Browsing Center for Genomic Regulation (CRG) by Title

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  • C/EBPalpha activates pre-existing and de novo macrophage enhancers during induced pre-B cell transdifferentiation and myelopoiesis
    van Oevelen, Chris; Collombet, Samuel; Vicent, Guillermo Pablo; Hoogenkamp, Maarten; Lepoivre, Cyrille; Badeaux, Aimee; Bussmann, Lars; Sardina, Jose Luis; Thieffry, Denis; Beato, Miguel; Shi, Yang; Bonifer, Constanze; Graf, T. (Thomas) (Elsevier, 2015)
    Transcription-factor-induced somatic cell conversions are highly relevant for both basic and clinical research yet their mechanism is not fully understood and it is unclear whether they reflect normal differentiation ...
  • C/EBPα induces highly efficient macrophage transdifferentiation of B lymphoma and leukemia cell lines and impairs their tumorigenicity
    Rapino, Francesca, 1982-; Robles, Eloy F.; Richter-Larrea, Jose A.; Kallin, Eric M.; Martinez-Climent, Jose A.; Graf, T. (Thomas) (Cell Press, 2013)
    Earlier work demonstrated that the transcription factor C/EBPα can convert immature and mature murine B lineage cells into functional macrophages. Testing >20 human lymphoma and leukemia B cell lines, we found that most ...
  • C/EBPα mediates the growth inhibitory effect of progestins on breast cancer cells
    Nacht, A. Silvina; Ferrari, Roberto; Zaurín Quer, Roser; Scabia, Valentina; Carbonell-Caballero, Jose; Le Dily, François; Quilez Oliete, Javier; Leopoldi, Alexandra; Brisken, Cathrin; Beato, Miguel; Vicent, Guillermo Pablo (EMBO Press, 2019)
    Steroid hormones are key gene regulators in breast cancer cells. While estrogens stimulate cell proliferation, progestins activate a single cell cycle followed by proliferation arrest. Here, we use biochemical and genome-wide ...
  • CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions
    Barteri, Fabio; Valenzuela, Alejandro; Farré, Xavier; Juan, David; Muntané, Gerard; Esteve Altava, Borja; Navarro i Cuartiellas, Arcadi, 1969- (Oxford University Press, 2023)
    Motivation: Coincidence of Convergent Amino Acid Substitutions (CAAS) with phenotypic convergences allow pinpointing genes and even individual mutations that are likely to be associated with trait variation within their ...
  • Cab45 is required for Ca(2+)-dependent secretory cargo sorting at the trans-Golgi network
    Blume, Julia von; Alleaume, Anne-Marie; Kienzle, Christine; Carreras Sureda, Amado, 1986-; Valverde, M. A. (Miguel Ángel), 1963-; Malhotra, Vivek (Rockefeller University Press, 2012)
    Ca(2+) import into the lumen of the trans-Golgi network (TGN) by the secretory pathway calcium ATPase1 (SPCA1) is required for the sorting of secretory cargo. How is Ca(2+) retained in the lumen of the Golgi, and what is ...
  • Cabut/dTIEG associates with the transcription factor Yorkie for growth control
    Ruíz Romero, Marina; Blanco, Enrique; Paricio, Nuria; Serras Rigalt, Florenci; Corominas Guiu, Montserrat (EMBO Press, 2015)
    The Drosophila transcription factor Cabut/dTIEG (Cbt) is a growth regulator, whose expression is modulated by different stimuli. Here, we determine Cbt association with chromatin and identify Yorkie (Yki), the transcriptional ...
  • Caenorhabditis elegans processes sensory information to choose between freeloading and self-defense strategies
    Schiffer, Jodie A.; Servello, Francesco A.; Heath, William R.; Amrit, Francis Raj Ghandi; Stumbur, Stephanie V; Eder, Matthias; Martin, Olivier M. F.; Johnsen, Sean B.; Stanley, Julia A.; Tam, Hannah; Brennan, Sara J.; McGowan, Natalie G.; Vogelaar, Abigail L.; Xu, Yuyan; Serkin, William T.; Ghazi, Arjumand; Stroustrup, Nicholas; Apfeld, Javier (eLife, 2020)
    Hydrogen peroxide is the preeminent chemical weapon that organisms use for combat. Individual cells rely on conserved defenses to prevent and repair peroxide-induced damage, but whether similar defenses might be coordinated ...
