The differential subcellular localization of soybean transcripts, an additional regulatory mechanism of gene activity.

backgroundOur understanding of gene function is often driven by its expression and, a fortiori, based on its RNA abundance in a cell, a tissue, or an organ. This assumption often neglects the limited correlation between RNA and protein abundance, largely due to post-transcriptional and pre-translational regulation. Among these regulatory processes, the spatial distribution of RNA molecules within cells has been reported as a major contributor of cellular function in microbial and animal systems. However, our understanding of the differential cellular distribution of transcripts in plants is very limited.

resultsIn this manuscript, using Molecular Cartography™ and Xenium, two high-resolution and sensitive spatial transcriptomic technologies, we comprehensively analyze the differential mapping of millions of plant transcripts in the nuclear and cytoplasmic compartments of various soybean nodule cell types. Our analysis reveals distinct distributions of transcripts between the nuclear and the cytoplasmic compartments of the soybean nodule cell. We also detect variability in cytoplasmic distribution among transcripts encoded by different genes and across cell types.

conclusionsOur findings reveal the strong diversity in the spatial distribution of transcripts in and between differentiated plant cells. It suggests that transcript localization serves as an additional regulatory layer beyond transcriptional control. By modulating nuclear export and cytoplasmic positioning, plant cells may fine-tune translational efficiency and gene function. This study underscores the importance of incorporating spatial information into transcriptomic analyses and provides new insights into the regulatory architecture of plant RNA biology.