Browsing by Author "Irimia, Manuel"

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  • ExOrthist: a tool to infer exon orthologies at any evolutionary distance
    Márquez, Yamile; Mantica, Federica; Cozzuto, Luca; Burguera, Demián; Hermoso Pulido, Antonio; Ponomarenko, Julia; Roy, Scott W.; Irimia, Manuel (BioMed Central, 2021)
    Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes. However, no corresponding tool allows the detection of exon homology relationships. Here, we present ...
  • Gene regulatory networks of epidermal and neural fate choice in a chordate
    Leon, Anthony; Subirana, Lucie; Magre, Kevin; Cases, Ildefonso; Tena, Juan J.; Irimia, Manuel; Gómez Skarmeta, José Luis; Escriva, Hector; Bertrand, Stéphanie (Oxford University Press, 2022)
    Neurons are a highly specialized cell type only found in metazoans. They can be scattered throughout the body or grouped together, forming ganglia or nerve cords. During embryogenesis, centralized nervous systems develop ...
  • Genetic regulation of RNA splicing in human pancreatic islets
    Atla, Goutham; Bonàs-Guarch, Silvia; Cuenca-Ardura, Mirabai; Beucher, Anthony; Crouch, Daniel J.M.; García-Hurtado, Javier; Moran, Ignasi; T2DSystems Consortium; Irimia, Manuel; Prasad, Rashmi B.; Gloyn, Anna L.; Marselli, Lorella; Suleiman, Mara; Berney, Thierry; Koning, Eelco J.P. de; Kerr-Conte, Julie; Pattou, Francois; Todd, John A.; Piemonti, Lorenzo; Ferrer, Jorge (BioMed Central, 2022)
    Background: Non-coding genetic variants that influence gene transcription in pancreatic islets play a major role in the susceptibility to type 2 diabetes (T2D), and likely also contribute to type 1 diabetes (T1D) risk. For ...
  • 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, 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 ...
  • Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings
    Almudi, 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. ...
  • Huntington's disease-specific mis-splicing unveils key effector genes and altered splicing factors
    Elorza, Ainara; Márquez, Yamile; Cabrera, Jorge; Sánchez-Trincado, José Luis; Santos-Galindo, María; Hernández, Ivó H.; Picó, Sara; Díaz-Hernández, Juan I.; García-Escudero, Ramón; Irimia, Manuel; Lucas, José J. (Oxford University Press, 2021)
    Correction of mis-splicing events is a growing therapeutic approach for neurological diseases such as spinal muscular atrophy or neuronal ceroid lipofuscinosis 7, which are caused by splicing-affecting mutations. Non-mutation ...
  • Insplico: effective computational tool for studying splicing order of adjacent introns genome-wide with short and long RNA-seq reads
    Gohr, André; Iñiguez, Luis P.; Torres Méndez, Antonio, 1992-; Bonnal, Sophie; Irimia, Manuel (Oxford University Press, 2023)
    Although splicing occurs largely co-transcriptionally, the order by which introns are removed does not necessarily follow the order in which they are transcribed. Whereas several genomic features are known to influence ...
  • Major roles for pyrimidine dimers, nucleotide excision repair, and ATR in the alternative splicing response to UV irradiation
    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 ...
  • Matt: Unix tools for alternative splicing analysis
    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 ...
  • Misregulation of an activity-dependent splicing network as a common mechanism underlying autism spectrum disorders
    Quesnel-Vallières, Mathieu; Dargaei, Zahra; Irimia, Manuel; Gonatopoulos-Pournatzis, Thomas; Ip, Joanna Y.; Wu, Mingkun; Sterne-Weiler, Thimothy; Nakagawa, Shinichi; Woodin, Melanie A.; Blencowe, Benjamin J.; Cordes, Sabine P. (Elsevier, 2016)
    A key challenge in understanding and ultimately treating autism is to identify common molecular mechanisms underlying this genetically heterogeneous disorder. Transcriptomic profiling of autistic brains has revealed ...
  • Molecular basis of differential 3' splice site sensitivity to anti-tumor drugs targeting U2 snRNP
    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 ...
  • Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain
    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 ...
  • Neuronal-specific microexon splicing of TAF1 mRNA is directly regulated by SRRM4/nSR100
    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' ...
  • Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture
    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 ...
  • Parallel evolution of a splicing program controlling neuronal excitability in flies and mammals
    Torres Méndez, Antonio, 1992-; Pop, Sinziana; Bonnal, Sophie; Almudi, Isabel; Avola, Alida; Roberts, Ruairí J. V.; Paolantoni, Chiara; Alcaina-Caro, Ana; Martín-Anduaga, Ane; Haussmann, Irmgard U.; Morin, Violeta; Casares, Fernando; Soller, Matthias; Kadener, Sebastian; Roignant, Jean-Yves; Prieto-Godino, Lucia; Irimia, Manuel (American Association for the Advancement of Science (AAAS), 2022)
    Alternative splicing increases neuronal transcriptomic complexity throughout animal phylogeny. To delve into the mechanisms controlling the assembly and evolution of this regulatory layer, we characterized the neuronal ...
  • Parallel evolution of amphioxus and vertebrate small-scale gene duplications
    Brasó-Vives, Marina, 1990-; Marlétaz, Ferdinand; Echchiki, Amina; Mantica, Federica; Acemel, Rafael D.; Gómez Skarmeta, José Luis; Hartasánchez Frenk, Diego Andrés, 1982-; Le Targa, Lorlane; Pontarotti, Pierre; Tena, Juan J.; Maeso, Ignacio; Escriva, Hector; Irimia, Manuel; Robinson-Rechavi, Marc (BioMed Central, 2022)
    Background: Amphioxus are non-vertebrate chordates characterized by a slow morphological and molecular evolution. They share the basic chordate body-plan and genome organization with vertebrates but lack their 2R whole-genome ...
  • RES complex is associated with intron definition and required for zebrafish early embryogenesis
    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. ...
  • Retention of paternal DNA methylome in the developing zebrafish germline
    Skvortsova, Ksenia; Tarbashevich, Katsiaryna; Stehling, Martin; Lister, Ryan; Irimia, Manuel; Raz, Erez; Bogdanovic, Ozren (Nature Research, 2019)
    Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell (PGC) formation. However, it is currently unclear how evolutionarily ...
  • Silencing of SRRM4 suppresses microexon inclusion and promotes tumor growth across cancers
    Head, Sarah A.; Hernandez-Alias, Xavier; Yang, Jae-Seong; Ciampi, Ludovica; Beltran-Sastre, Violeta; Torres Méndez, Antonio, 1992-; Irimia, Manuel; Schaefer, Martin H.; Serrano Pubull, Luis, 1982- (Public Library of Science (PLoS), 2021)
    RNA splicing is widely dysregulated in cancer, frequently due to altered expression or activity of splicing factors (SFs). Microexons are extremely small exons (3-27 nucleotides long) that are highly evolutionarily conserved ...
  • The Integrator complex regulates differential snRNA processing and fate of adult stem cells in the highly regenerative planarian Schmidtea mediterranea
    Schmidt, David; Reuter, Hanna; Hüttner, Katja; Ruhe, Larissa; Rabert, Franziska; Seebeck, Florian; Irimia, Manuel; Solana, Jordi; Bartscherer, Kerstin (Public Library of Science (PLoS), 2018)
    In multicellular organisms, cell type diversity and fate depend on specific sets of transcript isoforms generated by post-transcriptional RNA processing. Here, we used Schmidtea mediterranea, a flatworm with extraordinary ...