Time‐ and space‐resolved transcriptional regulation in Arabidopsis thaliana

Mar 14, 2026Plant biology (Stuttgart, Germany)

How gene activity changes over time and in different parts of Arabidopsis thaliana

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Abstract

Intermediate regulatory proteins in Arabidopsis thaliana are of significantly lower abundance compared to other transcripts in the transcriptome.

Transcription factors, kinases, and E3 ligases connect various environmental signals to metabolic outputs.
Over half of the expressed kinases, E3 ligases, and transcription factors exhibit variability in expression based on time and location in mature leaves.
Dynamic expression patterns of these regulators help plants manage metabolism while enabling specific stress responses.
The high variability in the Arabidopsis transcriptome suggests that sampling time and cellular context are crucial for experimental accuracy.

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General metabolism and responses to internal or external signals are tightly regulated in plants. We hypothesise that a network of intermediate regulatory proteins including transcription factors, kinases, and E3 ligases connect input signals like light, temperature, circadian clock, and ontogenetic pathways to output pathways. We therefore investigate the transcriptional dynamics of these regulators. RNA sequencing was performed on 3-week-old Arabidopsis thaliana Col-0 rosettes grown under 12 h/12 h light/dark conditions sampled every 2 h over 24 h to match publicly available single-cell data of same age plants. Both were analysed to identify the abundance of intermediate regulators in time and space. Intermediate regulators are of significantly lower abundance compared with other transcripts in the Arabidopsis transcriptome. More than half of expressed kinases, E3 ligases and transcriptions factors vary in either time, space or both in mature leaves. Dynamic expression patterns of regulators allow plants to maintain tightly regulated metabolism while providing sufficient room for specific stress responses. High plasticity of the Arabidopsis transcriptome highlights the importance of considering sampling time-of-day and cellular resolution for experiments.

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Time‐ and space‐resolved transcriptional regulation in Arabidopsis thaliana

Abstract

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