Hello all,
I would like to know if gene-X::GFP represents a transcriptional fusion or a translational one?
Also when something says “Driven by”, it refers to the promoter driving the reporter?
Finally, would it specifically mention gene-X:GFP as a reporter if it was a translational fusion?
Thank you very much !
Mehul
If the nomenclature is following correctly, then listing a transgene as gene-X::XFP indicates transcriptional reporter, with the promoter of gene-X driving the fluorescent protein. If all caps are used (GENE-X::XFP), this indicates a translational fusion. And to be 100% accurate, if the promoter of gene-X is used, it should be written as gene-X::GENE-X::XFP. sometimes you’ll see Pgene-X::GENE-X::XFP, where the P stands for promoter.
and yes, driven by indicates the promoter used.
I don’t really agree with Steve: the form gene-x::gfp means that sequence from the gene-x locus has been fused to the gfp gene, but that’s all it means. Critically, it doesn’t mean that all of this sequence is noncoding. The term GENE-X::GFP does refer to a fusion protein including (part of) the protein encoded by gene-x fused to GFP, but the transgene driving expression of GENE-X::GFP is nonetheless a gene, and should be written lowercase and in italics, and thus takes the form gene-x::gfp for the reasons in the beginning of this paragraph.
As Steve notes, you do also see constructs written as Pgene-x::gfp, meaning that the promoter for gene-x has been fused to the gfp gene, and this does mean that it’s a transcriptional rather than a translational fusion (although it may nonetheless include the first few codons of gene-x), and I suppose that one could name a translational fusion Pgene-x::gene-x::gfp, but while that may seem to be the most descriptive and most desirable option I don’t think that’s very commonly done, and I believe the same construct could still be named gene-x::gfp while following the nomenclature.
The most important point here may be that people believing themselves to be reasonable and logical nonetheless are following different rules. For any given construct it’s important to go back to the literature and find out just what it contains, because you can’t rely on the person who named it having followed either the guidelines Steve set forth or the ones I advise. And if you are publishing a construct, describe it well enough so that a reader can figure out what it contains - don’t rely on them to correctly discern its contents from the name you gave it.
Thank you very much for your informative replies. It is certainly a lot of help.
Perhaps someday, everyone will follow the guidelines to make life simpler. For now, the keywords being, look back at the literature - and sometimes even thats not very helpful 
Thanks for correcting me, Hillel. I just re-read the guidelines on WormBase, and here is the informative summary:
* Gene fusions incorporated in transgenes that consist of a C. elegans gene or part thereof fused to a reporter such as lacZ or GFP are indicated by the C. elegans gene name followed by two colons and the reporter, all italicized: [i]pes-1::lacZ[/i], [i]mab-9::GFP.[/i] [b]No specific recommendations have been made for distinguishing between transcriptional and translational fusions. [/b] (my emphasis)I hope that the worm community can adopt a uniform standard for distinguishing translation and transcriptional fusion. Does anyone have a suggestion of whom we should contact to set up such a standard? (I have been developing an undergraduate lab which requires using multiple translational GFP fusions and have been frustrated by my inability to easily determine whether a stock is a transcriptional or translational fusion, even with the CGC records in hand.)
Janet Duerr
This is a very important discussion. In my own experience, I always indicates transcriptional fusion as
Punc-119::GFP,
and translational fusion as Punc-119::UNC-119-GFP. So “P” means promoter and "–"means protein fusion.
That is how I tend to think of it as well. Or sometimes I have seen it is myo-1p::Gfp indicating it as a transcriptional fusion.
As for referring to the literature, unfortunately, sometimes even that is vague. E.g I recently came across what should have been a translational fusion but is actually a NLS-GFP.
Perhaps wormbase could have a separate checkbox for transcriptional and translational fusions in the Trangene section.