I work with a non-model system and I am trying to identify the mRNA targets of a specific RNA-binding protein using IP and RNAseq. I have been unable to find an antibody that will bind my native protein for IP. So instead, I would like to clone and tag my protein, followed by coupled transcription/translation, so that I can IP using tagged beads instead. My issue is that I haven't found any papers that do this. Will my cloned RBP still be able to bind its targets if I do this?
If I understand correctly, the question is whether the production of an RNA-binding protein by an in vitro coupled transcription/translation kit will be impossible because the protein as it is produced will bind to the transcribed RNA, blocking further translation.
With little effort, I found a paper in which this had been done. No doubt there are others. So it does appear to be possible.
Article An in Vitro Technique to Identify the RNA Binding-Site Seque...
You could over-expressed your tagged-protein in your original host cells and then do IP. If your tag doesn't affect your protein conformation and RNA-protein binding, you should be fine to proceed the experiment.