I am doing research on the chemotoxic assay in C. elegans. One of the strains I used has a significant difference between RNAi and knockout strains. The RNAi strain is significantly different compared to the wildtype, but the knockout strain has no difference compared to the wild type. The gene is a transcription factor. The knockout strain is proved by PCR and the RNAi feeding plasmid is sequencing proved correct. Is it possible that the knockout strain already adapted to the genetic background so the compensation pathway starts work somehow?
Thank you so much.
Hello this might be of interest to you.
It has been shown recently that genetic compensation response (GCR) is triggered through a component of the NMD (nonse-mediated decay) pathway causing a compensation in the knockout but not the knockdown therefore leading to a discrepancy between the phenotype obtained from the two techniques:
Article PTC-bearing mRNA elicits a genetic compensation response via...
Hi,
El-Brolosy and colleagues in a recent article has tried to explained the underlying mechanistic differences in compensatory pathways between gene knock-out an gene knock-down.
https://www.nature.com/articles/s41684-019-0397-4
Hope this helps!
RNAi has become an essential tool in C. elegans research. RNAi in C. elegans by microinjecting with dsRNA, feeding with bacteria expressing dsRNA and soaking in dsRNA solution, as well as high-throughput methods for RNAi-based screens.
Article RNA Interference in Caenorhabditis Elegans
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