Cause of 3' bias in polyA selection step in RNASeq library prep

Question

[rnaseqbias]

Hello. What is the cause of 3' bias in the polyA selection step in RNASeq library preparation? (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4310221/figure/F6/) I have searched around on the internet but could not find the mechanism and cause explicitly explained. Is there a mathematical model for the bias?

Thank you.

[GenoMax]

Since poly-A tails are at the 3'-end of RNA molecules it is not surprising this happens.

[rnaseqbias]

Is the bias because of biochemical or mechanical reasons? If it is a purely biochemical process, then the 3' bias should also show up if ribo-depletion is used instead of polyA selection to get rid of ribosomal RNA.(But as far as I know this is not the case.) So is there a mechanical aspect to this where the polyA grabbing induces breakage?

Answer 1

[h.mon]

What is the cause of 3' bias in the polyA selection step in RNASeq library preparation?

RNA degradation.

Is there a mathematical model for the bias?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616752/