  • Calibrating seed-based heuristics to map short reads with sesame
    Filion, Guillaume; Cortini, Ruggero; Zorita, Eduard (Frontiers, 2020)
    The increasing throughput of DNA sequencing technologies creates a need for faster algorithms. The fate of most reads is to be mapped to a reference sequence, typically a genome. Modern mappers rely on heuristics to gain ...
  • Can bioinformatics help in the identification of moonlighting proteins?
    Hernández, Sergi; Franco, Luís; Calvo Vidal, Verónica Alejandra; Ferragut, Gabriela; Hermoso Pulido, Antonio; Amela, Isaac; Gómez, Antonio; Querol, Enrique; Cedano, Juan (Portland Press, 2014)
    Protein multitasking or moonlighting is the capability of certain proteins to execute two or more unique biological functions. This ability to perform moonlighting functions helps us to understand one of the ways used by ...
  • Cancer LncRNA census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
    Carlevaro-Fita, Joana; Lanzós, Andrés; Feuerbach, Lars; Hong, Chen; Mas Ponte, David; Pedersen, Jackob S.; PCAWG Drivers and Functional Interpretation Working Group; Johnson, Rory; PCAWG Consortium (Nature Research, 2020)
    Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive ...
  • Cancer network activity associated with therapeutic response and synergism
    Serra Musach, Jordi; Capdevila Busquets, Eva; Jaeger, Samira; Aloy, Patrick, 1972-; Pujana, Miguel Angel (BioMed Central, 2016)
    Background: Cancer patients often show no or only modest benefit from a given therapy. This major problem in oncology is generally attributed to the lack of specific predictive biomarkers, yet a global measure of cancer ...
  • Cancer type-dependent genetic interactions between cancer driver alterations indicate plasticity of epistasis across cell types
    Park, Solip; Lehner, Ben, 1978- (Wiley Blackwell, 2015)
    Cancers, like many diseases, are normally caused by combinations of genetic alterations rather than by changes affecting single genes. It is well established that the genetic alterations that drive cancer often interact ...
  • Candida pathogens induce protective mitochondria-associated type I interferon signalling and a damage-driven response in vaginal epithelial cells
    Pekmezovic, Marina; Hovhannisyan, Hrant, 1992-; Gresnigt, Mark S.; Iracane, Elise; Oliveira Pacheco, João; Siscar Lewin, Sofía; Seemann, Eric; Qualmann, Britta; Kalkreuter, Till; Müller, Sylvia; Kamradt, Thomas; Mogavero, Selene; Brunke, Sascha; Butler, Geraldine; Gabaldón Estevan, Juan Antonio, 1973-; Hube, Bernhard (Nature Research, 2021)
    Vaginal candidiasis is an extremely common disease predominantly caused by four phylogenetically diverse species: Candida albicans; Candida glabrata; Candida parapsilosis; and Candida tropicalis. Using a time course infection ...
  • Cannabinoid type-1 receptor blockade restores neurological phenotypes in two models for Down syndrome
    Navarro-Romero, Alba; Vázquez-Oliver, Anna; Gomis González, Maria, 1988-; Garzón-Montesinos, Carlos; Falcón-Moya, Rafael; Pastor, Antonio; Martín García, Elena, 1975-; Pizarro Lozano, Mª Nieves; Busquets Garcia, Arnau, 1985-; Revest, Jean-Michel; Piazza, Pier Vincenzo; Bosch, Fatima; Dierssen, Mara; Torre Fornell, Rafael de la; Rodríguez-Moreno, Antonio; Maldonado, Rafael, 1961-; Ozaita Mintegui, Andrés, 1969- (Elsevier, 2019)
    Intellectual disability is the most limiting hallmark of Down syndrome, for which there is no gold-standard clinical treatment yet. The endocannabinoid system is a widespread neuromodulatory system involved in multiple ...
