This WP1 advances RNA characterization through the development of advanced genomic technologies and innovative applications. By integrating cutting-edge sequencing and multi-omic platforms, CRISPR-based interrogation tools, and spatial approaches, this work package builds the technological and analytical foundation of the Flagship. Its objective is to generate high-resolution insights into RNA biology and enable translational applications across research, clinical genomics, and One-Health contexts.

Genomic and multi-omic Technologies
We develop advanced genomic platforms that bridge experimental research and clinical genomics, integrating long-read and short-read sequencing workflows. These technologies operate across research and real-world settings, from hospitals to environmental and One-Health applications. Our infrastructure combines multi-omic integration—spanning transcriptomics, 3D chromatin architecture, and spatial omics—with deep phenotypic and clinical data, enabling comprehensive molecular profiling of complex diseases. Supported by dedicated bioinformatic systems and data governance frameworks, our activities align with national and European genomic strategies (such as 1+million genome, GDI and Genome of Europe).

CRISPR-based functional interrogation of RNA
We develop CRISPR-based platforms to functionally interrogate RNA-mediated mechanisms in cellular and 3D organoid models. These tools enable systematic target discovery across coding and non-coding RNAs, including the investigation of RNA modifications and regulatory pathways. By linking genomic perturbation to phenotypic outcomes, this activity strengthens mechanistic insight and supports translational research.

Nanopore-based RNA profiling
We develop experimental and computational workflows for single-molecule and single-isoform transcript profiling using Nanopore-based RNA sequencing in research and clinical samples. These platforms enable context-specific characterization of RNA isoforms and transposable element (TE) transcripts, alongside advanced epitranscriptomic analysis, with systematic assessment of RNA modifications and their impact on RNA fate and metabolism. By resolving transcript structures at full-length resolution, we redefine disease-associated transcriptomes—particularly in cancer—revealing regulatory and transcriptional mechanisms that have remained largely inaccessible to conventional short-read technologies.

Spatial and 4D RNA Imaging
We develop advanced spatial and 4D genomic approaches to study RNA at sub-cellular resolution, integrating nuclear architecture mapping with next-generation fluorescence microscopy and single-molecule imaging strategies. These technologies enable dynamic and multi-scale visualization of coding and non-coding RNAs across cellular and tissue contexts, supporting the study of RNA localization, chromatin organization, and regulatory interactions in both physiological settings and in disease contexts.