RNA-triggered fluorescence controlled by RNA switches for real-time RNA expression tracking in living plants

Tracking RNA expression dynamics in living plants is critical for understanding gene regulation, yet real-time visualization remains a significant challenge. We have addressed this issue by de novo engineering an RNA-triggered fluorescence (RTF) reporter system precisely controlled by programmable RNA switches and achieved dynamic imaging of RNA expression at the cellular level and the whole-plant scale. The RNA switch-RTF system enabled the dynamic real-time tracking of developmentally regulated, tissue-specific, circadian, and stress-responsive mRNAs, as well as the movement of a mobile mRNA and an aphid-secreted cross-kingdom long non-coding RNA. By providing a powerful platform for real-time RNA imaging in vivo , our approach opens new avenues for studying gene regulation, signaling, and mobility in plants, with potential applications in synthetic biology and crop improvement.