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An in situ sequencing approach maps PLASTOCHRON1 at the boundary between indeterminate and determinate cells

Reinout Laureyns, Jessica Joossens (UGent) , Denia Herwegh (UGent) , Julie Pevernagie (UGent) , Benjamin Pavie, Kirin Demuynck (UGent) , Kevin Debray (UGent) , Griet Coussens (UGent) , Laurens Pauwels (UGent) , Tom Van Hautegem (UGent) , et al.
(2022) PLANT PHYSIOLOGY. 188(2). p.782-794
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Abstract
The plant shoot apex houses the shoot apical meristem, a highly organized and active stem-cell tissue where molecular signaling in discrete cells determines when and where leaves are initiated. We optimized a spatial transcriptomics approach, in situ sequencing (ISS), to colocalize the transcripts of 90 genes simultaneously on the same section of tissue from the maize (Zea mays) shoot apex. The RNA ISS technology reported expression profiles that were highly comparable with those obtained by in situ hybridizations (ISHs) and allowed the discrimination between tissue domains. Furthermore, the application of spatial transcriptomics to the shoot apex, which inherently comprised phytomers that are in gradual developmental stages, provided a spatiotemporal sequence of transcriptional events. We illustrate the power of the technology through PLASTOCHRON1 (PLA1), which was specifically expressed at the boundary between indeterminate and determinate cells and partially overlapped with ROUGH SHEATH1 and OUTER CELL LAYER4 transcripts. Also, in the inflorescence, PLA1 transcripts localized in cells subtending the lateral primordia or bordering the newly established meristematic region, suggesting a more general role of PLA1 in signaling between indeterminate and determinate cells during the formation of lateral organs. Spatial transcriptomics builds on RNA ISH, which assays relatively few transcripts at a time and provides a powerful complement to single-cell transcriptomics that inherently removes cells from their native spatial context. Further improvements in resolution and sensitivity will greatly advance research in plant developmental biology.
Keywords
Plant Science, Genetics, Physiology, SPATIAL TRANSCRIPTOMICS, EXPRESSION PATTERNS, GENE-EXPRESSION, MAIZE, CYTOKININ, TISSUE, AUXIN, INDICATE, PROTEIN, FATE

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Citation

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MLA
Laureyns, Reinout, et al. “An in Situ Sequencing Approach Maps PLASTOCHRON1 at the Boundary between Indeterminate and Determinate Cells.” PLANT PHYSIOLOGY, vol. 188, no. 2, 2022, pp. 782–94, doi:10.1093/plphys/kiab533.
APA
Laureyns, R., Joossens, J., Herwegh, D., Pevernagie, J., Pavie, B., Demuynck, K., … Nelissen, H. (2022). An in situ sequencing approach maps PLASTOCHRON1 at the boundary between indeterminate and determinate cells. PLANT PHYSIOLOGY, 188(2), 782–794. https://doi.org/10.1093/plphys/kiab533
Chicago author-date
Laureyns, Reinout, Jessica Joossens, Denia Herwegh, Julie Pevernagie, Benjamin Pavie, Kirin Demuynck, Kevin Debray, et al. 2022. “An in Situ Sequencing Approach Maps PLASTOCHRON1 at the Boundary between Indeterminate and Determinate Cells.” PLANT PHYSIOLOGY 188 (2): 782–94. https://doi.org/10.1093/plphys/kiab533.
Chicago author-date (all authors)
Laureyns, Reinout, Jessica Joossens, Denia Herwegh, Julie Pevernagie, Benjamin Pavie, Kirin Demuynck, Kevin Debray, Griet Coussens, Laurens Pauwels, Tom Van Hautegem, Michiel Bontinck, Josh Strable, and Hilde Nelissen. 2022. “An in Situ Sequencing Approach Maps PLASTOCHRON1 at the Boundary between Indeterminate and Determinate Cells.” PLANT PHYSIOLOGY 188 (2): 782–794. doi:10.1093/plphys/kiab533.
Vancouver
1.
Laureyns R, Joossens J, Herwegh D, Pevernagie J, Pavie B, Demuynck K, et al. An in situ sequencing approach maps PLASTOCHRON1 at the boundary between indeterminate and determinate cells. PLANT PHYSIOLOGY. 2022;188(2):782–94.
IEEE
[1]
R. Laureyns et al., “An in situ sequencing approach maps PLASTOCHRON1 at the boundary between indeterminate and determinate cells,” PLANT PHYSIOLOGY, vol. 188, no. 2, pp. 782–794, 2022.
@article{8731761,
  abstract     = {{The plant shoot apex houses the shoot apical meristem, a highly organized and active stem-cell tissue where molecular signaling in discrete cells determines when and where leaves are initiated. We optimized a spatial transcriptomics approach, in situ sequencing (ISS), to colocalize the transcripts of 90 genes simultaneously on the same section of tissue from the maize (Zea mays) shoot apex. The RNA ISS technology reported expression profiles that were highly comparable with those obtained by in situ hybridizations (ISHs) and allowed the discrimination between tissue domains. Furthermore, the application of spatial transcriptomics to the shoot apex, which inherently comprised phytomers that are in gradual developmental stages, provided a spatiotemporal sequence of transcriptional events. We illustrate the power of the technology through PLASTOCHRON1 (PLA1), which was specifically expressed at the boundary between indeterminate and determinate cells and partially overlapped with ROUGH SHEATH1 and OUTER CELL LAYER4 transcripts. Also, in the inflorescence, PLA1 transcripts localized in cells subtending the lateral primordia or bordering the newly established meristematic region, suggesting a more general role of PLA1 in signaling between indeterminate and determinate cells during the formation of lateral organs. Spatial transcriptomics builds on RNA ISH, which assays relatively few transcripts at a time and provides a powerful complement to single-cell transcriptomics that inherently removes cells from their native spatial context. Further improvements in resolution and sensitivity will greatly advance research in plant developmental biology.}},
  author       = {{Laureyns, Reinout and Joossens, Jessica and Herwegh, Denia and Pevernagie, Julie and Pavie, Benjamin and Demuynck, Kirin and Debray, Kevin and Coussens, Griet and Pauwels, Laurens and Van Hautegem, Tom and Bontinck, Michiel and Strable, Josh and Nelissen, Hilde}},
  issn         = {{1532-2548}},
  journal      = {{PLANT PHYSIOLOGY}},
  keywords     = {{Plant Science,Genetics,Physiology,SPATIAL TRANSCRIPTOMICS,EXPRESSION PATTERNS,GENE-EXPRESSION,MAIZE,CYTOKININ,TISSUE,AUXIN,INDICATE,PROTEIN,FATE}},
  language     = {{eng}},
  number       = {{2}},
  pages        = {{782--794}},
  title        = {{An in situ sequencing approach maps PLASTOCHRON1 at the boundary between indeterminate and determinate cells}},
  url          = {{http://doi.org/10.1093/plphys/kiab533}},
  volume       = {{188}},
  year         = {{2022}},
}
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