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

Sahar Hani (1) , Laura Cuyas (1, 2) , Pascale David (1) , David Secco (3) , James Whelan (3) , Marie-Christine Thibaud (1) , Rémy Merret (4) , Florian Mueller (5) , Nathalie Pochon (1) , Hélène Javot (1) , Orestis Faklaris (6) , Eric Maréchal (7) , Edouard Bertrand (8) , Laurent Nussaume (9)

1 BIAM - Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB)
2 Centre Mondial de l'Innovation Roullier
3 La Trobe University [Melbourne]
4 LGDP - Laboratoire Génome et développement des plantes
5 Imagerie et Modélisation - Imaging and Modeling
6 CRBM - Centre de recherche en Biologie cellulaire de Montpellier
7 LIPID
8 IGMM - Institut de Génétique Moléculaire de Montpellier
9 EBMP - Environnement, Bioénergie, Microalgues et Plantes

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 ~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.

Domaines: Sciences du Vivant [q-bio]

Sahar Hani, Laura Cuyas, Pascale David, David Secco, James Whelan, et al.. Live single-cell transcriptional dynamics via RNA labelling during the phosphate response in plants. Nature Plants, 2021, 7 (8), pp.1050-1064. ⟨10.1038/s41477-021-00981-3⟩. ⟨hal-03320179⟩