Browsing Center for Genomic Regulation (CRG) by Title

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  • N6-methyladenosine modification is not a general trait of viral RNA genomes
    Baquero Pérez, Belinda; Yonchev, Ivaylo D.; Delgado-Tejedor, Anna; Medina, Rebeca; Puig-Torrents, Mireia; Sudbery, Ian; Begik, Oguzhan; Wilson, Stuart A.; Novoa, Eva Maria; Díez Antón, Juana, 1962- (Nature Research, 2024)
    Despite the nuclear localization of the m6A machinery, the genomes of multiple exclusively-cytoplasmic RNA viruses, such as chikungunya (CHIKV) and dengue (DENV), are reported to be extensively m6A-modified. However, these ...
  • NADPH oxidase 4 (Nox4) deletion accelerates liver regeneration in mice
    Herranz-Itúrbe, Macarena; López-Luque, Judit; Gonzalez-Sanchez, Ester; Caballero-Díaz, Daniel; Crosas-Molist, Eva; Martín-Mur, Beatriz; Gut, Marta; Esteve-Codina, Anna; Jaquet, Vincent; Jiang, Joy X.; Török, Natalie J.; Fabregat, Isabel (Elsevier, 2021)
    Liver is a unique organ in displaying a reparative and regenerative response after acute/chronic damage or partial hepatectomy, when all the cell types must proliferate to re-establish the liver mass. The NADPH oxidase ...
  • Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing
    Begik, Oguzhan; Diensthuber, Gregor; Liu, Huanle; Delgado-Tejedor, Anna; Kontur, Cassandra; Niazi, Adnan Muhammad; Valen, Eivind; Giraldez, Antonio J.; Beaudoin, Jean-Denis; Mattick, John S.; Novoa, Eva Maria (Nature Research, 2023)
    RNA polyadenylation plays a central role in RNA maturation, fate, and stability. In response to developmental cues, polyA tail lengths can vary, affecting the translation efficiency and stability of mRNAs. Here we develop ...
  • NEAT1 long isoform is highly expressed in chronic lymphocytic leukemia irrespectively of cytogenetic groups or clinical outcome
    Ronchetti, Domenica; Favasuli, Vanessa; Monti, Paola; Cutrona, Giovanna; Fabris, Sonia; Silvestris, Ilaria; Agnelli, Luca; Colombo, Monica; Menichini, Paola; Matis, Serena; Gentile, Massimo; Nurtdinov, Ramil; Guigó Serra, Roderic; Baldini, Luca; Fronza, Gilberto; Ferrarini, Manlio; Morabito, Fortunato; Neri, Antonino; Taiana, Elisa (MDPI, 2020)
    The biological role and therapeutic potential of long non-coding RNAs (lncRNAs) in chronic lymphocytic leukemia (CLL) are still open questions. Herein, we investigated the significance of the lncRNA NEAT1 in CLL. We examined ...
  • Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome
    Zapata Ortiz, Luis, 1985-; Pich, Oriol; Serrano Pubull, Luis, 1982-; Kondrashov, Fyodor A., 1979-; Ossowski, Stephan; Schaefer, Martin H. (BioMed Central, 2018)
    Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic ...
  • Nek9 phosphorylation defines a new role for TPX2 in Eg5-dependent centrosome separation before nuclear envelope breakdown
    Eibes, Susana; Gallisà-Suñé, Núria; Rosas Salvans, Miquel, 1987-; Martínez-Delgado, Paula; Vernos, Isabelle, 1959-; Roig, Joan (Elsevier, 2018)
    Centrosomes [1, 2] play a central role during spindle assembly in most animal cells [3]. In early mitosis, they organize two symmetrical microtubule arrays that upon separation define the two poles of the forming spindle. ...
