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Peer-reviewedCC BYScience Advances

Single-nucleus transcriptomics resolves multiple fate dynamics between inflorescence meristem and primary stem

  • Sebastián R Moreno1
  • Martin O. Lenz2,1
  • Elliot M. Meyerowitz3,1
  • James C W Locke1
  • Henrik Jönsson4,1
4 affiliations
  1. 1Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
  2. 2Cambridge Advanced Imaging Centre, Downing Site, University of Cambridge, Cambridge, CB2 3DY, UK
  3. 3Division of Biology and Biological Engineering and Howard Hughes Medical Institute, 156-29 California Institute of Technology, Pasadena, CA 91125. U.S.A
  4. 4Centre for Environmental and Climate Science, Lund University, Lund, Sweden
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Abstract

The shoot apical meristem (SAM), located at the plant apex, is accountable for the formation of above-ground organs such as leaves, stem and flowers. Although transcriptional profiling has elucidated some cell-types observed within stems or flowers, the differentiation transcriptional dynamics from shoot stem cells to multiple cell identities remain unknown. We employed a single-nucleus RNA-sequencing approach to assess the transcriptional heterogeneity and cell differentiation processes within the SAM. By collecting dissected inflorescence meristems, we constructed an inflorescence single-nucleus SAM atlas from Arabidopsis thaliana . Our analysis unveiled regulatory elements for most previously known cell types such as the boundary domain, vasculature, early primordia, epidermis and internal stem cells. We also identified previously unobserved transcriptional profiles, revealing that the stem cortex is defined early within forming primordia. Moreover, trajectory inference analysis allowed us to capture spatial control of S-phase machinery by floral homeotic genes and differentiation gene expression dynamics from internal shoot stem cells toward internal layers such as cortex, cambium, xylem and phloem. The results advance our understanding of the cellular and transcriptional heterogeneity underlying the cell-fate transcriptional dynamics shaping shoot organs and architecture.

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Cite

BibTeXRIS
BibTeX
@article{moreno2026singlenucleus,
  title = {{Single-nucleus transcriptomics resolves multiple fate dynamics between inflorescence meristem and primary stem}},
  author = {Sebastián R Moreno and Martin O. Lenz and Elliot M. Meyerowitz and James C W Locke and Henrik Jönsson},
  journal = {Science Advances},
  year = {2026},
  month = jun,
  doi = {10.1126/sciadv.aee2988},
  url = {https://doi.org/10.1126/sciadv.aee2988},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Single-nucleus transcriptomics resolves multiple fate dynamics between inflorescence meristem and primary stem
AU  - Sebastián R Moreno
AU  - Martin O. Lenz
AU  - Elliot M. Meyerowitz
AU  - James C W Locke
AU  - Henrik Jönsson
PY  - 2026
DA  - 2026/06/19
JO  - Science Advances
DO  - 10.1126/sciadv.aee2988
UR  - https://doi.org/10.1126/sciadv.aee2988
AB  - The shoot apical meristem (SAM), located at the plant apex, is accountable for the formation of above-ground organs such as leaves, stem and flowers. Although transcriptional profiling has elucidated some cell-types observed within stems or flowers, the differentiation transcriptional dynamics from shoot stem cells to multiple cell identities remain unknown. We employed a single-nucleus RNA-sequencing approach to assess the transcriptional heterogeneity and cell differentiation processes within the SAM. By collecting dissected inflorescence meristems, we constructed an inflorescence single-nucleus SAM atlas from Arabidopsis thaliana . Our analysis unveiled regulatory elements for most previously known cell types such as the boundary domain, vasculature, early primordia, epidermis and internal stem cells. We also identified previously unobserved transcriptional profiles, revealing that the stem cortex is defined early within forming primordia. Moreover, trajectory inference analysis allowed us to capture spatial control of S-phase machinery by floral homeotic genes and differentiation gene expression dynamics from internal shoot stem cells toward internal layers such as cortex, cambium, xylem and phloem. The results advance our understanding of the cellular and transcriptional heterogeneity underlying the cell-fate transcriptional dynamics shaping shoot organs and architecture.
SN  - 2375-2548
ER  -