Browsing Center for Genomic Regulation (CRG) by Title

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  • A complex secretory program orchestrated by the inflammasome controls paracrine senescence
    Acosta, Juan Carlos; Banito, Ana; Wuestefeld, Torsten; Georgilis, Athena; Janich, Peggy, 1981-; Morton, Jennifer P.; Athineos, Dimitris; Kang, Tae-Won; Lasitschka, Felix; Andrulis, Mindaugas; Pascual, Gloria; Morris, Kelly J.; Khan, Sadaf; Jin, Hong; Dharmalingam, Gopuraja; Snijders, Ambrosius P.; Carroll, Thomas; Capper, David; Pritchard, Catrin; Inman, Gareth J.; Longerich, Thomas; Sansom, Owen J.; Aznar Benitah, Salvador; Zender, Lars; Gil, Jesús (Nature Publishing Group, 2013)
    Oncogene-induced senescence (OIS) is crucial for tumour suppression. Senescent cells implement a complex pro-inflammatory response termed the senescence-associated secretory phenotype (SASP). The SASP reinforces senescence, ...
  • A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing
    Alioto, Tyler; Derdak, Sophia; Ribeca, Paolo; Castro Giner, Francesc; Beltran, Sergi; Raineri, Emanuele; Dabad, Marc; Heath, Simon; Gut, Marta; Gut, Ivo Glynne (Nature Research, 2015)
    As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different ...
  • A comprehensive proteomics-based interaction screen that links DYRK1A to RNF169 and to the DNA damage response
    Roewenstrunk, Julia Maria, 1981-; Di Vona, Chiara, 1981-; Chen, Jie; Borràs, Eva; Dong, Chao; Arató, Krisztina, 1981-; Sabidó Aguadé, Eduard, 1981-; Huen, Michael S. Y.; Luna Gargantilla, Susana de la (Nature Research, 2019)
    Dysregulation of the DYRK1A protein kinase has been associated with human disease. On the one hand, its overexpression in trisomy 21 has been linked to certain pathological traits of Down syndrome, while on the other, ...
  • A comprehensive view of the ß-arrestinome
    Crépieux, Pascale; Poupon, Anne; Langonné Gallay, Nathalie; Reiter, Éric R.; Delgado Blanco, Javier; Schaefer, Martin H.; Bourquard, Thomas; Serrano Pubull, Luis, 1982-; Kiel, Christina (Frontiers, 2017)
    G protein-coupled receptors (GPCRs) are membrane receptors critically involved in sensing the environment and orchestrating physiological processes. As such, they transduce extracellular signals such as hormone, ...
  • A computational approach for the discovery of protein-RNA networks
    Marchese, Domenica, 1986-; Livi, Carmen Maria; Tartaglia, Gian Gaetano (Humana Press (Springer Imprint), 2016)
    Protein–RNA interactions play important roles in a wide variety of cellular processes, ranging from transcriptional and posttranscriptional regulation of genes to host defense against pathogens. In this chapter we present ...
  • A computational clonal analysis of the developing mouse limb bud
    Marcon, Luciano, 1983-; Arqués, Carlos G.; Torres, Miguel S.; Sharpe, James (Public Library of Science (PLoS), 2011)
    A comprehensive spatio-temporal description of the tissue movements underlying organogenesis would be an extremely useful resource to developmental biology. Clonal analysis and fate mappings are popular experiments to study ...
  • A computational pipeline to learn gene expression predictive models from epigenetic information at enhancers or promoters
    González Ramírez, Mar, 1991-; Blanco, Enrique; Di Croce, Luciano (Elsevier, 2023)
    Here, we present a computational pipeline to obtain quantitative models that characterize the relationship of gene expression with the epigenetic marking at enhancers or promoters in mouse embryonic stem cells. Our protocol ...
  • A Concentration-Dependent Liquid Phase Separation Can Cause Toxicity upon Increased Protein Expression
    Bolognesi, Benedetta; Lorenzo Gotor, Maria de las Nieves; Dhar, Riddhiman; Cirillo, Davide; Baldrighi, Marta; Gaetano Tartaglia, Gian; Lehner, Ben, 1978- (Elsevier, 2016)
    Multiple human diseases are associated with a liquid-to-solid phase transition resulting in the formation of amyloid fibers or protein aggregates. Here, we present an alternative mechanism for cellular toxicity based on a ...
  • A conserved expression signature predicts growth rate and reveals cell & lineage-specific differences
    Jiang, Zhisheng; Generoso, Serena Francesca, 1988-; Badia, Marta; Payer, Bernhard; Carey, Lucas, 1980- (Public Library of Science (PLoS), 2021)
    Isogenic cells cultured together show heterogeneity in their proliferation rate. To determine the differences between fast and slow-proliferating cells, we developed a method to sort cells by proliferation rate, and performed ...
  • A coordinated response at the transcriptome and interactome level is required to ensure uropathogenic Escherichia coli survival during bacteremia
    Sanchez de Groot, Natalia; Torrent Burgas, Marc (MDPI, 2019)
    Localized infections or disruption of the skin barrier can enable the entry of bacteria into the bloodstream, possibly leading to acute inflammation and sepsis. There is currently no holistic view on how bacteria can survive ...
  • A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila
    Verd Fernández, Berta, 1984-; Clark, Erik; Wotton, Karl R.; Janssens, Hilde; Jiménez Guri, Eva; Crombach, Anton; Jaeger, Johannes, 1973- (Public Library of Science (PLoS), 2018)
    Insects determine their body segments in two different ways. Short-germband insects, such as the flour beetle Tribolium castaneum, use a molecular clock to establish segments sequentially. In contrast, long-germband insects, ...
