RNA2Fun (RNA secondary structures and their relationship with function: application to non-coding RNAs) is a research project funded by the European Union – NextGenerationEU through the Italian National Recovery and Resilience Plan (NRRP) – PRIN 2022 PNRR.
RNA2Fun integrates advanced bioinformatics with state-of-the-art wet lab approaches to develop new strategies for predicting RNA-mediated regulatory circuitries and for understanding pathological aggregation processes driven by aberrant protein–RNA interactions, with a focus on neurodegenerative disorders.
A central biological case study is pCharme, a lncRNA involved in muscle differentiation that forms nuclear condensates with the multifunctional RNA/DNA-binding protein MATRIN3 (MATR3). By combining computational predictions and CRISPR-based validation, RNA2Fun aims to identify structural determinants of function that can be transferred to other RNAs.
Objectives
- Build and curate an open dataset of experimentally supported RNA secondary structures (including pseudoknots) enriched with functional annotations.
- Develop computational methods to predict, compare, and search RNA secondary structure motifs linked to molecular interactions.
- Produce and validate CRISPR-engineered cellular models to test the functional role of predicted structural domains in pCharme.
Project structure (Work Packages)
WP1 — Dataset and structural representations
Creation and maintenance of an RNA dataset with experimentally validated secondary structures and associated meta-data (function, interactions, phylogeny). Development of multiple abstractions/representations and derived features, with specific attention to molecules interacting with MATR3 and to pCharme domains.
WP2 — Structure prediction and benchmarking
Selection of folding methods (including pseudoknot-capable approaches), prediction of representative ncRNAs from different families, and benchmarking against validated structures using multiple comparison strategies and abstractions. Analysis of relationships between primary and secondary structure in selected ncRNA classes.
WP3 — pCharme secondary structure and interaction-driven modeling
Prediction and analysis of lncRNA secondary structures with emphasis on protein-binding properties. Comparative genomics of pCharme across organisms, identification of candidate intronic portions, and quantitative evaluation of candidate deletions to guide downstream experimental validation.
WP4 — Experimental validation in cellular models
Biological validation of computationally predicted RNA secondary structures within functionally relevant lncRNA modules. Gene editing design and generation of pCharme mutant hiPSC lines (KO, intronic deletions and refined module deletions) and phenotypic readouts upon in-vitro differentiation.
WP5 — Management and dissemination
Project management, scientific coordination, dissemination, and long-term maintenance of software and open resources.
Open Science
RNA2Fun follows Open Access and FAIR principles. Software, datasets, and research outputs are released through public repositories and listed in the Open Data & Software section.