Publications

Publication highlights

  • Pervasive evolution of tissue-specificity of ancestral bilaterian genes

    Nature Ecology Evolution , Apr 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 bilaterian species, and investigated the evolution of tissue-specific expression patterns of highly conserved genes between vertebrates and insects. More than 50%…

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  • Pancreatic microexons regulate islet function and glucose homeostasis

    Nature Metabolism, Feb 2023

    Pancreatic islets control glucose homeostasis by the balanced secretion of insulin and other hormones, and their abnormal function causes diabetes or hypoglycaemia. Here we uncover a conserved programme of alternative microexons included in mRNAs of islet cells, particularly in genes involved in vesicle transport and exocytosis. Islet microexons are regulated…

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  • Origin and evolution of the neural microexon programme

    Nature Ecology Evolution, Mar 2019

    Neuronal microexons represent the most conserved class of alternative splicing in vertebrates, and are critical for proper brain development and function. Here, we discover neural microexon programmes in non-vertebrate species and trace their origin to bilaterian ancestors through the emergence of a previously uncharacterized protein domain, which evolved…

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Recent publications

  • Evolutionary diversification of ancestral genes across vertebrates and insects. Mantica, F. and Irimia, M. (2024) bioRxiv. https://doi.org/10.1101/2024.06.11.598551.

  • Evolution of tissue-specific expression of ancestral genes across vertebrates and insects. Mantica, F., Iñiguez, L. P., Marquez, Y., Permanyer, J., Torres-Mendez, A., Cruz, J., Franch-Marro, X., Tulenko, F., Burguera, D., Bertrand, S., Doyle, T., Nouzova, M., Currie, P. D., Noriega, F. G., Escriva, H., Arnone, M. I., Albertin, C. B., Wotton, K. R., Almudi, I., … Irimia, M. (2024). Nature Ecology & Evolution. https://doi.org/10.1038/s41559-024-02398-5

  • Alternative splicing decouples local from global PRC2 activity. Arecco, N., Mocavini, I., Blanco, E., Ballaré, C., Libman, E., Bonnal, S., Irimia, M., & Di Croce, L. (2024). Molecular Cell, 84(6), 1049–1061.e8.

  • Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States. Ciampi, L., Serrano, L., & Irimia, M. (2024). Molecular Systems Biology, 20(4), 296–310.

  • Mouse oocytes sequester aggregated proteins in degradative super-organelles. Zaffagnini, G., Cheng, S., Salzer, M. C., Pernaute, B., Duran, J. M., Irimia, M., Schuh, M., & Böke, E. (2024). Cell, 187(5), 1109–1126.e21.

  • Pleiotropic contribution of rbfox1 to psychiatric and neurodevelopmental phenotypes in two zebrafish models. Antón-Galindo, E., Adel, M. R., García-González, J., Leggieri, A., López-Blanch, L., Irimia, M., Norton, W. H. J., Brennan, C. H., Fernàndez-Castillo, N., & Cormand, B. (2024). Translational Psychiatry, 14(1), 99.

  • Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences.Yu, D., Ren, Y., Uesaka, M., Beavan, A. J. S., Muffato, M., Shen, J., Li, Y., Sato, I., Wan, W., Clark, J. W., Keating, J. N., Carlisle, E. M., Dearden, R. P., Giles, S., Randle, E., Sansom, R. S., Feuda, R., Fleming, J. F., Sugahara, F., … Pascual-Anaya, J. (2024). Nature Ecology & Evolution, 8(3), 519–535.

2024

  • SF3B1 mutation-mediated sensitization to H3B-8800 splicing inhibitor in chronic lymphocytic leukemia. López-Oreja, I., Gohr, A., Playa-Albinyana, H., Giró, A., Arenas, F., Higashi, M., Tripathi, R., López-Guerra, M., Irimia, M., Aymerich, M., Valcárcel, J., Bonnal, S., & Colomer, D. (2023). Life Science Alliance, 6(11).

  • Specific processing of meiosis-related transcript is linked to final maturation in human oocytes. Pietroforte, S., Barragan Monasterio, M., Ferrer-Vaquer, A., Irimia, M., Ibáñez, E., Popovic, M., Vassena, R., & Zambelli, F. (2023). Molecular Human Reproduction, 29(7).

  • Insplico: effective computational tool for studying splicing order of adjacent introns genome-wide with short and long RNA-seq reads. Gohr, A., Iñiguez, L. P., Torres-Méndez, A., Bonnal, S., & Irimia, M. (2023). Nucleic Acids Research, 51(10), e56.

