Browsing by Author "Marti-Renom, Marc A."

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  • 3D modeling of chromatin structure: is there a way to integrate and reconcile single cell and population experimental data?
    Le Dily, François; Serra, François; Marti-Renom, Marc A. (Wiley, 2017)
    The genome is organized in a hierarchical fashion within the nucleus in interphase. This nonrandom folding of the chromatin fiber is thought to play important roles in the processing of the genetic information. Therefore, ...
  • 3D reconstruction of genomic regions from sparse interaction data
    Mendieta Esteban, Julen, 1992-; Di Stefano, Marco; Castillo Andreo, David; Farabella, Irene; Marti-Renom, Marc A. (Oxford University Press, 2021)
    Chromosome conformation capture (3C) technologies measure the interaction frequency between pairs of chromatin regions within the nucleus in a cell or a population of cells. Some of these 3C technologies retrieve interactions ...
  • 4D genome rewiring during oncogene-induced and replicative senescence
    Sati, Satish; Serra, François; Castillo Andreo, David; Marti-Renom, Marc A.; Cavalli, Giacomo (Cell Press, 2020)
    To understand the role of the extensive senescence-associated 3D genome reorganization, we generated genome-wide chromatin interaction maps, epigenome, replication-timing, whole-genome bisulfite sequencing, and gene ...
  • 4D nucleome modeling
    Marti-Renom, Marc A.; Paulsen, Jonas; Jost, Daniel; Marti-Renom, Marc A. (Elsevier, 2021)
    The intrinsic dynamic nature of chromosomes is emerging as a fundamental component in regulating DNA transcription, replication, and damage-repair among other nuclear functions. With this increased awareness, reinforced ...
  • Binless normalization of Hi-C data provides significant interaction and difference detection independent of resolution
    Spill, Yannick G.; Castillo Andreo, David; Vidal, Enrique; Marti-Renom, Marc A. (Nature Research, 2019)
    Chromosome conformation capture techniques, such as Hi-C, are fundamental in characterizing genome organization. These methods have revealed several genomic features, such as chromatin loops, whose disruption can have ...
  • 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 ...
  • Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion
    Serna-Pujol, Núria; Salinas, Mònica; Mugianesi, Francesca; Le Dily, François; Marti-Renom, Marc A.; Jordan, Albert (Oxford University Press, 2022)
    Up to seven members of the histone H1 family may contribute to chromatin compaction and its regulation in human somatic cells. In breast cancer cells, knock-down of multiple H1 variants deregulates many genes, promotes the ...
  • Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation
    Vilarrasa-Blasi, Roser; Soler-Vila, Paula; Verdaguer-Dot, Núria; Russiñol, Núria; Di Stefano, Marco; Chapaprieta, Vicente; Clot, Guillem; Farabella, Irene; Cuscó Pons, Pol, 1987-; Kulis, Marta; Agirre, Xabier; Prosper, Felipe; Beekman, Renée; Beà, Sílvia; Colomer Pujol, Dolors; Stunnenberg, Hendrik G.; Gut, Ivo Glynne; Campo, Elias; Marti-Renom, Marc A.; Martin-Subero, José Ignacio (Nature Research, 2021)
    To investigate the three-dimensional (3D) genome architecture across normal B cell differentiation and in neoplastic cells from different subtypes of chronic lymphocytic leukemia and mantle cell lymphoma patients, here we ...
  • Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes
    Miguel Escalada, Irene; Bonàs-Guarch, Silvia; Mendieta Esteban, Julen, 1992-; Atla, Goutham; Farabella, Irene; Morgan, Claire C.; García-Hurtado, Javier; Morán, Ignasi; Torrents, David; Mercader Bigas, Josep Maria; Marti-Renom, Marc A.; Ferrer, Jorge (Nature Research, 2019)
    Genetic studies promise to provide insight into the molecular mechanisms underlying type 2 diabetes (T2D). Variants associated with T2D are often located in tissue-specific enhancer clusters or super-enhancers. So far, ...
