Live single-cell transcriptional dynamics via RNA labelling during the phosphate response in plants

Plants are constantly adapting to ambient fluctuations through spatial and temporal transcriptional responses. Here, we implemented the latest-generation RNA imaging system and combined it with microfluidics to visualize transcriptional regulation in living Arabidopsis plants. This enabled quantitative measurements of the transcriptional activity of single loci in single cells, in real time and under changing environmental conditions. Using phosphate-responsive genes as a model, we found that active genes displayed high transcription initiation rates (one initiation event every similar to 3 s) and frequently clustered together in endoreplicated cells. We observed gene bursting and large allelic differences in single cells, revealing that at steady state, intrinsic noise dominated extrinsic variations. Moreover, we established that transcriptional repression triggered in roots by phosphate, a crucial macronutrient limiting plant development, occurred with unexpectedly fast kinetics (on the order of minutes) and striking heterogeneity between neighbouring cells. Access to single-cell RNA polymerase II dynamics in live plants will benefit future studies of signalling processes.

Automated summary

In this study, real-time visualization of transcriptional regulation in living Arabidopsis plants was achieved using the latest-generation RNA imaging system combined with microfluidics. The research revealed quantitative measurements of transcriptional activity at single loci in single cells, gene bursting, and large allelic differences, as well as the dominance of intrinsic noise in transcriptional control. Additionally, fast kinetics of transcriptional repression triggered by phosphate in roots and heterogeneity between neighboring cells were observed, providing valuable insights for future studies of signaling processes in plants.