Organizing your space: The potential for integrating spatial transcriptomics and 3D imaging data in plants

Plant cells communicate information for the regulation of development and responses to external stresses. A key form of this communication is transcriptional regulation, accomplished via complex gene networks operating both locally and systemically. To fully understand how genes are regulated across plant tissues and organs, high resolution, multi-dimensional spatial transcriptional data must be acquired and placed within a cellular and organismal context. Spatial transcriptomics (ST) typically provides a two-dimensional spatial analysis of gene expression of tissue sections that can be stacked to render three-dimensional data. For example, X-ray and light-sheet microscopy provide sub-micron scale volumetric imaging of cellular morphology of tissues, organs, or potentially entire organisms. Linking these technologies could substantially advance transcriptomics in plant biology and other fields. Here, we review advances in ST and 3D microscopy approaches and describe how these technologies could be combined to provide high resolution, spatially organized plant tissue transcript mapping. Combining spatial transcriptomics with 3D imaging technologies can demonstrate how genes are regulated across plant cells in a multi-dimensional space.

Automated summary

Plant cells communicate through transcriptional regulation and gene networks to control development and respond to external stresses. Acquiring high resolution, multi-dimensional spatial transcriptomic data and placing it within a cellular and organismal context is crucial for understanding gene regulation across plant tissues and organs. Combining spatial transcriptomics with 3D imaging technologies can provide insights into how genes are regulated in a multi-dimensional space.