Abstract
The responses of plants to their environment are often dependent on the spatiotemporal dynamics of transcriptional regulation. While live-imaging tools have been used extensively to quantitatively capture rapid transcriptional dynamics in living animal cells, the lack of implementation of these technologies in plants has limited concomitant quantitative studies in this kingdom. Here, we applied the PP7 and MS2 RNA-labelling technologies for the quantitative imaging of RNA polymerase II activity dynamics in single cells of living plants as they respond to experimental treatments. Using this technology, we counted nascent RNA transcripts in real time in Nicotiana benthamiana (tobacco) and Arabidopsis thaliana. Examination of heat shock reporters revealed that plant tissues respond to external signals by modulating the proportion of cells that switch from an undetectable basal state to a high-transcription state, instead of modulating the rate of transcription across all cells in a graded fashion. This switch-like behaviour, combined with cell-to-cell variability in transcription rate, results in mRNA production variability spanning three orders of magnitude. We determined that cellular heterogeneity stems mainly from stochasticity intrinsic to individual alleles instead of variability in cellular composition. Together, our results demonstrate that it is now possible to quantitatively study the dynamics of transcriptional programs in single cells of living plants.
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Data availability
Raw and analysed data are available upon request. All plasmids used in this study are listed in Supplementary Table 1 and were submitted to the AddGene public repository. Arabidopsis seeds are listed in Supplementary Table 3 and are available from the Arabidopsis Biological Resource Center stock centre and/or upon request from the Niyogi laboratory. Source data are provided with this paper.
Code availability
All code used to analyse raw data can be found in the public GitHub repositories https://github.com/GarciaLab/mRNADynamics and https://github.com/GarciaLab/PlantPP7.
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Acknowledgements
We thank R. Phillips, A. Roeder, P. Quail, S. Wakao, C. Gee, J. Brunkard and A. Flamholz for comments on the manuscript; members of the Garcia laboratory: M. Turner and G. Martini for sharing their knowledge and materials related to the nanocages experiment and Y. J. Kim for discussing results, G. Martini in particular for setting up the microscope temperature chamber; C. Baker, S. Wakao and D. Westcott from the Niyogi laboratory for their RT–qPCR advice; A. Schwartz, J. O’Brien and F. Federici for sharing plasmids; A. Lin and J. Liu provided useful feedback regarding calculations; and M. Kobayashi for help and for making the Niyogi laboratory run smoothly. H.G.G. was supported by the Burroughs Wellcome Fund Career Award at the Scientific Interface, the Sloan Research Foundation, the Human Frontiers Science Program, the Searle Scholars Program, the Shurl and Kay Curci Foundation, the Hellman Foundation, the National Institutes for Health Director’s New Innovator Award (DP2 OD024541-01), and a National Science Foundation CAREER Award (1652236). K.K.N. is an investigator of the Howard Hughes Medical Institute. S.A. was supported by H.G.G. and K.K.N. A.R. was supported by H.G. and National Science Foundation Graduate Research Fellowships Program (DGE 1752814).
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S.A., H.G.G. and K.K.N. designed experiments. S.A. performed experiments and analysed the data. S.A., A.R. and H.G.G. wrote the analysis code. S.A., H.G.G. and K.K.N. wrote the paper.
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Supplementary Information
Supplementary calculations, Figs. 1–26 and tables.
Supplementary Video 1
Constitutive GAPC2 reporter in tobacco.
Supplementary Video 2
Inducible HSP70 reporter in tobacco.
Supplementary Video 3
Inducible HSP101 reporter in Arabidopsis.
Supplementary Video 4
Inducible HsfA2 reporter in Arabidopsis.
Supplementary Video 5
Constitutive EF-Tu reporter in Arabidopsis.
Supplementary Video 6
Two spot inducible HSP101 reporter in Arabidopsis.
Source data
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Statistical source data
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Statistical source data
Source Data Fig. 5
Statistical source data
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Alamos, S., Reimer, A., Niyogi, K.K. et al. Quantitative imaging of RNA polymerase II activity in plants reveals the single-cell basis of tissue-wide transcriptional dynamics. Nat. Plants 7, 1037–1049 (2021). https://doi.org/10.1038/s41477-021-00976-0
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DOI: https://doi.org/10.1038/s41477-021-00976-0
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