The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues

Joseph Swift, Kathleen Greenham, Joseph R. Ecker, Gloria M. Coruzzi, C. Robertson McClung

Research output: Contribution to journalReview articlepeer-review

2 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)764-778
Number of pages15
JournalPlant Journal
Volume109
Issue number4
DOIs
StatePublished - Feb 2022

Bibliographical note

Funding Information:
Work in the area of Plant Cell System Dynamics was supported by NSF grants IOS‐1547796 (to CRM), DBI‐2042159 (to KG), and an NIH grant NIGMS R01‐GM121753 (to GC). In addition, two conferences in the area of Plant Cell System Dynamics have been supported by NSF IOS‐2005283 [for Plant Molecular Biology Gordon Research Conference: Spatial and temporal dynamics in Plant Biology, 2022 (to CRM)] and NSF IOS‐1824578 [for Plant Molecular Biology Gordon Research Conference: Dynamic Plant Systems, 2018 (to GC)] and also by a Zegar Family Foundation Grant. JRE is an Investigator of the Howard Hughes Medical Institute. JS is an Open Philanthropy Awardee of the Life Sciences Research Foundation.

Publisher Copyright:
© 2021 Society for Experimental Biology and John Wiley & Sons Ltd.

Keywords

  • circadian
  • development
  • environmental signaling
  • single-cell
  • temporal regulatory networks
  • transcriptome dynamics

PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

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