Browsing by Author "Permanyer, Jon"

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  • A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons
    Torres Méndez, Antonio; Bonnal, Sophie; Marquez, Yamile; Roth, Jonathan; Iglesias, Marta; Permanyer, Jon; Almudi, Isabel; O'Hanlon, Dave; Guitart, Tanit; Soller, Matthias; Gingras, Anne-Claude; Gebauer, Fátima; Rentzsch, Fabian; Blencowe, Benjamin J.; Valcárcel, J. (Juan); Irimia Martínez, Manuel (Nature Research, 2019)
    The mechanisms by which entire programmes of gene regulation emerged during evolution are poorly understood. Neuronal microexons represent the most conserved class of alternative splicing in vertebrates, and are critical ...
  • ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics
    García-Castro, Helena; Kenny, Nathan J.; Iglesias, Marta; Álvarez Campos, Patricia; Mason, Vincent; Elek, Anamaria; Schönauer, Anna; Sleight, Victoria A.; Neiro, Jakke; Aboobaker, Aziz; Permanyer, Jon; Irimia Martínez, Manuel; Sebé-Pedrós, Arnau; Solana, Jordi (BioMed Central, 2021)
    Single-cell sequencing technologies are revolutionizing biology, but they are limited by the need to dissociate live samples. Here, we present ACME (ACetic-MEthanol), a dissociation approach for single-cell transcriptomics ...
  • An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms
    Tapial Rodríguez, Javier, 1990-; Ha, Kevin C. H.; Sterne-Weiler, Thimothy; Gohr, André; Braunschweig, Ulrich; Hermoso Pulido, Antonio; Quesnel-Vallières, Mathieu; Permanyer, Jon; Sodaei, Reza, 1988-; Marquez, Yamile; Cozzuto, Luca; Wang, Xinchen; Gómez-Velázquez, Melisa; Rayon, Teresa; Manzanares, Miguel; Ponomarenko, Julia; Blencowe, Benjamin J.; Irimia Martínez, Manuel (Cold Spring Harbor Laboratory Press (CSHL Press), 2017)
    Alternative splicing (AS) generates remarkable regulatory and proteomic complexity in metazoans. However, the functions of most AS events are not known, and programs of regulated splicing remain to be identified. To address ...
  • Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals
    de Mendoza, Alex; Suga, Hiroshi; Permanyer, Jon; Irimia Martínez, Manuel; Ruiz Trillo, Iñaki (eLife, 2015)
    Cell-type specification through differential genome regulation is a hallmark of complex multicellularity. However, it remains unclear how this process evolved during the transition from unicellular to multicellular organisms. ...
  • Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals
    de Mendoza, Alex; Suga, Hiroshi; Permanyer, Jon; Irimia Martínez, Manuel; Ruíz Trillo, Iñaki (eLife, 2015)
    Cell-type specification through differential genome regulation is a hallmark of complex multicellularity. However, it remains unclear how this process evolved during the transition from unicellular to multicellular organisms. ...
  • Environmental enrichment induces epigenomic and genome organization changes relevant for cognition
    Espeso Gil, Sergio, 1985-; Holik, Aliaksei Z.; Bonnin, Sarah; Jhanwar, Shalu, 1986-; Chandrasekaran, Sandhya; Pique Regi, Roger; Albaigès-Ràfols, Júlia; Maher, Michael; Permanyer, Jon; Irimia Martínez, Manuel; Friedländer, Marc R.; Pons Espinal, Meritxell, 1986-; Akbarian, Schahram; Dierssen, Mara; Maass, Philipp G.; Hor, Charlotte N.; Ossowski, Stephan (Frontiers, 2021)
    In early development, the environment triggers mnemonic epigenomic programs resulting in memory and learning experiences to confer cognitive phenotypes into adulthood. To uncover how environmental stimulation impacts the ...
  • Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes
    Burguera, Demián; Márquez, Yamile; Racioppi, Claudia; Permanyer, Jon; Torres Méndez, Antonio; Esposito, Rosaria; Albuixech Crespo, Beatriz; Fanlo, Lucía; D'Agostino, Ylenia; Gohr, André; Navas Pérez, Enrique; Riesgo, Ana; Cuomo, Claudia; Benvenuto, Giovanna; Christiaen, Lionel A.; Martí, Elisa; D'Aniello, Salvatore; Spagnuolo, Antonietta; Ristoratore, Filomena; Arnone, Maria Ina; García Fernàndez, Jordi; Irimia Martínez, Manuel (Nature Publishing Group, 2017)
    Epithelial-mesenchymal interactions are crucial for the development of numerous animal structures. Thus, unraveling how molecular tools are recruited in different lineages to control interplays between these tissues is key ...
  • Genome-wide transcriptomic changes reveal the genetic pathways involved in insect migration
    Doyle, Toby; Jiménez Guri, Eva; Hawkes, Will L.S.; Massy, Richard; Mantica, Federica; Permanyer, Jon; Cozzuto, Luca; Hermoso Pulido, Antonio; Baril, Tobias; Hayward, Alexander; Irimia Martínez, Manuel; Chapman, Jason W.; Bass, Chris; Wotton, Karl R. (Wiley, 2022)
    Insects are capable of extraordinary feats of long-distance movement that have profound impacts on the function of terrestrial ecosystems. The ability to undertake these movements arose multiple times through the evolution ...
  • The X-linked splicing regulator MBNL3 has been co-opted to restrict placental growth in eutherians
    Spruce, Thomas; Plass Pórtulas, Mireya, 1982-; Gohr, André; Ray, Debashish; Martínez de Lagrán Cabredo, María; Rot, Gregor; Nóvoa, Ana; Burguera, Demián; Permanyer, Jon; Miret-Cuesta, Marta; Zheng, Hong; Swanson, Maurice S.; Morris, Quaid; Mallo, Moises; Dierssen, Mara; Hughes, Timothy R.; Pernaute, Barbara; Irimia Martínez, Manuel (Public Library of Science (PLoS), 2022)
    Understanding the regulatory interactions that control gene expression during the development of novel tissues is a key goal of evolutionary developmental biology. Here, we show that Mbnl3 has undergone a striking process ...

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