  • Genes enriched in A/T-ending codons are co-regulated and conserved across mammals. Benisty, H., Hernandez-Alias, X., Weber, M., Anglada-Girotto, M., Mantica, F., Radusky, L., Senger, G., Calvet, F., Weghorn, D., Irimia, M., Schaefer, M. H., & Serrano, L. (2023). Cell Systems, 14(4), 312–323.e3.

  • Pleiotropic contribution of rbfox1 to psychiatric and neurodevelopmental phenotypes in a zebrafish model. Antón-Galindo, E., Adel, M., García-Gonzalez, J., Leggieri, A., López-Blanch, L., Irimia, M., Norton, W. H., Brennan, C. H., Fernàndez-Castillo, N., & Cormand, B. (2023). bioRxiv, https://doi.org/10.1101/2023.02.23.529711.

  • A novel regulatory mechanism of actin cytoskeleton dynamics through a neural microexon in DAAM1 is necessary for memory formation. Poliński, P., Cuesta, M. M., Zamora-Moratalla, A., Mantica, F., Cantero-Recasens, G., Normanno, D., Rabago, L. I., Morenilla-Palao, C., Ordoño, P., Bonnal, S., Riera, R. G., De Lagrán Cabredo, M. M., Fernández-Blanco, Á., Rodríguez-Marin, C., Permanyer, J., Fölsz, O., Sierra, C., Legutko, D., Wojnacki, J., … Irimia, M. (2023). bioRxiv, https://doi.org/10.1101/2023.01.12.523772.

  • Alternative splicing decouples local from global PRC2 activity. Arecco, N., Mocavini, I., Blanco, E., Ballaré, C., Bonnal, S., Irimia, M., & Di Croce, L. (2023). bioRxiv, https://doi.org/10.1101/2023.04.30.538846.

2023

  • Human EWS-FLI protein recapitulates in Drosophila the neomorphic functions that induce Ewing sarcoma tumorigenesis. Molnar, C., Reina, J., Herrero, A., Heinen, J. P., Méndiz, V., Bonnal, S., Irimia, M., Sánchez-Jiménez, M., Sánchez-Molina, S., Mora, J., & Gonzalez, C. (2022). PNAS Nexus, 1(4), gac222.

  • Parallel evolution of amphioxus and vertebrate small-scale gene duplications. Brasó-Vives, M., Marlétaz, F., Echchiki, A., Mantica, F., Acemel, R. D., Gómez-Skarmeta, J. L., Hartasánchez, D. A., Le Targa, L., Pontarotti, P., Tena, J. J., Maeso, I., Escriva, H., Irimia, M., & Robinson-Rechavi, M. (2022). Genome Biology, 23(1), 243.

  • Genetic regulation of RNA splicing in human pancreatic islets. Atla, G., Bonàs-Guarch, S., Cuenca-Ardura, M., Beucher, A., Crouch, D. J. M., Garcia-Hurtado, J., Moran, I., T2DSystems Consortium, Irimia, M., Prasad, R. B., Gloyn, A. L., Marselli, L., Suleiman, M., Berney, T., de Koning, E. J. P., Kerr-Conte, J., Pattou, F., Todd, J. A., Piemonti, L., & Ferrer, J. (2022). Genome Biology, 23(1), 196.

  • The 3D-Evo Space: Evolution of Gene Expression and Alternative Splicing Regulation. Mantica, F., & Irimia, M. (2022). Annual Review of Genetics, 56, 315–337.

  • Systematic exploration of dynamic splicing networks reveals conserved multistage regulators of neurogenesis. Han, H., Best, A. J., Braunschweig, U., Mikolajewicz, N., Li, J. D., Roth, J., Chowdhury, F., Mantica, F., Nabeel-Shah, S., Parada, G., Brown, K. R., O’Hanlon, D., Wei, J., Yao, Y., Zid, A. A., Comsa, L. C., Jen, M., Wang, J., Datti, A., … Blencowe, B. J. (2022). Molecular Cell, 82(16), 2982–2999.e14.

  • Computational Analysis of Alternative Splicing Using VAST-TOOLS and the VastDB Framework. Gohr, A., Mantica, F., Hermoso-Pulido, A., Tapial, J., Márquez, Y., & Irimia, M. (2022). Methods in Molecular Biology, 2537, 97–128.