  • A de novo CSDE1 variant causing neurodevelopmental delay, intellectual disability, neurologic and psychiatric symptoms in a child of consanguineous parents
    Gangfuß, Andrea; Lochmüller, Hanns; Töpf, Ana; O'Hehir, Emily; Horvath, Rita; Kölbel, Heike; Schweiger, Bernd; Schara-Schmidt, Ulrike; Roos, Andreas (Wiley, 2022)
    CSDE1 encodes the cytoplasmic cold shock domain-containing protein E1 (CSDE1), which is highly conserved across species and functions as an RNA-binding protein involved in translationally coupled mRNA turnover. CSDE1 ...
  • A de novo FOXP1 truncating mutation in a patient originally diagnosed as C syndrome
    Urreizti, Roser; Damanti, Sarah; Esteve, Carla; Franco Valls, Héctor; Castilla-Vallmanya, Laura; Tonda, Raúl; Cormand, Bru; Vilageliu, Lluïsa; Opitz, John M.; Neri, Giovanni; Grinberg, Daniel; Balcells, Susana (Nature Research, 2018)
    De novo FOXP1 mutations have been associated with intellectual disability (ID), motor delay, autistic features and a wide spectrum of speech difficulties. C syndrome (Opitz C trigonocephaly syndrome) is a rare and genetically ...
  • A de novo nonsense mutation in MAGEL2 in a patient initially diagnosed as Opitz-C: similarities between Schaaf-Yang and Opitz-C syndromes
    Urreizti, Roser; Cueto González, Anna María; Franco Valls, Héctor; Mort Farre, Sílvia; Roca Ayats, Neus; Ponomarenko, Julia; Cozzuto, Luca; Company, Carlos; Bosio, Mattia; Ossowski, Stephan; Montfort, Magda; Hecht, Jochen; Tizzano, Eduardo F.; Cormand, Bru; Vilageliu, Lluïsa; Opitz, John M.; Neri, Giovanni; Grinberg, Daniel; Balcells, Susana (Nature Publishing Group, 2017)
    Opitz trigonocephaly C syndrome (OTCS) is a rare genetic disorder characterized by craniofacial anomalies, variable intellectual and psychomotor disability, and variable cardiac defects with a high mortality rate. Different ...
  • A decade of structural variants: description, history and methods to detect structural variation
    Escaramís, Geòrgia; Docampo, Elisa; Rabionet, Raquel (Oxford University Press, 2015)
    In the past decade, the view on genomic structural variation (SV) has been changed completely. SVs, previously considered rare events, are now recognized as the largest source of interindividual genetic variation affecting ...
  • A deep learning method that identifies cellular heterogeneity using nanoscale nuclear features
    Carnevali, Davide; Zhong, Limei; González-Almela, Esther; Viana, Carlotta; Rotkevich, Mikhail; Wang, Aiping; Franco-Barranco, Daniel; González-Marfil, Aitor; Neguembor, Maria Victoria; Castells García, Àlvaro, 1991-; Arganda-Carreras, Ignacio; Cosma, Maria Pia (Springer, 2024)
    Cellular phenotypic heterogeneity is an important hallmark of many biological processes and understanding its origins remains a substantial challenge. This heterogeneity often reflects variations in the chromatin structure, ...
  • A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
    Jiao, Wei; Atwal, Gurnit; Polak, Paz; Karlic, Rosa; Cuppen, Edwin; PCAWG Tumor Subtypes and Clinical Translation Working Group; Danyi, Alexandra; Ridder, Jeroen de; van Herpen, Carla; Lolkema, Martijn P.; Steeghs, Neeltje; Getz, Gad; Morris, Quaid; Stein, Lincoln D.; PCAWG Consortium; Stobbe, Miranda D. (Nature Research, 2020)
    In cancer, the primary tumour's organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as ...
  • A developmentally programmed splicing failure contributes to DNA damage response attenuation during mammalian zygotic genome activation
    Wyatt, Christopher Douglas Robert, 1988-; Pernaute, Barbara; Gohr, André; Miret-Cuesta, Marta; Goyeneche, Lucia; Rovira, Quirze; Salzer, Marion C.; Boke, Elvan; Bogdanovic, Ozren; Bonnal, Sophie; Irimia Martínez, Manuel (American Association for the Advancement of Science (AAAS), 2022)
    Transition from maternal to embryonic transcriptional control is crucial for embryogenesis. However, alternative splicing regulation during this process remains understudied. Using transcriptomic data from human, mouse, ...
  • A diacidic motif determines unconventional secretion of wild-type and ALS-linked mutant SOD1
    Cruz-Garcia, David; Brouwers, Nathalie; Duran, Juan M.; Mora, Gabriel; Curwin, Amy; Malhotra, Vivek (Rockefeller University Press, 2017)
    The nutrient starvation-specific unconventional secretion of Acb1 in Saccharomyces cerevisiae requires ESCRT-I, -II, and -III and Grh1. In this study, we report that another signal sequence lacking cytoplasmic protein, ...
  • A DNA methylation map of human cancer at single base-pair resolution
    Vidal Ocabo, Enrique; Sayols, Sergi; Moran, Sebastian; Guillaumet-Adkins, Amy; Schroeder, Michael Philipp, 1986-; Royo, Romina; Orozco, Modesto; Gut, Marta; Gut, Ivo Glynne; López Bigas, Núria; Heyn, Holger; Esteller, Manel (Nature Publishing Group, 2017)
    Although single base-pair resolution DNA methylation landscapes for embryonic and different somatic cell types provided important insights into epigenetic dynamics and cell-type specificity, such comprehensive profiling ...

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