Browsing by Author "Irimia, Manuel"

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  • A developmentally programmed splicing failure contributes to DNA damage response attenuation during mammalian zygotic genome activation
    Wyatt, Christopher Douglas Robert, 1988-; Pernaute, Barbara; Gohr, André; Miret-Cuesta, Marta; Goyeneche, Lucia; Rovira, Quirze; Salzer, Marion C.; Boke, Elvan; Bogdanovic, Ozren; Bonnal, Sophie; Irimia, Manuel (American Association for the Advancement of Science (AAAS), 2022)
    Transition from maternal to embryonic transcriptional control is crucial for embryogenesis. However, alternative splicing regulation during this process remains understudied. Using transcriptomic data from human, mouse, ...
  • A novel L1CAM isoform with angiogenic activity generated by NOVA2-mediated alternative splicing
    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 ...
  • 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, 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 ...
  • Absence of tangentially migrating glutamatergic neurons in the developing avian brain
    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 ...
  • 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, 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 ...
  • The alternative splicing factor Nova2 regulates vascular development and lumen formation
    Giampietro, Costanza; Wyatt, Christopher Douglas Robert, 1988-; 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 ...
  • Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals
    Martín, Guiomar; Márquez, Yamile; Mantica, Federica; Duque, Paula; Irimia, Manuel (BioMed Central, 2021)
    Background: Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, ...
  • Amphioxus functional genomics and the origins of vertebrate gene regulation
    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 ...
  • An alternative splicing event amplifies evolutionary differences between vertebrates
    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 ...
  • 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, 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 ...
  • Ancient genomic regulatory blocks are a source for regulatory gene deserts in vertebrates after whole-genome duplications
    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 ...
  • Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals
    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. ...
  • Conservative route to genome compaction in a miniature annelid
    Irimia, Manuel; Vellutini, Bruno C.; Marlétaz, Ferdinand; Cetrangolo, Viviana; Cvetesic, Nevena; Thiel, Daniel; Henriet, Simon; Grau Bové, Xavier; Carrillo-Baltodano, Allan M.; Gu, Wenjia; Kerbl, Alexandra; Marquez, Yamile; Bekkouche, Nicolas; Chourrout, Daniel; Gómez Skarmeta, José Luis; Irimia, Manuel; Lenhard, Boris; Worsaae, Katrine; Hejnol, Andreas (Nature Research, 2020)
    The causes and consequences of genome reduction in animals are unclear because our understanding of this process mostly relies on lineages with often exceptionally high rates of evolution. Here, we decode the compact ...
  • Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians
    Solana, Jordi; Irimia, Manuel; Ayoub, Salah; Rodriguez Orejuela, Marta; Zywitza, Vera; Jens, Marvin; Tapial Rodríguez, Javier, 1990-; 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; ...
  • Cooperative epithelial phagocytosis enables error correction in the early embryo
    Hoijman, Esteban; Häkkinen, Hanna-Maria; Tolosa-Ramon, Queralt; Jiménez-Delgado, Senda; Wyatt, Christopher Douglas Robert, 1988-; Miret-Cuesta, Marta; Irimia, Manuel; Callan-Jones, Andrew; Wieser, Stefan; Ruprecht, Verena (Nature Research, 2021)
    Errors in early embryogenesis are a cause of sporadic cell death and developmental failure1,2. Phagocytic activity has a central role in scavenging apoptotic cells in differentiated tissues3-6. However, how apoptotic cells ...
  • Day-night and seasonal variation of human gene expression across tissues
    Wucher, Valentin; Sodaei, Reza, 1988-; Amador, Raziel; Irimia, Manuel; Guigó Serra, Roderic (Public Library of Science (PLoS), 2023)
    Circadian and circannual cycles trigger physiological changes whose reflection on human transcriptomes remains largely uncharted. We used the time and season of death of 932 individuals from GTEx to jointly investigate ...
  • 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, 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 origin and functional divergence of totipotent cell homeobox genes in eutherian mammals
    Maeso, Ignacio; Dunwell, Thomas L.; Wyatt, Christopher Douglas Robert, 1988-; 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 ...
  • 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, 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 ...
  • Exon junction complex shapes the transcriptome by repressing recursive splicing
    Blazquez, Lorea; Emmett, Warren; Faraway, Rupert; Pineda, Jose Mario Bello; Bajew, Simon, 1994-; 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 ...