Why histone mRNA can be found in polyA RNA-seq?

Question

[Andrew Liu]

Histone mRNAs were found in my RNA-seq data, but actually histone mRNAs are lacking of polyA tails. Thus I'm wondering how they can be found? Or maybe histone mRNAs are short and it's easy to mapped to multiple locations, then leads to a mapping mistake? THANK YOU!

[dsull]

Some ideas I have (others feel free to chime in).

Did your protocol use rRNA depletion or polyA enrichment? Is it possible that your library is contaminated? (there's typically always going to some degree of it, which could explain why you see some non-polyA-mRNA).

mRNA length doesn't matter -- it's the read length that matters. If you use short single-end reads, then you're more likely to get a mapping mistake.

In short: can you provide us with more details about how the RNA-seq protocol was carried out? What are the abundance of the histone mRNAs?