Time- and space-resolved transcriptional regulation in Arabidopsis thaliana.

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.