Browsing by Author "Di Croce, Luciano"

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  • 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 ...
  • Bioinformatic analysis of epigenetic regulatory mechanisms in development and disease
    González Ramírez, Mar (2021-04-09)
    Appropriate regulation of gene expression is necessary for correct development and homeostasis of organisms. Epigenetic mechanisms represent an additional layer of information, besides the genetic sequence, crucial for the ...
  • Characterization of BEND3, a novel interactor of deubiquitanase USP21
    Teichmann, Sophie (Universitat Pompeu Fabra, 2014-02-10)
    La monoubiquitinación de la histona H2A cumple un rol esencial en la represión génica. Diversas enzimas desubiquitinantes (DUBs) han sido identificadas, que remueven específicamente la ubiquitina de H2A en distintos contextos ...
  • CHD4 ensures stem cell lineage fidelity during skeletal muscle regeneration
    Sreenivasan, Krishnamoorthy; Rodríguez de la Rosa, Alejandra; Kim, Johnny; Mesquita, Diana; Segalés Dalmau, Jessica; Gómez del Arco, Pablo; Espejo, Isabel; Ianni, Alessandro; Di Croce, Luciano; Relaix, Frederic; Redondo, Juan Miguel; Braun, Thomas; Serrano Sánchez, Antonio L.; Perdiguero, Eusebio, 1968-; Muñoz Cánoves, Pura, 1962- (Elsevier, 2021)
    Regeneration of skeletal muscle requires resident stem cells called satellite cells. Here, we report that the chromatin remodeler CHD4, a member of the nucleosome remodeling and deacetylase (NuRD) repressive complex, is ...
  • Chromatin and RNA maps reveal regulatory long noncoding RNAs in mouse
    Bogu, Gireesh K., 1984-; Vizán, Pedro; Stanton, Lawrence W.; Beato, Miguel; Di Croce, Luciano; Marti-Renom, Marc A. (American Society for Microbiology, 2015)
    Discovering and classifying long noncoding RNAs (lncRNAs) across all mammalian tissues and cell lines remains a major challenge. Previously, mouse lncRNAs were identified using transcriptome sequencing (RNA-seq) data from ...
  • Chromatin capture links the metabolic enzyme AHCY to stem cell proliferation
    Aranda Aragón, Sergio; Alcaine Colet, Anna, 1992-; Blanco, Enrique; Borràs, Eva; Caillot, Claire; Sabidó Aguadé, Eduard, 1981-; Di Croce, Luciano (American Association for the Advancement of Science (AAAS), 2019)
    Profiling the chromatin-bound proteome (chromatome) in a simple, direct, and reliable manner might be key to uncovering the role of yet uncharacterized chromatin factors in physiology and disease. Here, we have designed ...
  • Chromatin-bound IκB-alpha regulates a subset of polycomb target genes in differentiation and cancer
    Mulero, María Carmen; Islam, Abul, 1978-; Margalef González, Pol, 1985-; Pecoraro, Matteo, 1984-; Toll Abelló, Agustín; Drechsel, Nils Jan Daniel, 1980-; Charneco, Cristina; Bellora Pereyra, Nicolás; Gallardo Hernández, Fernando; López Arribillaga, Erika, 1986-; Asensio Juan, Elena; Rodilla, Verónica; González, Jessica; Iglesias Coma, Mar; Albà Soler, Mar; Di Croce, Luciano; Villà i Freixa, Jordi; López Bigas, Núria; Keyes, William M., 1973-; Bigas Salvans, Anna; Espinosa Blay, Lluís (Elsevier, 2013)
    IκB proteins are the primary inhibitors of NF-κB. Here, we demonstrate that sumoylated and phosphorylated IκBα accumulates in the nucleus of keratinocytes and interacts with histones H2A and H4 at the regulatory region of ...
  • Chromatin-bound proteome profiling by genome capture
    Aranda Aragón, Sergio; Borràs, Eva; Sabidó Aguadé, Eduard, 1981-; Di Croce, Luciano (Elsevier, 2020)
    De novo identification of chromatin interactors can reveal unexpected pathways relevant to physiology and human disease. Inspired by the DNA mediated chromatin pull-down (Dm-ChP) technology (also known as iPOND [isolation ...
  • Creating the AML-specific t(9;11) chromosomal translocation model to study the structural basis of leukemia development in mouse cells
    Sparavier, Aleksandra (2022-06-10)
    Chromosomal translocation are large-scale genome rearrangements found in several cancers. They are formed when two (or more) non-homologous chromosomes interchange large parts as a result of erroneous DNA repair after ...
  • Differential contribution to gene expression prediction of histone modifications at enhancers or promoters
    González Ramírez, Mar, 1991-; Ballaré, Cecilia Julia; Mugianesi, Francesca; Beringer, Malte; Santanach Buxaderas, Alexandra, 1988-; Blanco, Enrique; Di Croce, Luciano (Public Library of Science (PLoS), 2021)
    The ChIP-seq signal of histone modifications at promoters is a good predictor of gene expression in different cellular contexts, but whether this is also true at enhancers is not clear. To address this issue, we develop ...
