Determine RNA transcription from common transcriptome data

Question

[June]

Hello almighty biostars,

Does anyone know a program that can infer the RNA transcription speed/turnaround/strength from common gene expression data? Common means the profiling is measured on endogenous RNA samples and doesn't involve any chemistry incorporation.

Thank you a lot, June

[rpolicastro]

RNA-seq only measures the steady-state level of mRNA which is a combination of syththesis rate/frequency and mRNA stability. It would be difficult to get kinetics information from just RNA-seq alone since it would be difficult to separate out these factors, and you have no quantifiable data from non-productive transcription. I generally see this done experimentally (e.g. pulse-chase, nascent RNA-seq, etc.) or computationally in scRNA-seq data with trajectory inference using RNA-velocity.

[June]

Hi rpolicastro,

Thanks for the explanation. In my case, I have several bulk RNA sequencing samples coming from the same germline, some of them are primary tumor, and some are from metastatic sites. Will it be strange if I declare in paper that the samples with more RNA diversities, or with more pre-mRNA shares, tend to be more transcription active?

Looking forward to your comments, June

[Dunois]

Could it work if you had time series data of sufficient temporal resolution?

[rpolicastro]

Even with longitudinal RNA-seq data it would be difficult to get kinetics information because you wouldn't really know whether changes in transcript levels are attributed to changes in mRNA stability or transcription rate/frequency.