RNA modifications have been tacitly considered constitutive, structural’ features, unlikely to play an active role in regulating gene expression. However, this view has dramatically changed in the recent years. Pioneering studies have revealed that RNA modifications are far more widespread than previously thought, are subjected to dynamic regulation, and can have a major impact on RNA processing, stability, translation and localization, leading to the birth of the term ‘epitranscriptomics’.
The ‘epitranscriptome’ offers a novel layer of regulation, as it is capable of determining the fate of RNA molecules in terms of their localization, degradation and translation, thus tuning the cellular landscape in a space-, time- and signal-dependent manner. However, to date, transcriptome-wide maps are only available for ~5% of known RNA modifications, most of them being not quantitative and/or lacking single nucleotide resolution. For this reason, our laboratory has put significant efforts into the development of novel methods to study RNA modifications using native RNA nanopore sequencing. Specifically, we have made available the algorithms to detect m6A (Cruciani et al., bioRxiv 2023; Liu et al, Nat Comm 2019) and pseudouridine RNA modifications (Begik et al., Nat Biotech 2021), novel barcoding and demultiplexing methods for native RNA nanopore sequencing data (Smith et al., Genome Res 2020), workflows for analyzing native RNA nanopore datasets (Cozzuto et al., Front in Genet 2020), and novel method to apply native RNA nanopore sequencing to small RNA populations such as tRNAs (Lucas*, Pryszcz* et al., Nat Biotech 2023).
We are now applying these methods to:
(i) understand the role that specific RNA modifications and specialized ribosomes play during early embryo development, cellular differentiation and stress responses (MICINN Spanish National funding 2021-2024);
(ii) decipher why and how dysregulation of RNA modifications leads to diverse human diseases (Merck Innovation Grant 2021-2024);
(iii) investigate the role that RNA modifications play in the transmission of environmental epigenetic information across generations (ERC Starting Grant 2022-2027);
(iv) exploit RNA modification dysregulation for diagnostic and prognostic purposes (LAB AECC grant 2021-2024).
