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2. Meta-unstable mRNAs in activated CD8⁺ T cells are defined by interlinked AU-rich elements and m⁶A mRNA methylationPaulo A. Gameiro, Iosifina P. Foskolou, Yumna A. Butt, Aniek A. M. Martens, Klara Kuret, Igor Ruiz de los Mozos, Nordin D. Zandhuis, Žan Hozjan, Veronica M. Kot, Rupert Faraway, Michiel Vermeulen, Monika C. Wolkers, Randall S. Johnson, Jernej Ule, 2026, izvirni znanstveni članek Objavljeno v DiRROS: 19.02.2026; Ogledov: 527; Prenosov: 242
 Celotno besedilo (4,79 MB)
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3. Integrative profiling of condensation-prone RNAs during early developmentTajda Klobučar, Jona Novljan, Ira Alexandra Iosub, Boštjan Kokot, Iztok Urbančič, D. Marc Jones, Anob M. Chakrabarti, Nicholas M. Luscombe, Jernej Ule, Miha Modic, 2026, izvirni znanstveni članek Povzetek: Complex RNA-protein networks play a pivotal role in the formation of many types of biomolecular condensates. How RNA features contribute to condensate formation, however, remains incompletely understood. Here, we integrate tailored transcriptomics assays to identify a distinct class of developmental condensation-prone RNAs termed “smOOPs” (semi-extractable, orthogonal-organic-phase-separation-enriched RNAs). These transcripts localize to larger intracellular foci, form denser RNA subnetworks than expected, and are heavily bound by RNA-binding proteins (RBPs). Using an explainable deep learning framework, we reveal that smOOPs harbor characteristic sequence composition, with lower sequence complexity, increased intramolecular folding, and specific RBP-binding patterns. Intriguingly, these RNAs encode proteins bearing extensive intrinsically disordered regions and are highly predicted to be involved in biomolecular condensates, indicating an interplay between RNA- and protein-based features in phase separation. This work advances our understanding of condensation-prone RNAs and provides a versatile resource to further investigate RNA-driven condensation principles.
Ključne besede: condensation-prone RNAs, RNA-RNA interactions, phase separation
Objavljeno v DiRROS: 17.02.2026; Ogledov: 482; Prenosov: 274
Celotno besedilo (8,91 MB)
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4. Collective homeostasis of condensation-prone proteins via their mRNAsRupert Faraway, Neve Costello Heaven, Holly Digby, Klara Kuret, Jure Rebselj, Oscar G. Wilkins, Anob M. Chakrabarti, Ira Alexandra Iosub, Neža Vadnjal, Rhys Dore, Lea Knez, Stefan Ameres, Clemens Plaschka, Jernej Ule, 2025, izvirni znanstveni članek Objavljeno v DiRROS: 19.01.2026; Ogledov: 500; Prenosov: 719
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6. Towards in silico CLIP-seq : predicting protein-RNA interaction via sequence-to-signal learningMarc Horlacher, Nils Wagner, Lambert Moyon, Klara Kuret, Nicolas Goedert, Marco Salvatore, Jernej Ule, Julien Gagneur, Ole Winther, Annalisa Marsico, 2023, izvirni znanstveni članek Objavljeno v DiRROS: 06.09.2023; Ogledov: 1584; Prenosov: 780
Celotno besedilo (3,88 MB)
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8. TDP-43 condensation properties specify its RNA-binding and regulatory repertoireMartina Hallegger, Anob M. Chakrabarti, Flora C. Y. Lee, Bo Lim Lee, Aram-Gustav Amalietti, Hana M. Odeh, Katie E. Copley, Jack D. Rubien, Bede Portz, Klara Kuret, Ina Huppertz, Frédérique Rau, Rickie Patani, Nicolas L. Fawzi, James Shorter, Nicholas M. Luscombe, Jernej Ule, 2021, izvirni znanstveni članek Objavljeno v DiRROS: 15.12.2021; Ogledov: 4143; Prenosov: 1772
Celotno besedilo (10,35 MB)
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