Browsing by Author "Irimia, Manuel"

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  • Angiolini, Francesca; Irimia, Manuel; Chigna, Claudia (eLife, 2019)
    The biological players involved in angiogenesis are only partially defined. Here, we report that endothelial cells (ECs) express a novel isoform of the cell-surface adhesion molecule L1CAM, termed L1-ΔTM. The splicing ...
  • Torres Méndez, Antonio; Bonnal, Sophie; Marquez, Yamile; Roth, Jonathan; Iglesias, Marta; Permanyer, Jon; Almudí, Isabel; O'Hanlon, Dave; Guitart, Tanit; Soller, Matthias; Gingras, Anne-Claude; Gebauer, Fátima; Rentzsch, Fabian; Blencowe, Benjamin J.; Valcárcel, J. (Juan); Irimia, 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 ...
  • García-Moreno, Fernando; Anderton, Edward; Jankowska, Marta; Begbie, Jo; Encinas, Juan Manuel; Irimia, Manuel; Molnár, Zoltán (Elsevier, 2018)
    Several neuronal populations orchestrate neocortical development during mammalian embryogenesis. These include the glutamatergic subplate-, Cajal-Retzius-, and ventral pallium-derived populations, which coordinate cortical ...
  • Giampietro, Costanza; Wyatt, Chris Douglas Robert; Irimia, Manuel; Ghigna, Claudia (Nature Publishing Group, 2015)
    Vascular lumen formation is a fundamental step during angiogenesis; yet, the molecular mechanisms underlying this process are poorly understood. Recent studies have shown that neural and vascular systems share common ...
  • Marlétaz, Ferdinand; Wyatt, Christopher Douglas Robert, 1988-; Burguera, Demián; Marquez, Yamile; Irimia, Manuel (Nature Research, 2018)
    Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus ...
  • Gueroussov, Serge; Gonatopoulos-Pournatzis, Thomas; Irimia, Manuel; Raj, Bushra; Lin, Zhen-Yuan; Gingras, Anne-Claude; Blencowe, Benjamin J. (American Association for the Advancement of Science (AAAS), 2015)
    Alternative splicing (AS) generates extensive transcriptomic and proteomic complexity. However, the functions of species- and lineage-specific splice variants are largely unknown. Here we show that mammalian-specific ...
  • Touceda-Suárez, María; Kita, Elizabeth M.; Acemel, Rafael D.; Firbas, Panos N.; Magri, Marta S.; Naranjo, Silvia; Tena, Juan J.; Gómez Skarmeta, José Luis; Maeso, Ignacio; Irimia, Manuel (Oxford University Press (OUP), 2020)
    We investigated how the two rounds of whole-genome duplication that occurred at the base of the vertebrate lineage have impacted ancient microsyntenic associations involving developmental regulators (known as genomic ...
  • de Mendoza, Alex; Suga, Hiroshi; Permanyer, Jon; Irimia, 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. ...
  • Solana, Jordi; Irimia, Manuel; Ayoub, Salah; Rodriguez Orejuela, Marta; Zywitza, Vera; Jens, Marvin; Tapial, Javier; Ray, Debashish; Morris, Quaid; Hughes, Timothy R.; Blencowe, Benjamin J.; Rajewsky, Nicolaus (eLife, 2016)
    In contrast to transcriptional regulation, the function of alternative splicing (AS) in stem cells is poorly understood. In mammals, MBNL proteins negatively regulate an exon program specific of embryonic stem cells; ...
  • Maeso, Ignacio; Dunwell, Thomas L.; Wyatt, Chris Douglas Robert; Marlétaz, Ferdinand; Vető, Borbála; Bernal, Juan A.; Quah, Shan; Irimia, Manuel; Holland, Peter W. H. (BioMed Central, 2016)
    BACKGROUND: A central goal of evolutionary biology is to link genomic change to phenotypic evolution. The origin of new transcription factors is a special case of genomic evolution since it brings opportunities for novel ...
  • 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, 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 ...
