Browsing by Author "Le Dily, François"

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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, ...
  • 90 YEARS OF PROGESTERONE: Molecular mechanisms of progesterone receptor action on the breast cancer genome
    Beato, Miguel; Wright, Roni H.G.; Le Dily, François (BioScientifica, 2020)
    Gene regulation by steroid hormones has been at the forefront in elucidating the intricacies of transcriptional regulation in eukaryotes ever since the discovery by Karlson and Clever that the insect steroid hormone ecdysone ...
  • A set of accessible enhancers enables the initial response of breast cancer cells to physiological progestin concentrations
    Zaurín Quer, Roser; Ferrari, Roberto; Nacht, A. Silvina; Carbonell-Caballero, Jose; Le Dily, François; Font Mateu, Jofre, 1977-; De Llobet, Lara Isabel; Vidal Ocabo, Enrique; Lioutas, Antonio, 1980-; Beato, Miguel; Vincent, Guillermo P. (Oxford University Press, 2021)
    Here, we report that in T47D breast cancer cells 50 pM progestin is sufficient to activate cell cycle entry and the progesterone gene expression program. At this concentration, equivalent to the progesterone blood levels ...
  • ATP, Mg2+, nuclear phase separation, and genome accessibility
    Wright, Roni H.G.; Le Dily, François; Beato, Miguel (Elsevier, 2019)
    Misregulation of the processes controlling eukaryotic gene expression can result in disease. Gene expression is influenced by the surrounding chromatin; hence the nuclear environment is also of vital importance. Recently, ...
  • 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 ...
  • CDK2-dependent activation of PARP-1 is required for hormonal gene regulation in breast cancer cells
    Wright, Roni H.G.; Castellano, Giancarlo; Bonet Martínez, Jaume, 1982-; Le Dily, François; Font Mateu, Jofre, 1977-; Ballaré, Cecilia Julia; Nacht, A. Silvina; Soronellas, Daniel; Oliva Miguel, Baldomero; Beato, Miguel (Cold Spring Harbor Laboratory Press (CSHL Press), 2012)
    Eukaryotic gene regulation implies that transcription factors gain access to genomic information via poorly understood processes involving activation and targeting of kinases, histone-modifying enzymes, and chromatin ...
  • Chromatin topology defines estradiol-primed progesterone receptor and PAX2 binding in endometrial cancer cells
    La Greca, Alejandro; Bellora Pereyra, Nicolás; Le Dily, François; Jara, Rodrigo; Nacht, A. Silvina; Quilez Oliete, Javier; Villanueva Cañas, José Luis, 1984-; Vidal, Enric; Merino, Gabriela; Fresno, Cristóbal; Reischle, Inti Tarifa; Vallejo, Griselda; Vicent, Guillermo Pablo; Fernández, Elmer; Beato, Miguel; Saragüeta, Patricia (eLife Sciences Publications, 2022)
    Estrogen (E2) and Progesterone (Pg), via their specific receptors (ERalpha and PR), are major determinants in the development and progression of endometrial carcinomas, However, their precise mechanism of action and the ...
  • 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 ...
  • CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response
    Stik, Grégoire; Vidal, Enrique; Barrero, Mercedes; Cuartero, Sergi; Vila-Casadesús, Maria; Mendieta Esteban, Julen, 1992-; Tian, Tian V.; Choi, Jinmi; Berenguer, Clara; Abad, Amaya; Borsari, Beatrice, 1992-; Le Dily, François; Cramer, Patrick; Martí Renom, Marc A.; Stadhouders, Ralph; Graf, T. (Thomas) (Nature Research, 2020)
    Three-dimensional organization of the genome is important for transcriptional regulation1-7. In mammals, CTCF and the cohesin complex create submegabase structures with elevated internal chromatin contact frequencies, ...
  • Hormone-control regions mediate steroid receptor-dependent genome organization
    Le Dily, François; Vidal, Enrique; Cuartero, Yasmina; Quilez Oliete, Javier; Nacht, A. Silvina; Vicent, Guillermo Pablo; Carbonell-Caballero, Jose; Sharma, Priyanka; Villanueva Cañas, José Luis, 1984-; Ferrari, Roberto; De Llobet, Lara Isabel; Verde, Gaetano; Wright, Roni H.G.; Beato, Miguel (Cold Spring Harbor Laboratory Press (CSHL Press), 2019)
    In breast cancer cells, some topologically associating domains (TADs) behave as hormonal gene regulation units, within which gene transcription is coordinately regulated in response to steroid hormones. Here we further ...
  • 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, ...