  • Direct interaction between Id1 and Zrf1 controls neural differentiation of embryonic stem cells
    Aloia, Luigi; Gutiérrez, Arantxa; Martín Caballero, Juan; Di Croce, Luciano (Wiley-Blackwell, 2015)
    Id proteins are dominant-negative regulators within the HLH family of proteins. In embryonic stem cells (ESCs), Id1 and Id3 maintain the pluripotent state by preventing neural differentiation. The Id1-interacting protein ...
  • Dnmt3a and dnmt3b associate with enhancers to regulate human epidermal stem cell homeostasis
    Rinaldi, Lorenzo, 1986-; Datta, Debayan; Serrat, Judit; Morey Ramonell, Lluís; Solanas, Guiomar; Avgustinova, Alexandra; Blanco, Enrique; Pons, José Ignacio; Matallanas, David; Kriegsheim, Alex von; Di Croce, Luciano; Aznar Benitah, Salvador (Elsevier, 2016)
    The genome-wide localization and function of endogenous Dnmt3a and Dnmt3b in adult stem cells are unknown. Here, we show that in human epidermal stem cells, the two proteins bind in a histone H3K36me3-dependent manner to ...
  • Dual regulatory role of Polycomblike-3 (PCL3/PHF19) in prostate cancer
    Jain, Payal (Universitat Pompeu Fabra, 2016-06-10)
    Polycomblike proteins (PCLs) have been shown to regulate Polycomb Repressive Complex 2 (PRC2) by enhancing its catalytic activity and guiding PRC2 to its target genes in embryonic stem cells. However, little is known about ...
  • Engaging chromatin: PRC2 structure meets function
    Chammas, Paul, 1992-; Mocavini, Ivano; Di Croce, Luciano (Nature Research, 2020)
    Polycomb repressive complex 2 (PRC2) is a key epigenetic multiprotein complex involved in the regulation of gene expression in metazoans. PRC2 is formed by a tetrameric core that endows the complex with histone methyltransferase ...
  • 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 ...
  • Functional and pathological roles of AHCY
    Vizán, Pedro; Di Croce, Luciano; Aranda Aragón, Sergio (Frontiers Media, 2021)
    Adenosylhomocysteinase (AHCY) is a unique enzyme and one of the most conserved proteins in living organisms. AHCY catalyzes the reversible break of S-adenosylhomocysteine (SAH), the by-product and a potent inhibitor of ...
  • GATA2 promotes hematopoietic development and represses cardiac differentiation of human mesoderm
    Castaño, Julio; Aranda Aragón, Sergio; Blanco, Enrique; Mereu, Elisabetta; Heyn, Holger; Di Croce, Luciano; Giorgetti, Alessandra (Elsevier, 2019)
    In vertebrates, GATA2 is a master regulator of hematopoiesis and is expressed throughout embryo development and in adult life. Although the essential role of GATA2 in mouse hematopoiesis is well established, its involvement ...
  • In vivo temporal resolution of acute promyelocytic leukemia progression reveals a role of Klf4 in suppressing early leukemic transformation
    Mas, Glòria; Santoro, Fabio; Blanco, Enrique; Gamarra Figueroa, Gianni Paolo; Le Dily, François; Frigè, Gianmaria; Vidal, Enrique; Mugianesi, Francesca; Ballaré, Cecilia Julia; Gutiérrez, Arantxa; Sparavier, Aleksandra; Marti-Renom, Marc A.; Minucci, Saverio; Di Croce, Luciano (Cold Spring Harbor Laboratory Press (CSHL Press), 2022)
    Genome organization plays a pivotal role in transcription, but how transcription factors (TFs) rewire the structure of the genome to initiate and maintain the programs that lead to oncogenic transformation remains poorly ...
  • Interplay between DNA and RNA modifications: a constantly evolving process
    Di Croce, Luciano; Fico, Annalisa; Di Croce, Luciano; Matarazzo, Maria R. (MDPI, 2020)
    The epigenome refers to the entirety of DNA methylations, histone modifications, nucleosome occupancy, and coding and non-coding RNAs (and their modifications) in different cell types [...].
  • Lamin B1 mapping reveals the existence of dynamic and functional euchromatin lamin B1 domains
    Pascual-Reguant, Laura; Blanco, Enrique; Galan Martínez, Silvia, 1992-; Le Dily, François; Cuartero, Yasmina; Serra Bardenys, Gemma, 1992-; Di Carlo, Valerio; Iturbide Martínez de Albéniz, Ane, 1989-; Cebrià i Costa, Joan Pau, 1989-; Nonell Mazelon, Lara, 1972-; García de Herreros, Antonio; Di Croce, Luciano; Marti-Renom, Marc A.; Peiró Sales, Sandra (Nature Publishing Group, 2018)
    Lamins (A/C and B) are major constituents of the nuclear lamina (NL). Structurally conserved lamina-associated domains (LADs) are formed by genomic regions that contact the NL. Lamins are also found in the nucleoplasm, ...

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