The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues. (6th December 2021)

• Record Type: Journal Article
• Authors: Swift, Joseph; Greenham, Kathleen; Ecker, Joseph R.; Coruzzi, Gloria M.; Robertson McClung, C.
• Is Part Of: Plant journal. Volume 109:Number 4(2022)
• Page Start: 764
• Page End: 778
• Publication Date: 2021-12-06
• Subjects: transcriptome dynamics -- single‐cell -- development -- circadian -- environmental signaling -- temporal regulatory networks; Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.15589
• Languages: English
• ISSNs: 0960-7412

Abstract

SUMMARY: As sessile organisms, plants are finely tuned to respond dynamically to developmental, circadian and environmental cues. Genome‐wide studies investigating these types of cues have uncovered the intrinsically different ways they can impact gene expression over time. Recent advances in single‐cell sequencing and time‐based bioinformatic algorithms are now beginning to reveal the dynamics of these time‐based responses within individual cells and plant tissues. Here, we review what these techniques have revealed about the spatiotemporal nature of gene regulation, paying particular attention to the three distinct ways in which plant tissues are time sensitive. (i) First, we discuss how studying plant cell identity can reveal developmental trajectories hidden in pseudotime. (ii) Next, we present evidence that indicates that plant cell types keep their own local time through tissue‐specific regulation of the circadian clock. (iii) Finally, we review what determines the speed of environmental signaling responses, and how they can be contingent on developmental and circadian time. By these means, this review sheds light on how these different scales of time‐based responses can act with tissue and cell‐type specificity to elicit changes in whole plant systems. Significance Statement: Plants are dynamic systems. Reflecting this, genome‐wide patterns of gene regulation vary both spatially and temporally. Here, we discuss how transcription dynamics are driven by developmental, circadian or environmental cues, with a focus on how they can unfold in a cell‐ and tissue‐specific manner. A major future challenge will be to model networks that integrate across different temporal and spatial scales, which we propose be recognized as a new field of Plant Cell System Dynamics.