  • Neonatal diabetes mutations disrupt a chromatin pioneering function that activates the human insulin gene
    Akerman, Ildem; Maestro, Miguel Ángel; De Franco, Elisa; Grau, Vanessa; Flanagan, Sarah; García-Hurtado, Javier; Mittler, Gerhard; Ravassard, Philippe; Piemonti, Lorenzo; Ellard, Sian; Hattersley, Andrew T.; Ferrer, Jorge (Elsevier, 2021)
    Despite the central role of chromosomal context in gene transcription, human noncoding DNA variants are generally studied outside of their genomic location. This limits our understanding of disease-causing regulatory ...
  • Network analysis of Down syndrome and SARS-CoV-2 identifies risk and protective factors for COVID-19
    De Toma, Ilario; Dierssen, Mara (Nature Research, 2021)
    SARS-CoV-2 infection has spread uncontrollably worldwide while it remains unknown how vulnerable populations, such as Down syndrome (DS) individuals are affected by the COVID-19 pandemic. Individuals with DS have more risk ...
  • Network-based proteomic approaches reveal the neurodegenerative, neuroprotective and pain-related mechanisms involved after retrograde axonal damage
    Casas, Caty; Isús Díaz, Laura, 1989-; Herrando Grabulosa, Mireia; Mancuso, Francesco M.; Borrás, Eva; Sabidó Aguadé, Eduard, 1981-; Forés, Joaquim; Aloy, Patrick, 1972- (Nature Publishing Group, 2015)
    Neurodegenerative processes are preceded by neuronal dysfunction and synaptic disconnection. Disconnection between spinal motoneuron (MN) soma and synaptic target leads either to a retrograde degenerative process or to a ...
  • Neurodegeneration and cancer: where the disorder prevails
    Klus, Petr, 1985-; Cirillo, Davide; Botta Orfila, Teresa; Tartaglia, Gian Gaetano (Nature Publishing Group, 2015)
    It has been reported that genes up-regulated in cancer are often down-regulated in neurodegenerative disorders and vice versa. The fact that apparently unrelated diseases share functional pathways suggests a link between ...
  • Neurodegenerative diseases: quantitative predictions of protein-RNA interactions
    Cirillo, Davide; Agostini, Federico, 1985-; Klus, Petr, 1985-; Marchese, Domenica, 1986-; Rodríguez, Silvia; Bolognesi, Benedetta; Tartaglia, Gian Gaetano (Cold Spring Harbor Laboratory Press (CSHL Press), 2013)
    Increasing evidence indicates that RNA plays an active role in a number of neurodegenerative diseases. We recently introduced a theoretical framework, catRAPID, to predict the binding ability of protein and RNA molecules. ...
  • Neurodevelopmental disorders: 2023 update
    Carriba, Paulina; Lorenzon, Nicola; Dierssen, Mara (University of Münster, 2023)
    Several advances in the field of neurodevelopmental diseases (NDDs) have been reported by 2022. Of course, NDDs comprise a diverse group of disorders, most of which with different aetiologies. However, owing to the development ...
  • Neuromuscular junction changes in a mouse model of charcot-marie-tooth disease type 4C
    Cipriani, Silvia; Phan, Vietxuan; Médard, Jean-Jacques; Horvath, Rita; Lochmüller, Hanns; Chrast, Roman; Roos, Andreas; Spendiff, Sally (MDPI, 2018)
    The neuromuscular junction (NMJ) appears to be a site of pathology in a number of peripheral nerve diseases. Charcot-Marie-Tooth (CMT) 4C is an autosomal recessive, early onset, demyelinating neuropathy. Numerous mutations ...
  • Neuronal temperature perception induces specific defenses that enable C. elegans to cope with the enhanced reactivity of hydrogen peroxide at high temperature
    Servello, Francesco A.; Fernandes, Rute; Eder, Matthias; Harris, Nathan; Martin, Olivier M. F.; Oswal, Natasha; Lindberg, Anders; Derosiers, Nohelly; Sengupta, Piali; Stroustrup, Nicholas; Apfeld, Javier (eLife, 2022)
    Hydrogen peroxide is the most common reactive chemical that organisms face on the microbial battlefield. The rate with which hydrogen peroxide damages biomolecules required for life increases with temperature, yet little ...
