We have some mutant Drosophila containing a UAS-cDNA rescue construct. However, the mutant phenotype in these animals is gone. They have not been crossed to a Gal4 line, and the problem has persisted across multiple different UAS/mutation recombinant lines, and across expression systems (lexA/op lines with this cDNA and mutation have the same problem). Is there a precedent for this to occur?
I remember that this occurred once with one of our UAS-cDNA constructs. This may occur if by chance your transgene get inserted near an active gene leading to constitutive expression of construct independent of the Gal4
Yes, we have had this happen both observing subtle phenotypes and difficulty getting transgenics of more 'toxic' UAS constructs. So yes, this is a thing.
Yes, the GAL4-UAS system has been known to have leaky expression. To avoid this issue, I suggest using PhiC31 integration when creating transgenic lines. There are many mapped out "landing sites"/integration loci that are known to have minimal to no leaky expression.
Similar to the others, we also observed the rescue of mutant phenotypes just by the introduction of a UAS construct into the mutant background. The PhiC31 system can help you to avoid this phenomenon, but it is not immune against it, e.g. Mao et al. (2014, Development 141) reported a low activity of the 51D insertion site (see link; p1066 and p.1072).
http://dev.biologists.org/content/141/5/1064
Another potential issue is having a "twi>GFP" marked balancer in the background, as these are not directly driven by a twi enhancer, but are rather a UAS-GFP driven by twi>GAL4 on the same balancer. In effect it's a "hidden" GAL4 source that can cause problems
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