Identification and analysis of dynamic RNA hubs during early murine embryonic developmentKlobučar, Tajda (Avtor) Modic, Miha (Mentor) condensationRNA hubribonucleoproteinsRIC-seqmouse embryonic stem cellsEarly mouse embryonic development proceeds through tightly regulated transitions by specific molecular mechanisms and signalling pathways. Among the implicated mechanisms, complex RNA-protein networks are emerging as important factors. While ribonucleoproteins (RNPs) are known to play a crucial role in the formation of RNP granules and biomolecular condensates, it is still unknown how and which RNA features might contribute to their formation. Here, we identified a novel class of semi-extractable and OOPS-enriched transcripts (termed smOOPs) that are dynamic during early embryonic stem cell fate transitions. This group of transcripts exhibits elevated RBP occupancy and forms larger foci, showing characteristics of condensation propensity. Furthermore, RIC-seq revealed that smOOPs are more interconnected than expected by chance, suggesting a novel higher-order transcriptome organisation. With the newly generated high-quality and high-resolution datasets, we pinpointed an RNA hub Efl1, a highly interactive and dynamic RNA hub in naive to primed pluripotency transition. Genomic depletion of Efl1 hub resulted in minor differential expression of imprinted genes, while depletion of putative binder PTBP1 led to minimal changes in expression of its interactors. Importantly, this work has laid the foundation for mechanistic studies of RNA hubs, paving the way for deciphering functional role of RNA hubs in development and beyond.[T. Klobučar]20262026-06-26 07:15:08Doktorsko delo/naloga184080sl