  • Specialization of the photoreceptor transcriptome by Srrm3-dependent microexons is required for outer segment maintenance and vision. Ciampi, L., Mantica, F., López-Blanch, L., Permanyer, J., Rodriguez-Marín, C., Zang, J., Cianferoni, D., Jiménez-Delgado, S., Bonnal, S., Miravet-Verde, S., Ruprecht, V., Neuhauss, S. C. F., Banfi, S., Carrella, S., Serrano, L., Head, S. A., & Irimia, M. (2022). PNAS, 119(29), e2117090119.

  • Genome-wide transcriptomic changes reveal the genetic pathways involved in insect migration. Doyle, T., Jimenez-Guri, E., Hawkes, W. L. S., Massy, R., Mantica, F., Permanyer, J., Cozzuto, L., Hermoso Pulido, T., Baril, T., Hayward, A., Irimia, M., Chapman, J. W., Bass, C., & Wotton, K. R. (2022). Molecular Ecology, 31(16), 4332–4350.

  • Best practice standards for circular RNA research. Nielsen, A. F., Bindereif, A., Bozzoni, I., Hanan, M., Hansen, T. B., Irimia, M., Kadener, S., Kristensen, L. S., Legnini, I., Morlando, M., Jarlstad Olesen, M. T., Pasterkamp, R. J., Preibisch, S., Rajewsky, N., Suenkel, C., & Kjems, J. (2022). Nature Methods, 19(10), 1208–1220.

  • The X-linked splicing regulator MBNL3 has been co-opted to restrict placental growth in eutherians. Spruce, T., Plass, M., Gohr, A., Ray, D., Martínez de Lagrán, M., Rot, G., Nóvoa, A., Burguera, D., Permanyer, J., Miret, M., Zheng, H., Swanson, M. S., Morris, Q., Mallo, M., Dierssen, M., Hughes, T. R., Pernaute, B., & Irimia, M. (2022). PLoS Biology, 20(4), e3001615.

  • A developmentally programmed splicing failure contributes to DNA damage response attenuation during mammalian zygotic genome activation. Wyatt, C. D. R., Pernaute, B., Gohr, A., Miret-Cuesta, M., Goyeneche, L., Rovira, Q., Salzer, M. C., Boke, E., Bogdanovic, O., Bonnal, S., & Irimia, M. (2022). Science Advances, 8(15), eabn4935.

  • Gene Regulatory Networks of Epidermal and Neural Fate Choice in a Chordate. Leon, A., Subirana, L., Magre, K., Cases, I., Tena, J. J., Irimia, M., Gomez-Skarmeta, J. L., Escriva, H., & Bertrand, S. (2022). Molecular Biology and Evolution, 39(4), msac055.

  • Gene architecture directs splicing outcome in separate nuclear spatial regions. Tammer, L., Hameiri, O., Keydar, I., Roy, V. R., Ashkenazy-Titelman, A., Custódio, N., Sason, I., Shayevitch, R., Rodríguez-Vaello, V., Rino, J., Lev Maor, G., Leader, Y., Khair, D., Aiden, E. L., Elkon, R., Irimia, M., Sharan, R., Shav-Tal, Y., Carmo-Fonseca, M., & Ast, G. (2022). Molecular Cell, 82(5), 1021–1034.e8.

  • Parallel evolution of a splicing program controlling neuronal excitability in flies and mammals. Torres-Méndez, A., Pop, S., Bonnal, S., Almudi, I., Avola, A., Roberts, R. J. V., Paolantoni, C., Alcaina-Caro, A., Martín-Anduaga, A., Haussmann, I. U., Morin, V., Casares, F., Soller, M., Kadener, S., Roignant, J.-Y., Prieto-Godino, L., & Irimia, M. (2022). Science Advances, 8(4), eabk0445.

  • Is There a Prechordal Region and an Acroterminal Domain in Amphioxus? Ferran, J. L., Irimia, M., & Puelles, L. (2022). Brain, Behavior and Evolution, 96(4-6), 334–352.

2022

  • ExOrthist: a tool to infer exon orthologies at any evolutionary distance. Márquez, Y., Mantica, F., Cozzuto, L., Burguera, D., Hermoso-Pulido, A., Ponomarenko, J., Roy, S. W., & Irimia, M. (2021). Genome Biology, 22(1), 239.

  • Environmental Enrichment Induces Epigenomic and Genome Organization Changes Relevant for Cognition. Espeso-Gil, S., Holik, A. Z., Bonnin, S., Jhanwar, S., Chandrasekaran, S., Pique-Regi, R., Albaigès-Ràfols, J., Maher, M., Permanyer, J., Irimia, M., Friedländer, M. R., Pons-Espinal, M., Akbarian, S., Dierssen, M., Maass, P. G., Hor, C. N., & Ossowski, S. (2021). Frontiers in Molecular Neuroscience, 14, 664912.

  • ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics. García-Castro, H., Kenny, N. J., Iglesias, M., Álvarez-Campos, P., Mason, V., Elek, A., Schönauer, A., Sleight, V. A., Neiro, J., Aboobaker, A., Permanyer, J., Irimia, M., Sebé-Pedrós, A., & Solana, J. (2021). Genome Biology, 22(1), 89.

  • Huntington’s disease-specific mis-splicing unveils key effector genes and altered splicing factors. Elorza, A., Márquez, Y., Cabrera, J. R., Sánchez-Trincado, J. L., Santos-Galindo, M., Hernández, I. H., Picó, S., Díaz-Hernández, J. I., García-Escudero, R., Irimia, M., & Lucas, J. J. (2021). Brain, 144(7), 2009–2023.

  • Silencing of SRRM4 suppresses microexon inclusion and promotes tumor growth across cancers. Head, S. A., Hernandez-Alias, X., Yang, J.-S., Ciampi, L., Beltran-Sastre, V., Torres-Méndez, A., Irimia, M., Schaefer, M. H., & Serrano, L. (2021). PLoS Biology, 19(2), e3001138.

  • Cooperative epithelial phagocytosis enables error correction in the early embryo. Hoijman, E., Häkkinen, H.-M., Tolosa-Ramon, Q., Jiménez-Delgado, S., Wyatt, C., Miret-Cuesta, M., Irimia, M., Callan-Jones, A., Wieser, S., & Ruprecht, V. (2021). Nature, 590(7847), 618–623.

  • Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals. Martín, G., Márquez, Y., Mantica, F., Duque, P., & Irimia, M. (2021). Genome Biology, 22(1), 35.

  • Conservative route to genome compaction in a miniature annelid. Martín-Durán, J. M., Vellutini, B. C., Marlétaz, F., Cetrangolo, V., Cvetesic, N., Thiel, D., Henriet, S., Grau-Bové, X., Carrillo-Baltodano, A. M., Gu, W., Kerbl, A., Marquez, Y., Bekkouche, N., Chourrout, D., Gómez-Skarmeta, J. L., Irimia, M., Lenhard, B., Worsaae, K., & Hejnol, A. (2021). Nature Ecology & Evolution, 5(2), 231–242.

  • Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings. Almudi, I., Vizueta, J., Wyatt, C. D. R., de Mendoza, A., Marlétaz, F., Firbas, P. N., Feuda, R., Masiero, G., Medina, P., Alcaina-Caro, A., Cruz, F., Gómez-Garrido, J., Gut, M., Alioto, T. S., Vargas-Chavez, C., Davie, K., Misof, B., González, J., Aerts, S., … Casares, F. (2020). Nature Communications, 11(1), 2631.

2021

  • Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome Duplications. Touceda-Suárez, M., Kita, E. M., Acemel, R. D., Firbas, P. N., Magri, M. S., Naranjo, S., Tena, J. J., Gómez-Skarmeta, J. L., Maeso, I., & Irimia, M. (2020). Molecular Biology and Evolution, 37(10), 2857–2864.

  • Autism-Misregulated eIF4G Microexons Control Synaptic Translation and Higher Order Cognitive Functions. Gonatopoulos-Pournatzis, T., Niibori, R., Salter, E. W., Weatheritt, R. J., Tsang, B., Farhangmehr, S., Liang, X., Braunschweig, U., Roth, J., Zhang, S., Henderson, T., Sharma, E., Quesnel-Vallières, M., Permanyer, J., Maier, S., Georgiou, J., Irimia, M., Sonenberg, N., Forman-Kay, J. D., … Blencowe, B. J. (2020). Molecular Cell, 77(6), 1176–1192.e16.

  • Neuronal-specific microexon splicing of TAF1 mRNA is directly regulated by SRRM4/nSR100. Capponi, S., Stöffler, N., Irimia, M., Van Schaik, F. M. A., Ondik, M. M., Biniossek, M. L., Lehmann, L., Mitschke, J., Vermunt, M. W., Creyghton, M. P., Graybiel, A. M., Reinheckel, T., Schilling, O., Blencowe, B. J., Crittenden, J. R., & Timmers, H. T. M. (2020). RNA Biology, 17(1), 62–74.

2020

  • Retention of paternal DNA methylome in the developing zebrafish germline. Skvortsova, K., Tarbashevich, K., Stehling, M., Lister, R., Irimia, M., Raz, E., & Bogdanovic, O. (2019). Nature Communications, 10(1), 3054.