  • Blazquez, Lorea; Emmett, Warren; Faraway, Rupert; Pineda, Jose Mario Bello; Bajew, Simon; Gohr, André; Haberman, Nejc; Sibley, Christopher R.; Bradley, Robert K.; Irimia, Manuel; Ule, Jernej (Elsevier, 2018)
    Recursive splicing (RS) starts by defining an "RS-exon," which is then spliced to the preceding exon, thus creating a recursive 5' splice site (RS-5ss). Previous studies focused on cryptic RS-exons, and now we find that ...
  • Almudí, Isabel; Wyatt, Christopher Douglas Robert, 1988-; Cruz, Fernando; Gómez-Garrido, Jèssica; Gut, Marta; Alioto, Tyler; Irimia, Manuel; Casares, Fernando (Nature Research, 2020)
    The evolution of winged insects revolutionized terrestrial ecosystems and led to the largest animal radiation on Earth. However, we still have an incomplete picture of the genomic changes that underlay this diversification. ...
  • Muñoz, Manuel Javier; Nieto Moreno, Nicolás; Giono, Luciana E.; Cambindo Botto, Adrián E.; Dujardin, Gwendal; Bastianello, Giulia; Lavore, Stefania; Torres Méndez, Antonio; Menck, Carlos Frederico Martins; Blencowe, Benjamin J.; Irimia, Manuel; Foiani, Marco; Kornblihtt, Alberto R. (Elsevier, 2017)
    We have previously found that UV irradiation promotes RNA polymerase II (RNAPII) hyperphosphorylation and subsequent changes in alternative splicing (AS). We show now that UV-induced DNA damage is not only necessary but ...
  • Gohr, André; Irimia, Manuel (Oxford University Press, 2019)
    Summary: Tracking thousands of alternative splicing (AS) events genome-wide makes their downstream analysis computationally challenging and laborious. Here, we present Matt, the first UNIX command-line toolkit with focus ...
  • Vigevani, Luisa, 1985-; Gohr, André; Webb, Thomas R.; Irimia, Manuel; Valcárcel, J. (Juan) (Nature Publishing Group, 2017)
    Several splicing-modulating compounds, including Sudemycins and Spliceostatin A, display anti-tumor properties. Combining transcriptome, bioinformatic and mutagenesis analyses, we delineate sequence determinants of the ...
  • Albuixech Crespo, Beatriz; López Blanch, Laura; Burguera, Demián; Maeso, Ignacio; Sánchez Arrones, Luisa; Moreno Bravo, Juan Antonio; Somorjai, Ildikó Maureen Lara; Pascual Anaya, Juan; Puelles, Eduardo; Bovolenta, Paola; García Fernàndez, Jordi; Puelles, Luis; Irimia, Manuel; Ferrán, José Luis E. (Public Library of Science (PLoS), 2017)
    All vertebrate brains develop following a common Bauplan defined by anteroposterior (AP) and dorsoventral (DV) subdivisions, characterized by largely conserved differential expression of gene markers. However, it is still ...
  • Capponi, Simona; Stöffler, Nadja; Irimia, Manuel; Van Schaik, Frederik M.A.; Ondik, Mercedes M.; Biniossek, Martin L.; Lehmann, Lisa; Mitschke, Julia; Vermunt, Marit W.; Creygthon, Menno P.; Graybiel, Ann M.; Reinheckel, Thomas; Schilling, Oliver; Blencowe, Benjamin J.; Crittenden, Jill R.; Timmers, Marc (Taylor & Francis, 2020)
    Neuronal microexons represent the most highly conserved class of alternative splicing events and their timed expression shapes neuronal biology, including neuronal commitment and differentiation. The six-nt microexon 34' ...
  • Grau Bové, Xavier; Ruiz Trillo, Iñaki; Irimia, Manuel (BioMed Central, 2018)
    Background: Alternative splicing, particularly through intron retention and exon skipping, is a major layer of pre-translational regulation in eukaryotes. While intron retention is believed to be the most prevalent mode ...
  • Fernández, Juan Pablo; Moreno Mateos, Miguel Ángel; Gohr, André; Miao, Liyun; Chan, Shun Hang; Irimia, Manuel; Giraldez, Antonio J. (Public Library of Science (PLoS), 2018)
    Pre-mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome-wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA-binding proteins. ...