  • Canonical Wnt pathway controls mESC self-renewal through inhibition of spontaneous differentiation via β-catenin/TCF/LEF functions
    Aulicino, Francesco, 1987-; Pedone, Elisa, 1985-; Sottile, Francesco, 1988-; Lluis Vinas, Frederic; Marucci, Lucia; Cosma, Maria Pia (Elsevier, 2020)
    The Wnt/β-catenin signaling pathway is a key regulator of embryonic stem cell (ESC) self-renewal and differentiation. Constitutive activation of this pathway has been shown to increase mouse ESC (mESC) self-renewal and ...
  • CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing
    Carbonell Sala, Silvia; Perteghella, Tamara; Lagarde, Julien; Nishiyori, Hiromi; Palumbo, Emilio; Arnan Ros, Carme; Takahashi, Hazuki; Carninci, Piero; Uszczynska-Ratajczak, Barbara; Guigó Serra, Roderic (Nature Research, 2024)
    Long-read RNA sequencing is essential to produce accurate and exhaustive annotation of eukaryotic genomes. Despite advancements in throughput and accuracy, achieving reliable end-to-end identification of RNA transcripts ...
  • Carm1-arginine methylation of the transcription factor C/EBPα regulates transdifferentiation velocity
    Torcal Garcia, Guillem, 1991-; Kowenz-Leutz, Elisabeth; Tian, Tian V.; Klonizakis, Antonios; Lerner, Jonathan; Andrés Aguayo, Luisa de; Sapozhnikova, Valeriia; Berenguer, Clara; Plana Carmona, Marcos, 1993-; Vila-Casadesús, Maria; Bulteau, Romain; Francesconi, Mirko; Peiró Sales, Sandra; Mertins, Philipp; Zaret, Kenneth S.; Leutz, Achim; Graf, T. (Thomas) (eLife, 2023)
    Here, we describe how the speed of C/EBPα-induced B cell to macrophage transdifferentiation (BMT) can be regulated, using both mouse and human models. The identification of a mutant of C/EBPα (C/EBPαR35A) that greatly ...
  • CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis
    Ounzain, Samir; Micheletti, Rudi; Arnan Ros, Carme; Plaisance, Isabelle; Cecchi, Dario; Schroen, Blanche; Reverter, Ferran; Alexanian, Michael; Gonzales, Christine; Ng, Shi Yan; Bussotti, Giovanni, 1983-; Pezzuto, Iole; Notredame, Cedric; Heymans, Stephane; Guigó Serra, Roderic; Johnson, Rory; Pedrazzini, Thierry (Elsevier, 2015)
    Long noncoding RNAs (lncRNAs) are emerging as important regulators of developmental pathways. However, their roles in human cardiac precursor cell (CPC) remain unexplored. To characterize the long noncoding transcriptome ...
  • Cathepsin D as biomarker in cerebrospinal fluid of nusinersen-treated patients with spinal muscular atrophy
    Schorling, David; Kölbel, Heike; Hentschel, Andreas; Pechmann, Astrid; Meyer, Nancy; Wirth, Brunhilde; Rombo, Roman; SMArtCARE consortium; Sickmann, Albert; Kirschner, Janbernd; Schara-Schmidt, Ulrike; Lochmüller, Hanns; Roos, Andreas (Wiley, 2022)
    Background and purpose: The therapeutic landscape of spinal muscular atrophy (SMA) has changed dramatically during the past 4 years, but treatment responses differ remarkably between individuals, and therapeutic decision-making ...
  • catRAPID omics: a web server for large-scale prediction of protein-RNA interactions
    Agostini, Federico, 1985-; Zanzoni, Andreas; Klus, Petr, 1985-; Marchese, Domenica, 1986-; Cirillo, Davide; Tartaglia, Gian Gaetano (Oxford University Press, 2013)
    SUMMARY: Here we introduce catRAPID omics, a server for large-scale calculations of protein-RNA interactions. Our web server allows (i) predictions at proteomic and transcriptomic level; (ii) use of protein and RNA sequences ...

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