Mol. Cell. doi:10.1016/j.molcel.2017.09.030 (2017)


Cellular mRNA levels are controlled by modulating intrinsic synthesis and degradation pathways in response to changes in gene expression and environmental conditions. Cytoplasmic mRNAs undergo decay by removal of the protective 5′ cap and 3′ polyadenine tail followed by degradation by the 5′-3′exonuclease Xrn1. Monitoring Xrn1-mediated degradation in real time is complicated, because decay intermediates exist only transiently. Inspired by the identification of pseudo-knot (PK) structures in flaviviruses that are resistant to Xrn1-mediated cleavage, Horvathova et al. developed a fluorescent biosensor called 3′-RNA end accumulation during turnover (TREAT) by placing two viral PKs between the PP7 and MS2 RNA stem loops, protecting MS2, but not PP7, from Xrn1-mediated degradation. This biosensor enables the monitoring of RNA degradation by measuring the ratio of intact (PP7 and MS2) versus degraded products (MS2) in fixed cells using smFISH probes targeted to the PP7 and MS2 RNA and in live cells by labeling the PP7 and MS2 coat proteins with fluorescent proteins. The TREAT sensor revealed that addition of translation inhibitors such as puromycin or cyclohexamide increased RNA stability and that cytoplasmic degradation does not occur in processing bodies (P-bodies). Exciting opportunities are now possible for coupling TREAT with existing methodologies for single-molecule imaging of transcription and translation to visualize gene expression with unprecedented detail.