  • Neuronal-specific microexon splicing of TAF1 mRNA is directly regulated by SRRM4/nSR100
    Capponi, Simona; Stöffler, Nadja; Irimia Martínez, 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' ...
  • New factors for protein transport identified by a genome-wide CRISPRi screen in mammalian cells
    Bassaganyas Bars, Laia, 1985-; Popa, Stephanie J.; Horlbeck, Max; Puri, Claudia; Stewart, Sarah E.; Campelo, Felix; Ashok, Anupama, 1985-; Butnaru, Cristian M.; Brouwers, Nathalie; Heydari, Kartoosh; Ripoche, Jean; Weissman, Jonathan; Rubinsztein, David C.; Schekman, Randy; Malhotra, Vivek; Moreau, Kevin; Villeneuve, Julien (Rockefeller University Press, 2019)
    Protein and membrane trafficking pathways are critical for cell and tissue homeostasis. Traditional genetic and biochemical approaches have shed light on basic principles underlying these processes. However, the list of ...
  • New genes involved in Angelman syndrome-like: expanding the genetic spectrum
    Aguilera, Cinthia; Gabau, Elisabeth; Ramirez-Mallafré, Ariadna; Brun i Gasca, Carme; Dominguez-Carral, Jana; Delgadillo, Veronica; Laurie, Steven, 1973-; Derdak, Sophia; Padilla, Natàlia; Cruz, Xavier de la; Capdevila, Núria; Spataro, Nino, 1984-; Baena, Neus; Guitart, Miriam; Ruiz, Anna (Public Library of Science (PLoS), 2021)
    Angelman syndrome (AS) is a neurogenetic disorder characterized by severe developmental delay with absence of speech, happy disposition, frequent laughter, hyperactivity, stereotypies, ataxia and seizures with specific EEG ...
  • New murine Niemann-Pick type C models bearing a pseudoexon-generating mutation recapitulate the main neurobehavioural and molecular features of the disease
    Gómez Grau, Marta; Albaigès-Ràfols, Júlia; Casas, Josefina; Auladell, Carme; Dierssen, Mara; Vilageliu, Lluïsa; Grinberg, Daniel (Nature Publishing Group, 2017)
    Niemann-Pick disease type C (NPC) is a rare neurovisceral disease caused mainly by mutations in the NPC1 gene. This autosomal recessive lysosomal disorder is characterised by the defective lysosomal secretion of cholesterol ...
  • New origin firing is inhibited by APC/CCdh1 activation in S-phase after severe replication stress
    Ercilla, Amaia; Llopis, Alba; Feu, Sonia; Aranda Aragón, Sergio; Ernfors, Patrik; Freire, Raimundo; Agell, Neus (Oxford University Press, 2016)
    Defects in DNA replication and repair are known to promote genomic instability, a hallmark of cancer cells. Thus, eukaryotic cells have developed complex mechanisms to ensure accurate duplication of their genomes. While ...
  • New spinocerebellar ataxia subtype caused by SAMD9L mutation triggering mitochondrial dysregulation (SCA49)
    Corral Juan, Marc; Casquero, Pilar; Giraldo-Restrepo, Natalia; Laurie, Steven, 1973-; Martinez-Piñeiro, Alicia; Mateo-Montero, Raidili Cristina; Ispierto, Lourdes; Vilas, Dolores; Tolosa, Eduard; Volpini, Victor; Alvarez-Ramo, Ramiro; Sánchez, Ivelisse; Matilla Dueñas, Antoni (Oxford University Press, 2022)
    Spinocerebellar ataxias consist of a highly heterogeneous group of inherited movement disorders clinically characterized by progressive cerebellar ataxia variably associated with additional distinctive clinical signs. The ...

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