  • Identification of chromatin loops from Hi-C interaction matrices by CTCF-CTCF topology classification
    Galan Martínez, Silvia, 1992-; Serra, François; Marti-Renom, Marc A. (Oxford University Press, 2022)
    Genome-wide profiling of long-range interactions has revealed that the CCCTC-Binding factor (CTCF) often anchors chromatin loops and is enriched at boundaries of the so-called Topologically Associating Domains, which ...
  • Impact of chromosome fusions on 3D genome organization and gene expression in budding yeast
    Di Stefano, Marco; Di Giovanni, Francesca, 1985-; Pozharskaia, Vasilia; Gomar-Alba, Mercè; Baù, Davide; Carey, Lucas, 1980-; Marti-Renom, Marc A.; Mendoza, Manuel (Mendoza Palomares) (Genetics Society of America, 2020)
    The three-dimensional (3D) organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects remain debated. To determine how changes in chromosome positioning affect transcription ...
  • 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 ...
  • 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 Mazelón, Lara; 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, ...
  • Muscle progenitor specification and myogenic differentiation are associated with changes in chromatin topology
    Zhang, Nan; Mendieta Esteban, Julen, 1992-; Magli, Alessandro; Lilja, Karin C.; Perlingeiro, Rita C. R.; Marti-Renom, Marc A.; Tsirigos, Aristotelis; Dynlacht, Brian David (Nature Research, 2020)
    Using Hi-C, promoter-capture Hi-C (pCHi-C), and other genome-wide approaches in skeletal muscle progenitors that inducibly express a master transcription factor, Pax7, we systematically characterize at high-resolution the ...
  • Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana
    Di Stefano, Marco; Nützmann, Hans-Wilhelm; Marti-Renom, Marc A.; Jost, Daniel (Oxford University Press, 2021)
    The 3D genome is characterized by a complex organization made of genomic and epigenomic layers with profound implications on gene regulation and cell function. However, the understanding of the fundamental mechanisms driving ...
  • Specific contributions of cohesin-SA1 and cohesin-SA2 to TADs and polycomb domains in embryonic stem cells
    Cuadrado, Ana; Giménez-Llorente, Daniel; Kojic, Aleksandar; Rodríguez-Corsino, Miriam; Cuartero, Yasmina; Martín-Serrano, Guillermo; Gómez López, Gonzalo; Marti-Renom, Marc A.; Losada, Ana (Elsevier, 2019)
    Cohesin exists in two variants carrying either STAG/SA1 or SA2. Here we have addressed their specific contributions to the unique spatial organization of the mouse embryonic stem cell genome, which ensures super-enhancer-dependent ...
  • Structural study of the therapeutic potential of protein-ligand interactions
    Martínez-Jiménez, Francisco, 1988- (Universitat Pompeu Fabra, 2016-12-16)
    Most of the cellular functions are driven by small-molecules that selectively bind to their protein targets. Is such their importance, that the pharmacological intervention of proteins by small molecule drugs is frequently ...
  • The conformation of yeast chromosome III is mating type dependent and controlled by the recombination enhancer
    Belton, Jon-Matthew; Lajoie, Bryan R.; Audibert, Sylvain; Cantaloube, Sylvain; Lassadi, Imen; Goiffon, Isabelle; Baù, Davide; Marti-Renom, Marc A.; Bystricky, Kerstin; Dekker, Job (Cell Press, 2015)
    Mating-type switching in yeast occurs through gene conversion between the MAT locus and one of two silent loci (HML or HMR) on opposite ends of the chromosome. MATa cells choose HML as template, whereas MATα cells use HMR. ...
  • The impact of chromosome positioning in nuclear functions
    Di Giovanni, Francesca, 1985- (Universitat Pompeu Fabra, 2016-11-24)
    Chromatin is not randomly organized inside the eukaryotic nucleus in interphase. In budding yeast gene expression of some specific loci is affected by their positioning in the nucleus. Replication firing of early origins ...
  • The Role of chromatin-associated factors in genome topology
    Mugianesi, Francesca, 1992- (2022-06-08)
    Gene expression, epigenetic states and topological conformation are three fundamental aspects of genome organization that are tightly regulated in space and time. Epigenetic states, protein occupancy and chromatin modifications ...