When investigating the interaction between lincRNAs and coding RNAs, do I use the primary RNA sequence (before splicing occurs) containing the introns and exons, or the spliced sequence (without introns) of both of these RNAs (of example using the tool LncTar)?
That's an interesting question.
Increasing evidence in several models suggests that much of splicing activity is conducted in a co-transcriptional manner (see ref). My interpretation of this data is that mRNAs spend most of their lifetime spliced... I would therefore tend to think that using spliced sequences is the most representative rendition of the global cellular picture.
Do you have evidence that your lncRNA-mRNA interaction of interest occurs in the nucleus? In the periphery of chromatin? Co-transcriptionally? Then, there might be a rationale for using pre-mRNA sequences...
Best of luck,
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4102251/
Thanks so much for your help. I have no prior info on the potential interactions - I am using a list of differentially expressed lincRNAs and I want to predict if any of them may have regulated a list of differentially expressed mRNAs that I have.
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