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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.
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This content will become publicly available on June 20, 2026
The time machine: feedback loops, post‐transcriptional regulation, and environmental integration in the plant circadian oscillator
SUMMARY Daily rhythms in physiology are obvious and widespread. While for millennia it was thought that these cycles represent passive responses to environmental cycles, we now recognize that many of them are governed by circadian oscillators. In plants, these cell‐autonomous oscillators regulate daily processes such as photosynthesis, organ growth, and hormone production, as well as seasonal transitions like flowering. Furthermore, the circadian system gates plant responses to biotic and abiotic stresses, modulating susceptibility to pathogens and environmental extremes in a time‐of‐day‐dependent manner. Variants of circadian clock genes have been repeatedly selected during crop domestication and improvement, highlighting the importance of the circadian system to plants and its relevance for agriculture. Here, I review the history of circadian studies in plants and summarize our current understanding of the molecular nature of the circadian oscillator. I also discuss how this complex network both responds to and is buffered against changes in the environment. Next, I examine how circadian oscillators differ between various tissues and how their activities are coordinated throughout the plant body. Finally, I discuss emerging directions, such as ways in which this understanding can be applied to crop improvement in the face of climate change.
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- Award ID(s):
- 2309854
- PAR ID:
- 10614151
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- The Plant Journal
- Volume:
- 122
- Issue:
- 6
- ISSN:
- 0960-7412
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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