I was recently talking to a colleague about CRISPR knock-ins, and my colleague was referring to knock-ins as a transgene. However when I think of transgenes, I don’t think of CRISPR. I think of ExArrays. I’ve also heard of knock-ins referred to as insertions, but this makes me think of insertions via bombardment, integration of transgenes, or MosSci, etc.
So I was wondering what is the best way to describe a knock-in, especially when writing about it in a paper or a grant. Also, if it’s not a transgene what is it?
For the context of a paper or grant, I think you would want to say you’re looking at “endogenously labelled RAB-3” etc. with stress on the endogenous part.
If you’re describing the methods section, I would write “…was modified at the endogenous locus using CRISPR/Cas9 genome editing”
Transgene is a general term to describe any non-endogenous sequence element that is introduced into an organism. It includes both functional (e.g., GFP, degron) and non-functional (plasmid, cosmic, YAC) elements. Transgenes can be extrachromosomal or integrated (either randomly or targeted).
The method of introduction (CRISPR, bombardment, injection) is distinct from the transgene itself. For example, engineering a SNP mutation into the genome via CRISPR would not be considered a transgene.
Knock-in is a colloquial term - probably best to avoid in grants/papers (but I’m old-school; YMMV).
This is a great question! I think I would usually use transgene to describe something that wasn’t there before; so if I modify an endogenous locus it wouldn’t be a transgene in my mind, because you have merely changed something that already existed in the genome. I would probably say something akin to what Snug said when describing it in publication. However, if you use CRISPR to insert a complete cassette of promoter, GFP, and 3’UTR or something like that, then I’d probably call that a transgene. So the phrase is independent of the method, in a way.