In order to identify the pathway that is responsible for the turnover of a certain transcript of interest, we developed the xrFrag method (xrFrag = XRN1-resistant decay fragment).
Using the virus-derived xrRNA element, decay intermediates that arise due to the turnover of RNAs can be visualized.
We have successfully used the xrFrag method to analyze multiple mRNA decay pathways such as nonsense-mediated mRNA decay (NMD), miRNA-induced decay and degradation caused by AU-rich elements or cytokine 3' UTRs
If you are interested, here you can find the original publication: PubMed
The fully annotated vector sequence can be downloaded here
We are in the process of depositing many xrRNA-containing vectors to Addgene. More information will be available shortly.