Ribosome protected fragments on CDS V/S UTR

Question

[Chirag Nepal]

Hi there,

When I read the papers, I see people analyze RPF that is bound only on CDS. However, recent papers have shown that many ncrnas and UTRs have ribosomes associated on them. So, if you are comparing (wt vs treated cells) the RPF of any coding genes, is it OK if UTR is also included along with CDS in the downstream analysis. Or do you suggest not to include UTRs of gene when comparing (between wt and treated rnas) the RPF of gene?

thanks!

Answer 1

[jelena121]

I think it depends on what your question is? For example, if you're trying to compare differences in translation rates, it's unlikely that you will be interested in the UTR, and I think a few of the ribosomal profiling papers even exclude the first section of the CDS, because it will have an initiation peak that's not necessarily related to overall translation rates. However, it might be interesting to look at UTR associations to see whether there are peaks of binding associated there etc. But I wouldn't include it by default in a first-pass analysis unless there was a compelling reason to.