Decoding plant RNA localization sequences and structural signals (D-POLARIS)

Cellular RNA localization determines transcript fate by controlling its distribution between chromatin, nucleus and cytoplasm. Studies in animal cells have identified a limited number of sequence motifs linked to compartmentalization, but these motifs are often broadly defined and not readily generalizable across species, cell types or conditions. RNA molecules can adopt diverse spatial structures that are involved in various aspects of RNA metabolism. RNA structure has therefore been proposed as an additional layer that regulates RNA subcellular localization.I aim to deliver the first comprehensive decoding of RNA localization rules in plants by combining compartment-resolved RNA-seq fractionation, in vivo RNA structure profiling, massively parallel reporter assay (MPRA), and AI-driven analyses. Building on my preliminary compartment-resolved RNA-seq fractionation datasets from chromatin-associated, nuclear and cytosolic fractions under control and cold conditions, I will (1) generate compartment-resolved in vivo RNA secondary-structure maps in Arabidopsis, (2) use MPRA to identify and validate sequence–structure motifs that regulate subcellular localization using both traditional bioinformatic and AI-driven modelling to refine motif discovery. (3) Motifs identified through integrated analysis will be validated in native gene contexts via transient expression in Arabidopsis protoplasts and stable complementation of T-DNA mutants with wild-type and motif-altered constructs. Additionally, I will assess whether these motif-driven localization changes cause measurable phenotypic effects.The outputs will establish a promising conceptual framework for harnessing RNA localization as a regulatory layer of gene expression in plants. Hosted at the John Innes Centre, I shall benefit from advanced training in RNA biology, molecular genetics and AI-driven analysis, complemented by opportunities to boost my professional visibility, leadership capacity and employability.