maulana MI, Kammenga JE, Snoek BL, Sterken MG. Cryptic genetic variation of eQTL architecture revealed by genetic perturbation in C. elegans. G3 (Bethesda) 2023; 13:7067301. [PMID: 36861370 PMCID: PMC10151397 DOI: 10.1093/g3journal/jkad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 12/27/2022] [Accepted: 02/07/2023] [Indexed: 03/03/2023]
Abstract
Genetic perturbation in different genetic backgrounds can cause a range of phenotypes within a species. These phenotypic differences can be the result of the interaction between the genetic background and the perturbation. Previously we reported that perturbation of gld-1, an important player in developmental control of C. elegans, released cryptic genetic variation affecting fitness in different genetic backgrounds. Here we investigated the change in transcriptional architecture. We found 414 genes with a cis-eQTL and 991 genes with a trans-eQTL that were specifically found in the gld-1 RNAi treatment. In total, we detected 16 eQTL-hotspots, of which 7 were only found in the gld-1 RNAi treatment. Enrichment analysis of those 7 hotspots showed that the regulated genes were associated with neurons and the pharynx. Furthermore, we found evidence of accelerated transcriptional aging in the gld-1 RNAi treated nematodes. Overall, our results illustrate that studying CGV leads to the discovery of hidden polymorphic regulators.
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Affiliation(s)
- Marijke H van Wijk
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Joost A G Riksen
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Mark Elvin
- Peak Proteins, Alderley Park, Macclesfield, Cheshire, SK10 4TG, United Kingdom
| | - Gino B Poulin
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, M13 9PL, United Kingdom
| | - Muhammad I Maulana
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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