Browsing by Author "Irimia Martínez, Manuel"

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  • 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 ...
  • Evolution of tissue-specific expression of ancestral genes across vertebrates and insects
    Mantica, Federica; Iñiguez, Luis P.; Marquez, Yamile; Permanyer, Jon; Torres Méndez, Antonio; Cruz, Josefa; Franch-Marro, Xavier; Burguera, Demián; Martin, David; Irimia Martínez, Manuel (Nature Research, 2024)
    Regulation of gene expression is arguably the main mechanism underlying the phenotypic diversity of tissues within and between species. Here we assembled an extensive transcriptomic dataset covering 8 tissues across 20 ...
  • Evolution of tissue-specific transcriptomes across bilaterian animals
    Mantica, Federica (Universitat Pompeu Fabra, 2023-05-25)
    Regulated Gene Expression (rGE) and Alternative Splicing (rAS) are two of the main mechanisms contributing to tissue-phenotypic diversity within and between species. In this thesis, we aim at characterizing rGE and rAS ...
  • 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 Martínez, 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 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 ...
  • 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 Martínez, 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 ...
  • 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 Martínez, 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 Martínez, 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 Martínez, 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 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 ...
  • 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 Martínez, 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. ...
  • Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences
    Yu, Daqi; Irimia Martínez, Manuel; Pascual Anaya, Juan (Nature Research, 2024)
    Polyploidy or whole-genome duplication (WGD) is a major event that drastically reshapes genome architecture and is often assumed to be causally associated with organismal innovations and radiations. The 2R hypothesis ...
  • 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 Martínez, 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 Martínez, 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 Martínez, 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 Martínez, 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 Martínez, 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 Martínez, 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 Martínez, 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 ...
  • Mouse oocytes sequester aggregated proteins in degradative super-organelles
    Zaffagnini, Gabriele; Cheng, Shiya; Salzer, Marion C.; Pernaute, Barbara; Duran, Juan M.; Irimia Martínez, Manuel; Schuh, Melina; Böke, Elvan (Elsevier, 2024)
    Oocytes are among the longest-lived cells in the body and need to preserve their cytoplasm to support proper embryonic development. Protein aggregation is a major threat for intracellular homeostasis in long-lived cells. ...

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