  • Srrm234, but not canonical SR and hnRNP proteins, drive inclusion of Dscam exon 9 variable exons. Ustaoglu, P., Haussmann, I. U., Liao, H., Torres-Mendez, A., Arnold, R., Irimia, M., & Soller, M. (2019). RNA , 25(10), 1353–1365.

  • A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons. Torres-Méndez, A., Bonnal, S., Marquez, Y., Roth, J., Iglesias, M., Permanyer, J., Almudí, I., O’Hanlon, D., Guitart, T., Soller, M., Gingras, A.-C., Gebauer, F., Rentzsch, F., Blencowe, B. J., Valcárcel, J., & Irimia, M. (2019). Nature Ecology & Evolution, 3(4), 691–701.

  • A novel L1CAM isoform with angiogenic activity generated by NOVA2-mediated alternative splicing. Angiolini, F., Belloni, E., Giordano, M., Campioni, M., Forneris, F., Paronetto, M. P., Lupia, M., Brandas, C., Pradella, D., Di Matteo, A., Giampietro, C., Jodice, G., Luise, C., Bertalot, G., Freddi, S., Malinverno, M., Irimia, M., Moulton, J. D., Summerton, J., … Ghigna, C. (2019). eLife, 8.

  • ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development. Magomedova, L., Tiefenbach, J., Zilberman, E., Le Billan, F., Voisin, V., Saikali, M., Boivin, V., Robitaille, M., Gueroussov, S., Irimia, M., Ray, D., Patel, R., Xu, C., Jeyasuria, P., Bader, G. D., Hughes, T. R., Morris, Q. D., Scott, M. S., Krause, H., … Cummins, C. L. (2019). Nucleic Acids Research, 47(6), 2856–2870.

  • Matt: Unix tools for alternative splicing analysis. Gohr, A., & Irimia, M. (2019). Bioinformatics , 35(1), 130–132.

2019

  • The Integrator complex regulates differential snRNA processing and fate of adult stem cells in the highly regenerative planarian Schmidtea mediterranea. Schmidt, D., Reuter, H., Hüttner, K., Ruhe, L., Rabert, F., Seebeck, F., Irimia, M., Solana, J., & Bartscherer, K. (2018). PLoS Genetics, 14(12), e1007828.

  • Amphioxus functional genomics and the origins of vertebrate gene regulation. Marlétaz, F., Firbas, P. N., Maeso, I., Tena, J. J., Bogdanovic, O., Perry, M., Wyatt, C. D. R., de la Calle-Mustienes, E., Bertrand, S., Burguera, D., Acemel, R. D., van Heeringen, S. J., Naranjo, S., Herrera-Ubeda, C., Skvortsova, K., Jimenez-Gancedo, S., Aldea, D., Marquez, Y., Buono, L., … Irimia, M. (2018). Nature, 564(7734), 64–70.

  • Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing. Blazquez, L., Emmett, W., Faraway, R., Pineda, J. M. B., Bajew, S., Gohr, A., Haberman, N., Sibley, C. R., Bradley, R. K., Irimia, M., & Ule, J. (2018). Molecular Cell, 72(3), 496–509.e9.

  • Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture. Grau-Bové, X., Ruiz-Trillo, I., & Irimia, M. (2018). Genome Biology, 19(1), 135.

  • Autism-like phenotype and risk gene mRNA deadenylation by CPEB4 mis-splicing. Parras, A., Anta, H., Santos-Galindo, M., Swarup, V., Elorza, A., Nieto-González, J. L., Picó, S., Hernández, I. H., Díaz-Hernández, J. I., Belloc, E., Rodolosse, A., Parikshak, N. N., Peñagarikano, O., Fernández-Chacón, R., Irimia, M., Navarro, P., Geschwind, D. H., Méndez, R., & Lucas, J. J. (2018). Nature, 560(7719), 441–446.

  • RES complex is associated with intron definition and required for zebrafish early embryogenesis. Fernandez, J. P., Moreno-Mateos, M. A., Gohr, A., Miao, L., Chan, S. H., Irimia, M., & Giraldez, A. J. (2018). PLoS Genetics, 14(7), e1007473.

  • Absence of Tangentially Migrating Glutamatergic Neurons in the Developing Avian Brain. García-Moreno, F., Anderton, E., Jankowska, M., Begbie, J., Encinas, J. M., Irimia, M., & Molnár, Z. (2018). Cell Reports, 22(1), 96–109.

2018