Browsing by Author "Gómez Skarmeta, José Luis"

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  • An amphioxus neurula stage cell atlas supports a complex scenario for the emergence of vertebrate head mesoderm
    Grau Bové, Xavier; Subirana, Lucie; Meister, Lydvina; Soubigou, Anaël; Neto, Ana; Elek, Anamaria; Naranjo, Silvia; Fornas Carreño, Oscar; Gómez Skarmeta, José Luis; Tena, Juan J.; Irimia Martínez, Manuel; Bertrand, Stéphanie; Sebé-Pedrós, Arnau; Escriva, Hector (Nature Research, 2024)
    The emergence of new structures can often be linked to the evolution of novel cell types that follows the rewiring of developmental gene regulatory subnetworks. Vertebrates are characterized by a complex body plan compared ...
  • 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 Martínez, 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 ...
  • Characterization of new otic enhancers of the pou3f4 gene reveal distinct signaling pathway regulation and spatio-temporal patterns
    Robert Moreno, Alexandre; Naranjo, Silvia; de la Calle Mustienes, Elisa; Gómez Skarmeta, José Luis; Alsina i Español, Berta (Public Library of Science (PLoS), 2010)
    POU3F4 is a member of the POU-homedomain transcription factor family with a prominent role in inner ear development. Mutations in the human POU3F4 coding unit leads to X-linked deafness type 3 (DFN3), characterized by ...
  • Conservative route to genome compaction in a miniature annelid
    Irimia Martínez, 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; 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 ...
  • Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures
    García Pérez, Raquel, 1989-; Esteller Cucala, Paula; Mas, Glòria; Lobon Garcia, Irene; Di Carlo, Valerio; Riera, Meritxell; Kuhlwilm, Martin; Navarro i Cuartiellas, Arcadi, 1969-; Blancher, Antoine; Di Croce, Luciano; Gómez Skarmeta, José Luis; Juan, David; Marquès i Bonet, Tomàs, 1975- (Nature Research, 2021)
    Changes in the epigenetic regulation of gene expression have a central role in evolution. Here, we extensively profiled a panel of human, chimpanzee, gorilla, orangutan, and macaque lymphoblastoid cell lines (LCLs), using ...
  • 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 ...
  • Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes
    Martin, David; Guigó Serra, Roderic; Gómez Skarmeta, José Luis (Nature Research, 2011)
    Many genomic alterations associated with human diseases localize in noncoding regulatory elements located far from the promoters they regulate, making it challenging to link noncoding mutations or risk-associated variants ...
  • MacroH2As regulate enhancer-promoter contacts affecting enhancer activity and sensitivity to inflammatory cytokines
    Corujo, David; Malinverni, Roberto; Carrillo-Reixach, Juan; Meers, Oliver; Garcia-Jaraquemada, Arce; Le Pannérer, Marguerite-Marie, 1990-; Valero, Vanesa; Pérez, Ainhoa; Del Río-Álvarez, Álvaro; Royo, Laura; Pérez-González, Beatriz; Raurell Vila, Helena; Acemel, Rafael D.; Santos-Pereira, José M.; Gómez Skarmeta, José Luis; Pasquali, Lorenzo; Manyé, Josep; Armengol, Carolina; Buschbeck, Marcus (Elsevier, 2022)
    MacroH2A histone variants have a function in gene regulation that is poorly understood at the molecular level. We report that macroH2A1.2 and macroH2A2 modulate the transcriptional ground state of cancer cells and how they ...
  • Multiple enhancers located in a 1-Mb region upstream of POU3F4 promote expression during inner ear development and may be required for hearing
    Naranjo, Silvia; Voesenek, Krysta; Calle Mustienes, Elisa de la; Robert Moreno, Alexandre; Kokotas, Haris; Grigoriadou, Maria; Economides, John; Van Camp, Guy; Hilgert, Nele; Moreno, Felipe; Alsina i Español, Berta; Petersen, Michael B.; Kremer, Hannie; Gómez Skarmeta, José Luis (Springer, 2010)
    POU3F4 encodes a POU-domain transcription factor required for inner ear development. Defects in POU3F4 function are associated with X-linked deafness type 3 (DFN3). Multiple deletions affecting up to 900-kb upstream of ...
  • 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 Martínez, 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 ...
  • The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity
    Sebé-Pedrós, Arnau; Ballaré, Cecilia Julia; Parra-Acero, Helena; Chiva, Cristina; Tena, Juan J.; Sabidó Aguadé, Eduard, 1981-; Gómez Skarmeta, José Luis; Di Croce, Luciano; Ruíz Trillo, Iñaki (Elsevier, 2016)
    The unicellular ancestor of animals had a complex repertoire of genes linked to multicellular processes. This suggests that changes in the regulatory genome, rather than in gene innovation, were key to the origin of animals. ...
  • The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild
    Prado Martínez, Javier, 1987-; Hernando Herráez, Irene, 1985-; Lorente-Galdós, Belén, 1981-; Dabad, Marc; Ramírez, Oscar; Baeza Delgado, Carlos; Morcillo Suárez, Carlos, 1969-; Alkan, Can; Hormozdiari, Fereydoun; Raineri, Emanuele; Estellé, Jordi; Fernández Callejo, Marcos; Vallès, Mònica; Ritscher, Lars; Schöneberg, Torsten; Calle Mustienes, Elisa de la; Casillas, Sònia; Rubio Acero, Raquel; Melé Messeguer, Marta, 1982-; Engelken, Johannes; Cáceres Aguilar, Mario; Gómez Skarmeta, José Luis; Gut, Marta; Bertranpetit, Jaume, 1952-; Gut, Ivo Glynne; Abelló, Teresa; Eichler, Evan E.; Mingarro, Ismael; Lalueza Fox, Carles, 1965-; Navarro i Cuartiellas, Arcadi, 1969-; Marquès i Bonet, Tomàs, 1975- (BioMed Central, 2013)
    BACKGROUND: The only known albino gorilla, named Snowflake, was a male wild born individual from Equatorial Guinea who lived at the Barcelona Zoo for almost 40 years. He was diagnosed with non-syndromic oculocutaneous ...

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