Comprehensive mapping of Arabidopsis alternative splicing landscape reveals key insights into plant development and immunity

Barff, Teura, Sanchez Carrillo, I. B., Parra Gutiérrez, V. P., B. Plourde, M., Joly, D. L. et Germain, H. (2025). Comprehensive mapping of Arabidopsis alternative splicing landscape reveals key insights into plant development and immunity. The Plant Genome, 18 (2). Article e70022. ISSN 1940-3372 DOI 10.1002/tpg2.70022

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Résumé

Abstract
The different steps of alternative splicing (AS) in plants and its regulatory mechanisms have already been studied extensively. Its broader impact on cell identity, plant immunity-related genes, and their study as a whole remains to be investigated. Using transgenic plants, we sorted 11 different Arabidopsis thaliana cell types ranging from root to aerial organs using fluorescence-activated cell sorting. RNA-seq data were analyzed with vast-tools and enabled us to generate a high-resolution AS landscape across multiple cell types, all collected through the same experimental procedure. The analysis of cell type-specific gene expression and alternative splicing events highlights the importance of AS on transcription and AS regulation itself. AS is also shown to be tightly linked to cell identity. By using closely related cell types, we captured alternative splicing events involved in specific stages of plant development. The columella cells, among others, show intensified AS regulation and an interesting splicing profile, especially regarding immunity-related genes. Overall, our analysis brings a valuable tool in the study of cell type identity, plant immunity, and AS.

Plain Language Summary
Although the process used by organisms to encode various proteins from the same gene (alternative splicing) has been investigated, its effects on plant cell identity and plant immunity genes are still being explored. Using transgenic plants, we sorted 11 different cell types from roots to aerial parts using fluorescence-activated cell sorting. RNA sequencing provided detailed alternative splicing information across these cell types. Our analysis revealed that AS plays a crucial role in gene expression and regulation. By examining related cell types, we identified alternative splicing events specific to plant development stages. Notably, columella cells showed significant alternative splicing regulation, especially in immunity-related genes. This research provides valuable insights into cell type identity, plant immunity, and alternative splicing.

Type de document:	Article
Date de dépôt:	28 juill. 2025 15:10
Dernière modification:	28 juill. 2025 15:10
Version du document déposé:	Version officielle de l'éditeur
URI:	https://depot-e.uqtr.ca/id/eprint/12170

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