  • MyoD induces ARTD1 and nucleoplasmic poly-ADP-ribosylation during fibroblast to myoblast transdifferentiation
    Bisceglie, Lavinia; Hopp, Ann-Katrin; Gunasekera, Kapila; Wright, Roni H.G.; Le Dily, François; Vidal, Enrique; Dall'Agnese, Alessandra; Caputo, Luca; Nicoletti, Chiara; Puri, Pier Lorenzo; Beato, Miguel; Hottiger, Michael O. (Elsevier, 2021)
    While protein ADP-ribosylation was reported to regulate differentiation and dedifferentiation, it has so far not been studied during transdifferentiation. Here, we found that MyoD-induced transdifferentiation of fibroblasts ...
  • Nucleosome-driven transcription factor binding and gene regulation
    Ballaré, Cecilia Julia; Castellano, Giancarlo; Gaveglia, Laura; Althammer, Sonja Daniela; González-Vallinas Rostes, Juan, 1983-; Eyras Jiménez, Eduardo; Le Dily, François; Zaurín Quer, Roser; Soronellas, Daniel; Vicent, Guillermo Pablo; Beato, Miguel (Elsevier, 2013)
    In fission yeast cells, Cds1 is the effector kinase of the DNA replication checkpoint. We previously showed that when the DNA replication checkpoint is activated, the repressor Yox1 is phosphorylated and inactivated by ...
  • OneD: increasing reproducibility of Hi-C samples with abnormal karyotypes
    Vidal Ocabo, Enrique; Le Dily, François; Quilez Oliete, Javier; Stadhouders, Ralph; Cuartero, Yasmina; Graf, T. (Thomas); Martí Renom, Marc A.; Beato, Miguel; Filion, Guillaume (Oxford University Press, 2018)
    The three-dimensional conformation of genomes is an essential component of their biological activity. The advent of the Hi-C technology enabled an unprecedented progress in our understanding of genome structures. However, ...
  • Rapid reversible changes in compartments and local chromatin organization revealed by hyperosmotic shock
    Amat, Ramon; Böttcher, René; Le Dily, François; Vidal Ocabo, Enrique; Quilez Oliete, Javier; Cuartero, Yasmina; Beato, Miguel; Nadal Clanchet, Eulàlia de; Posas Garriga, Francesc (Cold Spring Harbor Laboratory Press (CSHL Press), 2019)
    Nuclear architecture is decisive for the assembly of transcriptional responses. However, how chromosome organization is dynamically modulated to permit rapid and transient transcriptional changes in response to environmental ...
  • Signaling by steroid hormones in the 3D nuclear space
    Le Dily, François; Beato, Miguel (MDPI, 2018)
    Initial studies showed that ligand-activated hormone receptors act by binding to the proximal promoters of individual target genes. Genome-wide studies have now revealed that regulation of transcription by steroid hormones ...
  • STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells
    Richart, Laia; Lapi, Eleonora; Pancaldi, Vera; Cuenca-Ardura, Mirabai; Carrillo-de-Santa Pau, Enrique; Madrid-Mencía, Miguel; Neyret-Kahn, Hélène; Radvanyi, François; Rodríguez, Juan Antonio; Cuartero, Yasmina; Serra, François; Le Dily, François; Valencia, Alfonso; Martí Renom, Marc A.; Real, Francisco X. (Oxford University Press, 2021)
    Cohesin exists in two variants containing STAG1 or STAG2. STAG2 is one of the most mutated genes in cancer and a major bladder tumor suppressor. Little is known about how its inactivation contributes to tumorigenesis. Here, ...
  • TFIIIC binding to alu elements controls gene expression via chromatin looping and histone acetylation
    Ferrari, Roberto; De Llobet, Lara Isabel; Di Vona, Chiara, 1981-; Le Dily, François; Vidal Ocabo, Enrique; Lloutas, Antonios; Quilez Oliete, Javier; Jochem, Laura; Cuts, Erin; Dieci, Giorgio; Vannini, Alessandro; Teichmann, Martin; de la Luna, Susana; Beato, Miguel (Elsevier, 2020)
    How repetitive elements, epigenetic modifications, and architectural proteins interact ensuring proper genome expression remains poorly understood. Here, we report regulatory mechanisms unveiling a central role of Alu ...
  • The impact of chromosomal fusions on 3D genome folding and recombination in the germ line
    Vara, Covadonga; Paytuví Gallart, Andreu; Cuartero, Yasmina; Álvarez-González, Lucía; Marín-Gual, Laia; Garcia, Francisca; Florit-Sabater, Beatriu; Capilla, Laia; Sanchéz-Guillén, Rosa Ana; Sarrate, Zaida; Cigliano, Riccardo Aiese; Sanseverino, Walter; Searle, Jeremy B.; Ventura, Jacint; Martí Renom, Marc A.; Le Dily, François; Ruiz Herrera, Aurora (Nature Research, 2021)
    The spatial folding of chromosomes inside the nucleus has regulatory effects on gene expression, yet the impact of genome reshuffling on this organization remains unclear. Here, we take advantage of chromosome conformation ...