Imaging mRNAs with corrected RNA stability

Abstract

MS2 system is widely used to image mRNAs in living cells, where the spatial distribution of mRNAs regulates various aspects of cell biology, including translation and RNA decay. To image an mRNA of interest, the mRNA’s 3’ untranslated region (UTR) is genetically fused with an array of MS2 stem loops, which recruit fluorescently labeled MS2 coat proteins. And each mRNA molecule appears as a diffraction‐limited spot under fluorescent microscope. Here, we report that the MS2 system renders some of the tagged mRNAs less stable and being degraded by the nonsense‐mediated mRNA decay (NMD) pathway. To resolve this issue, we improved the MS2 system by fusing the MS2 coat protein with the translation termination factor eRF3, which protects the mRNA from being degraded through the NMD pathway. Our improved MS2 system faithfully reports the mRNAs’ stability and localization, and will see wide applications in future studies of RNA biology.